TABLE OF CONTENTS

1. Fundamentals of Bacteriology
Microbiology 2. Bacterial Genetics
3. Bacterial Toxins
4. Staphylococcus
5. Streptococcus
6. Enterococcus and Bacillus
7. Clostridium
8. Mycobacteria
9. Non-Spore Forming Gram Positive Bacilli
10. Lactose Fermenting Gram Negative Bacilli
11. Non-lactose Fermenting Gram Negative Bacilli
12. Gram Negative Curved Rods
13. Gram Negative Diplococci
14. Gram Negative Coccobacilli
15. Spirochetes
 TABLE OF CONTENTS

16. Atypical Bacteria

Microbiology 17. Dimorphic Mycosis
18. Opportunistic Mycosis
19. Tinea
20. Gastrointestinal Protozoa
21. Systemic Protozoa
22. Nematodes
23. Cestodes
24. Trematodes
25. Ectoparasites
26. Approach to Virology
27. Basics of Virology
28. Cardiorespiratory Infections
29. Infectious Neuropathology
30. Infectious Dermatologic Disease
31. Opportunistic Infections
 TABLE OF CONTENTS

32. Antibiotics
Microbiology 33. Antifungals
 OUTLINE
1. Structural Bacterial Envelope 5. Bacterial Cultures
A. Cell Wall A. MacConkey Agar

Microbiology: B. Outer Membrane

C. Lipopolysaccharide
D. Lipooligosaccharide
B. Eosin Methylene Blue Agar
C. Chocolate Blood Agar
D. Sheep Blood Agar

Fundamentals of
E. Lipoteichoic Acid E. Eaton Agar
F. Periplasm F. Regan-Lowe, Bordet-Gengou Agar
G. Inner Membrane G. Cystine-Tellurite Agar

Bacteriology
H. Capsule H. Lӧffler Medium
2. Bacterial Adherence and Motility I. Charcoal Yeast Extract Agar
A. Flagellum J. Lӧwenstein-Jensen Agar
B. Pilus K. Middlebrook Agar
C. Endospore L. Mannitol Salt Agar
D. Glycocalyx M. Thiosulfate Citrate Bile Salt Sucrose Agar
E. Biofilm N. Bile Esculin Agar
3. Bacterial Form and Function O. Sabouraud Agar
A. Bacterial Morphology
B. Intracellular Bacteria
C. Anaerobic Bacteria
D. Aerobic Bacteria
E. Respiratory Burst
4. Gram Stain and Variant Staining
A. Process
B. Poor Staining on Gram Stain
C. Variant Staining
Microbiology: Fundamentals of Bacteriology Bootcamp.com

Cell Wall:
• Peptidoglycan: Peptides crosslinked by transpeptidase
• N-acetylmuramic Acid (NAM), N-acetylglucosamine (NAG): Carbohydrate
• Lipoteichoic Acid: (Gram + only)
• Mycolic Acid: (Acid fast only)
• ↑ Structural integrity
• Thick à Gram +, Thin à Gram -
Outer Membrane:
• Outer layer: Lipooligosaccharide (LOS), Lipopolysaccharide (LPS)
• Inner layer: Phospholipids
• Gram - only
Lipopolysaccharide (LPS):
• O-antigen: Outer domain, target for host antibodies (TLR4, CD14)
• Core domain: Linked between O-antigen and lipid A
• Lipid A: Phosphorylated glucosamine disaccharide w/ fatty acids, toxicity to host à Septic shock
Lipooligosaccharide (LOS):
• Similar to LPS, absence of O-antigen
• Neisseria and Haemophilus
Lipoteichoic Acid:
• Anchored to inner membrane, target for host antibodies (TLR2)
Periplasm:
• Space between outer and inner membrane
• Peptidoglycan and β-lactamase
Inner (Cytoplasmic) Membrane:
• Phospholipid bilayer à Hydrophobic layer
• Penicillin-binding proteins
• Enzymes à Essential for bacterial cell function
Capsule:
• Polysaccharide layer à Hydrophilic layer
• Protects against complement-mediated destruction and phagocytosis
• S. pneumoniae, Staphylococcus aureus, Neisseria meningitidis, Haemophilus influenza type b, E. coli, Pseudomonas aeruginosa, Salmonella, Klebsiella
• Poly-D-glutamate capsule in Bacillus anthracis
Microbiology: Fundamentals of Bacteriology Bootcamp.com

Flagellum:
• Motility
Pilus:
• Adhesion to host cells or other bacteria à Neisseria, E. coli
• Sex Pilus à Connects 2 bacteria à F-factor transmission during conjugation
Endospore:
• Protective layer surrounding spore à Protects against desiccation, radiation, temperature, and chemical damage
• Core à DNA, Dipicolinic acid
• Formed during stress (↓ Nutrient availability) à Metabolically inactive
• Bacillus, Clostridium
Glycocalyx:
• “Slime layer”
• Adhesion to foreign surfaces or host cells
Biofilm:
• Aggregation of bacteria, “stuck” together and/or to a surface
• Slimy extracellular matrix composed of extracellular polymeric substances
• Grouped protection from clearing mechanisms
• “Seeding” into systemic circulation
• S. epidermidis à Catheters and prosthetics (foreign body)
• Pseudomonas aeruginosa à Respiratory (VAP), contact lenses
• Nontypeable H. influenzae à Middle ear (AOM)
• Viridans streptococci à Native heart valves, dentition
Microbiology: Fundamentals of Bacteriology Bootcamp.com

Bacteria Morphology:
• Bacilli: Rod-shaped
• Cocci: Sphere-shaped
• Coccobacilli: Combination of rod-sphere-shape
• Spirochete: Spiral-shaped
Intracellular Bacteria:
• Obligate: Unable to generate ATP independent of host à Chlamydia, Rickettsia, Coxiella
• Facultative: Able to generate ATP independent of host à Mycobacterium, Listeria, Legionella, Yersinia, Neisseria, Salmonella, Brucella, Francisella
Anaerobic Bacteria:
• Obligate: Unable to grow in presence of oxygen à Gut flora à Bacteroides, Clostridium, Actinomyces
• Facultative: Able to grow in presence and absence of oxygen à Staphylococcus, Streptococcus, Bacillus cereus
Aerobic Bacteria:
• Only able to grow in the presence of oxygen à Pseudomonas, Mycobacterium, Bordetella, Nocardia
Respiratory Burst:
• Oxidative burst pathway à Generates reactive oxygen species (ROS) à Destroy pathogens w/in phagolysosomes
• NADPH Oxidase: O2 + NADPH à O2-ᐧ + NADP+
• Superoxide Dismutase: 2ᐧO2- à H2O2
• Myeloperoxidase: H2O2 + Cl- à HOClᐧ
• Chronic granulomatous disease à ↑ Risk for catalase + pathogen infection
• Pseudomonas aeruginosa à Pyocyanin à Generates ROS à Destroy competing pathogens
Microbiology: Fundamentals of Bacteriology Bootcamp.com

Process:
• Preparation: Begin with heat-fixed smear of bacteria
• Crystal dye stain: Peptidoglycan retains the violet-blue color
• Iodine: “Fixes” the crystal violet dye (Prevents easy removal)
• Acetone or ethanol: Decolorizer (Wash out of dye)
• Safranin: Counterstain
Poor Staining on Gram Stain:
• No cell wall à Mycoplasma, Ureaplasma
• ↓↓↓ Cell wall thickness à Leptospira
• ↑ Lipid content/Mycolic acid à Mycobacteria
• ↓ Peptidoglycan à Chlamydia
• ↓ Lipopolysaccharide à Treponema
• Intracellular à Poor staining à Legionella, Rickettsia, Bartonella, Anaplasma, Ehrlichia
• Bipolar staining (“closed safety pin”), classic on Giemsa stainà Yersinia enterocolitica
Variant Staining:
• Carbol fuchsin (Ziehl-Neelsen stain): ↑ Affinity for mycolic acid, stains red à Mycobacteria, Nocardia, Cryptosporidium
• Auramine-rhodamine stain: ↑ Affinity for mycolic acid, yellow-red fluorescence à Mycobacteria, Nocardia, Cryptosporidium
• Giemsa stain: Chlamydia, Histoplasma, “Owl-eye” inclusions (CMV), Parasites (Trypanosoma, Plasmodium)
• Periodic acid-Schiff (PAS): Stains glycogen red, Fungi, parasites, Whipple disease, Glycogen storage diseases, ⍺1AT def.
• Silver stain: Legionella, Bartonella, H. pylori, Fungi
• India ink: Stains capsule light on dark background (halo), Cryptococcus neoformans
• Mucicarmine stain: Stains capsule bright red, Cryptococcus neoformans, Blastomyces, Coccidioides
• Dark-field microscopy: Treponema
Microbiology: Fundamentals of Bacteriology Bootcamp.com

MacConkey Agar:
• E.coli, Klebsiella, Enterobacter, Citrobacter, Serratia à Pink/red colonies
• Non-lactose fermenters à Colorless
• Sorbitol-MacConkey Agar à Selective: E. coli O157:H7 does not turn pink/red
Eosin Methylene Blue Agar:
• E. coli à Green sheen colonies
• Klebsiella, Serratia à Purple/black colonies (Enterobacter and Citrobacter can be variable)
• Non-lactose fermenters à Colorless
Chocolate Blood Agar:
• Contains lysed red blood cells (not the same as blood agar)
• Contains Factor V (NAD+), X (hematin)
• Haemophilus influenzae, Neisseria
• Thayer Martin Media: Vancomycin, Trimethoprim, Colistin, Nystatin à Selective: Neisseria
Sheep Blood Agar:
• ⍺-hemolysis: Partial hemoglobin oxidation à Biliverdin/green hemolysis; Streptococcus pneumoniae, Viridans streptococci
• β-hemolysis: Complete hemoglobin breakdown à Translucency peripheral to bacteria; Staph aureus, Strep pyogenes, Strep agalactiae, E. coli, Listeria
• Ɣ-hemolysis: No hemolysis occurs à Agar unchanged peripheral to bacteria
• Haemophilus influenzae does not grow à Satellite phenomenon with hemolytic bacteria cross-streaking (S. aureus)
Eaton Agar: Mycoplasma pneumonia
Regan-Lowe Medium, Bordet-Gengou Agar: Bordetella pertussis
Cystine-Tellurite Agar: Corynebacterium diphtheriae à Black colonies with brown halo
Lӧffler Medium: Corynebacterium diphtheriae à Add methylene blue à Dark-blue metachromatic granules
Charcoal Yeast Extract Agar: Legionella pneumophila, Francisella, Nocardia
Lӧwenstein-Jensen Agar: Mycobacterium tuberculosis
Middlebrook Agar: Mycobacterium tuberculosis
Mannitol Salt Agar: Staphylococcus, Enterococcus; Most species will remain the color of the medium, S. aureus à golden/yellow colonies
Thiosulfate Citrate Bile Salts Sucrose Agar: Vibrio species; V. cholerae à yellow colonies, V. parahaemolyticus à green colonies
Bile Esculin Agar: Enterococcus species, Streptococcus bovis
Sabouraud Agar: Fungi
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0072

A researcher is attempting to identify an unknown bacterial organism that may be implicated in an outbreak of diarrheal illness in the
Northeast region of the United States. Samples collected from affected patients reveal the bacteria is a gram-positive bacillus. The
researcher then attempts to grow colonies of the unknown bacteria on sheep blood agar and perform a cross-streaking method with
Haemophilus influenzae. Satellite growth was observed peripheral to the growth of the unknown bacteria. Further analysis reveals that
the unknown bacteria was able to replicate within and outside of host cells and is not encapsulated.

Which of the following most resembles the pathogen causing the diarrheal outbreak?

⚪ A. Vibrio cholerae

⚪ B. Mycobacterium tuberculosis

⚪ C. Staphylococcus aureus

⚪ D. Bacillus anthracis

⚪ E. Listeria monocytogenes
 OUTLINE
1. DNA Structures and Genetic Material Exchange
A. Vertical Gene Transfer

Microbiology: 2.
B. Horizontal Gene Transfer
C. DNA Structures
Transformation

Bacterial Genetics
A. Mechanism
B. Classic Bacteria Demonstrating Competence
C. Considerations
3. Conjugation
A. Mechanism
B. High Frequency Recombination
C. Considerations
D. Aerobic Bacteria
E. Respiratory Burst
4. Transduction
A. Generalized Transduction
B. Specialized Transduction
C. Considerations
5. Transposition
A. Transposons
B. Considerations
Microbiology: Bacterial Genetics Bootcamp.com

Vertical Gene Transfer:

• Exchange of genetic material from parent to offspring
• Random Mutations à Slow, ↑ Virulence
• Antigenic Variation à Fast, ↑ Virulence
Horizontal Gene Transfer:
• Exchange of genetic material not from parent to offspring
• Transformation
• Conjugation
• Transduction
• Transposition
DNA Structures:
• Chromosome: Contains chromosomal DNA
• Plasmid: Nonchromosomal DNA, replicates independently, contains genes for antibiotic resistance and toxins
• Bacteriophage: Viruses that infect bacteria (Lytic, Lysogenic)
• Transposon: DNA sequence, cannot replicate independently, “jumps” between plasmid ßà chromosome ßà bacteriophage
Microbiology: Bacterial Genetics Bootcamp.com

Mechanism:
• Donor bacteria releases free segments of DNA to environment
• Free DNA (chromosomal or plasmid) segment from environment combines with recipient DNA
• New gene expression in recipient bacteria
Classic Bacteria Demonstrating Competence:
• Neisseria
• Haemophilus influenzae type b
• Streptococcus pneumoniae
Considerations:
• Non-competent bacteria will generally not be able to uptake bacterial DNA
• Deoxyribonuclease breaks down free DNA à Inhibits transformation
Microbiology: Bacterial Genetics Bootcamp.com

Mechanism:
• F factor plasmid within donor
• Donor (F+) bacteria contains genes for sex pilus
• Donor (F+) completely transfers plasmid DNA fragment to recipient (F-) via sex pilus
• Recipient plasmid is self-transmissible
• Single plasmid strand transferred (No chromosomal DNA) à Plasmids create complementary strands
• Results in both donor (F+) and recipient (F+)
High Frequency Recombination (Hfr):
• F factor integrated into donor (Hfr) chromosomal DNA
• Hfr donor incompletely transfers plasmid DNA fragment to recipient (F-) via sex pilus
• Recipient plasmid is not self-transmissible
• Results in a Hfr donor and recipient (F-)
Considerations:
• Antibiotic resistance
Microbiology: Bacterial Genetics Bootcamp.com

Generalized Transduction (Lytic):

• Bacteriophage infects donor bacterium à Injects bacteriophage DNA à Replication of bacteriophage DNA
• Bacteriophage progeny form with phage capsids à Some progeny mistakenly carry donor DNA (“packaging error”)
• Donor bacterium cell lysis and release of bacteriophage progeny
• Bacteriophage with donor DNA infects recipient bacteria à Transfers donor bacterial DNA
Specialized Transduction (Lysogenic):
• Bacteriophage infects donor bacterium à Injects bacteriophage DNA à Bacteriophage DNA incorporates into donor DNA (at specific location)
• Bacteriophage DNA remains in an inactive state à Eventually activated à Replication of bacteriophage DNA
• Bacteriophage progeny form with phage capsids
• Bacteriophage DNA is excised with flanking bacterial DNA regions to be carried by progeny
• Donor bacterium cell lysis and release of bacteriophage progeny
• Bacteriophage with donor DNA infects recipient bacteria à Transfers donor bacterial DNA
Considerations:
• Specialized à Encoding bacterial toxins à Botulinum, Cholera, Diphtheria, Erythrogenic, Shiga
Microbiology: Bacterial Genetics Bootcamp.com

Transposons:
• Genes that “jump” across plasmid, bacterial chromosome, bacteriophage DNA
• Excised from one location à Re-inserted into new location à Genetic diversity and variable expression of genes
Considerations:
• Antibiotic resistance (genetic diversity among plasmids with antibiotic resistance genes) à vanA gene
• Plasmids containing multiple antibiotic resistance genes
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0073

A group of researchers identify unique changes in pathogenic virulence among two strains of Streptococcus pneumoniae. Strain 1 is
referred to as cap08 and is known to be virulent. Strain 2 is referred to as uncap08 and is known to be nonvirulent. cap08 and uncap08
are injected into mice and survival is measured 72 hours after the injection. Data from the experiment is collected below.

Which of the following would most likely increase the survival of mice in experiment E?

Experiment Injected Strain(s) Total mice prior to Surviving mice

injection after injection

A Live uncap08 36 36

B Live cap08 36 1

C Heat killed cap08 35 35

⚪ A. Adding the live cap08 strain in experiment D
D Heat killed cap08 35 0
⚪ B. Removing the heat killed cap08 strain in experiment C Live uncap08

E Unknown* 35 0
⚪ C. Adding the heat killed cap08 strain in experiment E
*The unknown species in this experiment was isolated from mice at the end of experiment D.
⚪ D. Adding DNase to experiment D

⚪ E. Adding DNase to experiment E

 OUTLINE
1. Endotoxin
A. Properties

Microbiology: B. Mechanism
C. Pathogenic Associations
D. Considerations

Bacterial Toxins
2. Sepsis
A. Bacteriemia
B. Systemic Inflammatory Response Syndrome
C. Sepsis
D. Severe Sepsis
E. Multiorgan Dysfunction Syndrome
F. Septic Shock
3. Exotoxin
A. Properties
B. Mechanism
C. Pathogenic Associations
D. Considerations
Microbiology: Bacterial Toxins Bootcamp.com

Properties:
• Located in outer membrane (Gram negative)
• Lipopolysaccharide (LPS): O-antigen, core, lipid A
• Lipid A à Virulence factor
• ↓ Antigenicity, ↓ Toxicity
• Heat-stable
Mechanism:
• Endotoxin binds CD14/TLR4 receptor à Macrophage activation à IL-1, IL-6, TNF-⍺, NO à Fever, vasodilation, ↑ capillary permeability
• Complement activation à ↑ C3a (Anaphylatoxin) à ↑ Histamine à Vasodilation, ↑ capillary permeability
• Complement activation à ↑ C5a (Neutrophil chemotaxis) à Neutrophilic inflammatory infiltration
• Endothelial damage à ↑ Bradykinin à Vasodilation à Septic shock
• Endothelial damage à ↑ FIII (Tissue factor) à Binds FVIIa (Extrinsic)à Activation of FX à Common pathway à DIC
Pathogenic Associations:
• Septic shock
• Waterhouse-Friderichsen Syndrome
• Necrotizing enterocolitis
Considerations:
• No vaccination
• Encoded by bacterial chromosome
Microbiology: Bacterial Toxins Bootcamp.com

Bacteremia:
• Presence of bacteria in bloodstream +/- signs of infection
Systemic Inflammatory Response Syndrome (SIRS):
• Inflammatory reactions from various causes (including noninfectious)
• At least 2 of the 4 criteria below needed:
1. Temperature: >100.4℉ (38℃) or <96.8℉ (36℃)
2. Heart Rate: >90/min
3. Respiratory Rate: >20/min or PaCO2 <32mmHg
4. WBC count: >12,000/mm3 or <4,000/mm3 or >10% band cells
Sepsis:
• Dysregulation of patient response to infection
• Endotoxin-mediated in gram negative bacteria
• SIRS + Suspected/confirmed underlying infection (i.e., SIRS + Viable bacteremia)
Severe Sepsis:
• Sepsis + Dysfunction of at least 1 organ or system
Multiorgan Dysfunction Syndrome (MODS):
• Dysfunction of at least 2 organs or systems
• #1 cause à Sequela of severe sepsis or septic shock
Septic Shock:
• Persistent hypotension à Requiring vasopressors to maintain MAP
• Persistent lactic acidosis à Refractory to fluid resuscitation
• Presentation: Warm, dry skin (early) à Cold, clammy skin (late)
• ↑ Mixed venous O2 saturation
Microbiology: Bacterial Toxins Bootcamp.com

Properties:
• Gram positive and gram negative
• Polypeptide
• ↑ Antigenicity, ↑ Toxicity
• Heat-labile (exceptions exist)
Mechanism:
• Type I: Superantigen à Modulate MHC II-CD4+ receptor activity
• Type II: Cytotoxic
• Type III (MC): AB Toxin à Component A: Active (ADP ribosyltransferases are common), Component B: Binding and uptake
Pathogenic Associations:
• Bacillus anthracis à Anthrax toxin (Edema factor, lethal factor, protective antigen) à Anthrax
• Bordetella pertussis à Pertussis toxin à Pertussis (whooping cough)
• Bacillus cereus à Heat labile toxin à Gastroenteritis
• Clostridium botulinum à Botulinum toxin à Botulism
• Clostridium tetani à Tetanospasmin à Tetanus
• Clostridium perfringens à ⍺-toxin à Gas gangrene
• Corynebacterium diphtheriae à Diphtheria toxin à Diphtheria, myocarditis
• Enterotoxigenic E. coli à Heat labile toxin, Heat stable toxin à Gastroenteritis
• Enterohemorrhagic E. coli à Shiga-like toxin à Gastroenteritis, Hemolytic uremic syndrome
• Pseudomonas aeruginosa à Exotoxin A à Ecthyma gangrenosum
• Shigella spp. à Shiga toxin à Hemolytic uremic syndrome
• Staphylococcus aureus à Enterotoxin B, exfoliative toxin, TSST-1 à Gastroenteritis, SSSS, Bullous impetigo, Toxic shock syndrome
• Streptococcus pyogenes à Erythrogenic Exotoxin A, Streptolysin O à Scarlet fever, Toxic shock syndrome
• Vibrio cholera à Cholera toxin à Cholera
Considerations:
• Toxoid can be used for vaccination à Humoral IgG response
• Transmitted directly via plasmid (conjugation) or via bacteriophage (specialized transduction)
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0074

A 34-year-old postpartum female is transferred to the intensive care unit for hypotension. Twenty-two hours earlier a cesarean section had
been performed and the patient subsequently developed purulent postpartum endometritis evidenced by a fever, purulent uterine
discharge and uterine tenderness. A blood culture was obtained just prior to initiation of empiric antibiotic therapy with vancomycin and
gentamycin. Her vital signs abruptly deteriorated despite aggressive fluid resuscitation requiring immediate vasopressor infusion.

Blood cultures would later grow colonies on eosin methylene blue agar displaying a green metallic sheen appearance.

Given the limited information provided, which of the following is most likely contributing to this patient’s presentation?

⚪ A. Active bacterial secretion of a heat-labile toxin

⚪ B. Active bacterial secretion of a heat-stable toxin

⚪ C. Active bacterial secretion of a Shiga-like toxin

⚪ D. Bacteriolysis causing release of a heat-labile toxin

⚪ E. Bacteriolysis causing release of a heat-stable toxin

 OUTLINE
1. Staphylococcus Aureus
A. General Principles

Microbiology: B. Enzymes
C. Polypeptides
D. Polysaccharides

Staphylococcus
E. Toxins
F. Infectious Diseases
G. Antibiotics
2. Antibiotic Resistant Strains of Staphylococcus Aureus
A. MRSA
B. VRSA
C. Risk Factors
3. Staphylococcus Epidermidis
A. General Principles
B. Enzymes
C. Toxins
D. Foreign Body Infections
E. Antibiotics
4. Staphylococcus Saprophyticus
A. General Principles
B. Enzymes
C. Urinary Tract Infection (Uncomplicated)
D. Antibiotics
Microbiology: Staphylococcus Bootcamp.com

General Principles:
• Gram positive cocci à Clusters
• Culture growth usually “golden” or yellow, can grow in NaCl up to 10% (Mannitol salt agar), β-hemolytic
• Novobiocin sensitive, facultative anaerobe
Enzymes: Catalase, coagulase, hemolysins, hyaluronidase, penicillinase
Polypeptides:
• Protein A à Bind Fc region on IgG à ↓ Complement activation à ↓ C3b
• Modified penicillin-binding protein (MRSA)
Polysaccharides: Capsule à ↓ Phagocytosis
Toxins:
• Enterotoxin B à Superantigen (Type I) à Gastroenteritis
• Exfoliative toxin à Staphylococcal Scalded Skin Syndrome (SSSS)
• Panton-Valentine leukocidin à Leukocyte destruction à Soft tissue necrosis
• TSST-1 à Superantigen (Type I) à Toxic Shock Syndrome (TSS)
Staphylococcal Toxic Shock Syndrome: TSST-1 super antigen, Prolonged use of tampons, shock and end organ dysfunction
Staphylococcal Scalded Skin Syndrome: Exfoliative toxin cleaves desmoglein-1, Infants and young children, diffuse sloughing of skin
Parotitis: Firm, erythematous, peri-auricular edema, trismus, fever, chills, ↑ serum amylase
Gastroenteritis: Enterotoxin B (heat-stable), improper food handling, emesis, mild diarrhea, abdominal pain
IVDU Endocarditis: Constitutional symptoms, tricuspid regurgitation, septic emboli à Splinter hemorrhages, Janeaway lesions, Osler nodes, Roth spots
Osteomyelitis: Progressively worsening localized pain, worse with activity/palpation/percussion, +/- fever, +/- neurologic signs
Additional Diseases: Necrotizing fasciitis, impetigo, pneumonia, meningitis
Antibiotics:
• MSSA penicillinase-sensitive à Penicillin
• MSSA penicillinase-resistant à Oxacillin, nafcillin
• Clindamycin (if PCN allergy)
• MRSA à Vancomycin, linezolid, daptomycin
Microbiology: Staphylococcus Bootcamp.com

Methicillin-Resistant S. aureus (MRSA):

• Acquire mec gene on bacterial chromosome à PBP-2A
• PBP-2A has ↓ affinity for β-lactam antibiotics à ↑ Resistance to β-lactam antibiotics
• Transduction à mec gene transfer among S. aureus
• Typical resistance to methicillin, nafcillin, oxacillin, and cephalosporins
• Rx: Vancomycin (usually) à Daptomycin, linezolid
Vancomycin-Resistant S. aureus (VRSA):
• Acquire vanA from Vancomycin-resistant Enterococcus (VRE) à D-ala, D-lactate
• Transduction and/or conjugation à vanA gene transfer from VRE
• Rx: Daptomycin, linezolid
Risk Factors:
• Prolonged hospitalization, ICU admission, recent antibiotic use, immunocompromised
• Healthcare workers (exposure) à Contact precautions for MDR-bacteria
Microbiology: Staphylococcus Bootcamp.com

General Principles:
• Gram positive cocci à Clusters
• Does not ferment mannitol
• Novobiocin sensitive
• Facultative anaerobe
• Ɣ-hemolytic
Enzymes:
• Catalase, urease
• Coagulase negative
Toxins:
• PSM peptide toxin à Methicillin resistance
Foreign Body Infections:
• Fibrinogen + Fibronectin host protein coating à Binding site for S. epidermidis
• Extracellular polysaccharide matrix forms à Biofilm à Seeding into systemic circulation
• Frequently identified as contaminant on blood cultures
• Catheter, central line, prosthetic valves, cardiac devices, VP shunt
Antibiotics:
• Methicillin sensitive: Oxacillin, nafcillin, clindamycin
• Methicillin resistance: Vancomycin, daptomycin
Microbiology: Staphylococcus Bootcamp.com

General Principles:
• Gram positive cocci à Clusters
• Does not ferment mannitol
• Novobiocin resistant
• Facultative anaerobe
Enzymes:
• Catalase, urease à Does not reduce nitrate to nitrite
• Coagulase negative
Urinary Tract Infection (Uncomplicated):
• Second most common cause in young females (1st E.coli)
• ↑ Urinary frequency, urgency, dysuria, hematuria, suprapubic tenderness
• Nitrite negative
• Resistance to some E.coli UTI antibiotic regimens
Antibiotics:
• Nitrofurantoin
• Trimethoprim-sulfamethoxazole
• Local resistance patterns vary
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0075

A 34-day old male infant was brought to the emergency department with parents for multiple dermatologic lesions throughout the body that were
first noticed 4 days earlier and had progressively worsened. Parents reported that the infant had a low-grade fever over the preceding several
days with decreased oral feeding. There was no significant antenatal history reported. On physical examination there are multiple pustular lesions
present over the face, trunk, and back with purulent discharge. Auscultation of the lungs revealed coarse breath sounds. Further microbial
investigation including blood and wound cultures with antimicrobial sensitivities are performed revealing growth of methicillin-sensitive
staphylococcus aureus. Targeted antibiotic treatment is completed, and the patient is subsequently discharged home with family in stable
condition.

Two weeks later the patient returns with a cough, fever, and respiratory distress. Chest X-ray reveals a left-sided pulmonary infiltrate. Blood
cultures from this second admission would later grow methicillin-resistant staphylococcus aureus. Immunologic workup is performed, and a
portion of the results are shown below. Which of the following is most likely the pathogenic mechanism leading to recurrent staphylococcal
disease in this patient?
Diagnostic Test Detail-Result

Serum Immunoglobulins Normal for age.

⚪ A. Mutant bacterial DNA gyrase subunit (GyrB protein)
CD18 Normal for age.
⚪ B. Bacterial-mediated extracellular polysaccharide matrix formation
Dihydrorhodamine flow Minimal green fluorescence of rhodamine at conclusion
cytometry of this study.
⚪ C. Bacterial-mediated enzymatic inactivation of catalase
Nitroblue tetrazolium test Incubated leukocytes do not turn blue when exposed to
nitroblue tetrazolium.
⚪ D. Bacterial-mediated enzymatic decomposition of hydrogen peroxide

⚪ E. Bacterial-mediated urea hydrolysis

 OUTLINE
1. Streptococcus Pneumoniae
A. General Principles

Microbiology: B. Pathogenesis
C. Drug Resistant S. pneumonia
D. Diseases

Streptococcus
E. Asplenia
F. Antibiotics
G. Vaccinations
2. Viridans Group Streptococci
A. General Principles
B. Pathogenesis
C. Diseases
D. Antibiotics
3. Streptococcus Pyogenes (Group A)
A. General Principles
B. Pathogenesis
C. Diseases
D. Diagnostics
E. Antibiotics
4. Streptococcus Agalactiae
A. General Principles
B. Pathogenesis
C. Diseases
D. Diagnostics
E. Antibiotics
5. Additional Streptococci
A. Streptococcus Gallolyticus
B. Streptococcus Anginosus
Microbiology: Streptococcus Bootcamp.com
Microbiology: Streptococcus Bootcamp.com

General Principles:
• Gram positive “lancet”-shaped diplococci à Pairs or chains
• Catalase negative
• ⍺-hemolytic
• Optochin sensitive, facultative anaerobe
• Bile soluble
• Neufeld-Quellung reaction positive à Used for capsular serotyping
Pathogenesis:
• Nasopharynx colonization
• Polysaccharide capsule à ↓ Phagocytosis
• IgA1 protease à Cleaves mucosal IgA
• Pili à Adherence to cell surfaces, ↑ Inflammation
Drug-Resistant S. pneumonia (DRSP):
• Penicillin resistance à Alteration of penicillin-binding protein (PBP)
Pneumonia: MCC in adults, classically lobar, rusty-color sputum, CXR
Otitis Media: MCC in children
Meningitis: MCC in adults
Additional Diseases: Sinusitis, pharyngitis
Asplenia: ↑ Risk of infection w/ encapsulated pathogens (Streptococcus pneumoniae)
Antibiotics:
• Pneumonia + Penicillinase sensitive à Penicillin, Amoxicillin, Azithromycin, Levofloxacin
• Pneumonia + Penicillinase resistant à Vancomycin
• Acute Otitis Media à Amoxicillin-clavulanate
• Meningitis à Ceftriaxone and vancomycin (Covers Neisseria and H. influenzae)
Vaccinations:
• Pneumococcal conjugate (PCV13,15,20) à Infants, Elderly (Humoral IgG response)
• Pneumococcal capsule (PPSV23) à (Humoral IgM response)
Microbiology: Streptococcus Bootcamp.com

General Principles:
• S. mutans, S. mitis, and S. sanguinis
• Gram positive in chains
• Catalase negative
• ⍺-hemolytic
• Optochin resistant, facultative anaerobe
• Bile resistant
Pathogenesis:
• Oropharynx colonization
• Dextran à Adherence to surfaces, requires local fibrin deposition (damaged heart valves) (S. sanguinis)
• Biofilm à Adhesion to oral surfaces (S. mutans, S. mitis)
• Pili à Adherence to cell surfaces, ↑ Inflammation
Disease of Dentition and Gingiva: Subgingival plaque à Penetrates gingival epithelium
• Dental caries, gingivitis
Subacute Bacterial Endocarditis: Dental procedure/trauma à S. sanguinis bacteremia à Heart valve/prosthetic device seeding
• Antibiotic prophylaxis à High risk patients (Prosthetic heart valves, prior history of endocarditis)
Antibiotics:
• Endocarditis prophylaxis in high risk à Amoxicillin
Microbiology: Streptococcus Bootcamp.com

General Principles:
• Gram positive in pairs and chains
• Catalase negative
• β-hemolytic
• Bacitracin sensitive, facultative anaerobe
• Pyrrolidinyl arylamidase (PYR) positive
Pathogenesis:
• Nasopharynx colonization
• Erythrogenic exotoxin A, B, or C à Scarlett fever
• Streptococcal pyrogenic exotoxins (SPE) à Toxic shock syndrome
• Streptolysin, hyaluronidase à Damages host membranes and cells à Highly antigenic à Anti-streptolysin O Ab produced by host
• Hemolysins
• Hyaluronic acid capsule
• M protein: ↓ Opsonization, phagocytosis à Molecular mimicry à Acute rheumatic fever
• Protein F: Binds fibronectin à ↑ Adherence
Tonsillopharyngitis: Pharyngeal erythema +/- gray-white tonsillar exudates, usually age 5-15 y/o
• Additional: Otitis media, peritonsillar abscess
Scarlett Fever: Mediated by erythrogenic exotoxins, “Scarlet sandpaper” maculopapular rash, “strawberry” tongue
Soft Tissue Infections:
• Erysipelas: Superficial dermis, sharply demarcated
• Cellulitis: Deep dermis and subcutaneous tissue, poorly demarcated, induration
• Impetigo: “Honey-crusted lesions” (Majority caused by S. aureus)
• Necrotizing fasciitis: Pain out of proportion to degree of erythema, rapid progression, crepitus, skin necrosis, ↑ risk TSS
Streptococcal Toxic Shock Syndrome: Associated with necrotizing fasciitis and myositis, ↑ mortality rate (vs Staphylococcal TSS)
Acute Rheumatic Fever: Inflammatory sequela to GAS infection, cross reactivity of M protein Ab with host myocardial tissue
Poststreptococcal Glomerulonephritis: Inflammatory sequela to GAS infection, S. pyogenes antigen-immune complex deposition in glomerular BM
Diagnostics:
• Throat culture, rapid antigen detection (Rapid Strep Test)
• Serum antistreptolysin O (ASO), anti-deoxyribonuclease B (ADB) titer
Antibiotics:
• Penicillin, Ampicillin, Amoxicillin
• 1st and 2nd generation cephalosporins
Microbiology: Streptococcus Bootcamp.com

General Principles:
• Gram positive in pairs and chains
• Catalase negative
• β-hemolytic
• Bacitracin resistant, facultative anaerobe
• Pyrrolidinyl arylamidase (PYR) negative
• Hippurate positive
• CAMP factor à ↑ S. aureus hemolysis area on culture
Pathogenesis:
• Vaginal and GI colonization in mother à Ascend toward uterus à Chorioamnionitis, vertical transmission to newborn
• Sialic acid polysaccharide capsule
• Pilus à Adherence of mucosal surfaces
• Hemolysins
• C5a-ase
Neonatal Meningitis: Bulging fontanelle, lethargy, muscle hypotonia, poor appetite, hyperthermia (or hypothermia)
Neonatal Pneumonia: Respiratory distress, lethargy, pallor, hypotension, hyperthermia within the first 24 hours post-delivery
Diagnostics:
• Rectal and vaginal swabs in mother à Screen during pregnancy at 35-37 weeks à Positive culture à Intrapartum prophylaxis
Antibiotics:
• Ampicillin +/- Gentamycin
• Penicillin
• 1st and 2nd generation cephalosporins
• Clindamycin
Microbiology: Streptococcus Bootcamp.com

Streptococcus Gallolyticus (Group D):

• Gram positive in pairs and chains
• Catalase negative
• Ɣ-hemolytic (usually)
• Facultative anaerobe
• Bile resistant
• Does not grow in high salt concentrations (6.5% NaCl)
• S. bovis biotype 1 = S. gallolyticus
• GI colonization
• Subacute bacterial endocarditis à ↑ Risk of colorectal carcinoma
Streptococcus Anginosus (Group E):
• Gram positive, non-motile, in pairs and chains
• Catalase negative
• Facultative anaerobe
• Soft tissue infections, abscesses
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0076

A 9-year-old male presents to the emergency department with worsening swelling. His mother reports that he was treated with antibiotics 7 days ago for
a sore throat and now believes that he may be having an allergic reaction. She reports that his urine has been a dark brown color for the past 12 hours.
Vital signs reveal that the patient is afebrile with a blood pressure of 132/80 mmHg and a heart rate of 94/min. Physical examination reveals 2+ pretibial
edema bilaterally with diffuse edema in the periorbital and scrotal regions. Serum laboratory evaluation is shown below. Renal biopsy is planned and
reveals polymorphonuclear infiltration within the glomerular basement membrane and approaching the tubulointerstitial area along with mild thickening in
the arterial walls. Granular staining of the renal biopsy with C3c was positive on immunofluorescent microscopy. Which of the following features most
closely describes the bacteria responsible for this immune-mediated sequela in this patient?

Hemoglobin: 11.3 g/dL

Leukocyte count: 10,500/mm3
Platelet count: 155,000/mm3
Serum creatinine: 2.58 mg/dL
Sodium 134 mEq/L
Potassium 4.4 mEq/L
Antistreptolysin-O antibody: Positive titer
C3 22.5 mg/dL (ref: 84-175 mg/dL)
Gram Catalase Hemolysis PYR*
⚪ A. Stain capability status
A. + + β -
⚪ B.
B. + + Ɣ -
⚪ C.
C. + - β +
⚪ D.
D. + - Ɣ +
⚪ E.
E. + - ⍺ -
*Pyrrolidinyl arylamidase
 OUTLINE
1. Enterococcus (Group D)
A. General Principles

Microbiology: B. Pathogenesis
C. Vancomycin-Resistant Enterococci
D. Diseases

Enterococcus and
E. Antibiotics
2. Bacillus Anthracis
A. General Principles

Bacillus
B. Pathogenesis
C. Diseases
D. Prevention
E. Medical Management
3. Bacillus Cereus
A. General Principles
B. Pathogenesis
C. Diseases
D. Diagnostics
E. Antibiotics
Microbiology: Enterococcus and Bacillus Bootcamp.com
Microbiology: Enterococcus and Bacillus Bootcamp.com

General Principles:
• E. faecalis, E. faecium
• Gram positive diplococci à Pairs or chains
• Catalase negative
• Urease negative
• Ɣ-hemolytic
• Facultative anaerobe
• Pyrrolidinyl arylamidase (PYR) positive
• Bile resistant, Bile esculin agar
• Can grow in NaCl 6.5%, Mannitol salt agar
Pathogenesis:
• GI colonization à Recent GI or GU procedures
• Polysaccharide capsule à ↓ Phagocytosis
• Pili à Adherence to cell surfaces, ↑ Inflammation
• Biofilm à Adhesion to foreign substances (urinary catheter)
• Penicillin and early generation cephalosporin resistant
Vancomycin-Resistant Enterococcus (VRE): Nosocomial infection
Urinary Tract Infection: Hospitalized patient +/- catheterization, cannot convert nitrates to nitrites
Cholecystitis: Bile-resistant properties
Subacute Bacterial Endocarditis: Elderly patients, recent cystoscopy or colonoscopy
Antibiotics:
• Ampicillin +/- Gentamycin
• Vancomycin
• VRE à Linezolid, daptomycin
Microbiology: Enterococcus and Bacillus Bootcamp.com

General Principles:
• Gram positive non-motile bacilli à ”Bamboo stick” shape, “box car” arrangement
• Capsular halo (“Medusa head”)
• Catalase positive
• Spore forming
• Ɣ-hemolytic
• Can grow on blood agar
Pathogenesis:
• Transmission via spore inhalation, ingestion, or inoculation, generally from infected animals
• ↑ Risk in areas with low animal vaccination rates and exposure to animal hides
• Polypeptide D-glutamate capsule à ↓ Phagocytosis
• Anthrax toxin consists of 3 components à Edema factor, lethal factor, protective antigen
• Protective antigen: Binds cell surface à Permits entry of edema and lethal factor
• Edema factor: Binds calmodulin à ↑ cAMP
• Lethal factor: Cleaves amino terminus of MAPKK à Macrophage apoptosis
Cutaneous Anthrax:
• Most common form of disease, inoculation of spores
• ↑ Risk w/ IVDU
• Pruritic papule with central vesicle/bulla à Painless necrotic black eschar with surrounding non-pitting edema
Pulmonary Anthrax:
• “Woolsorter’s disease”, inhalation of spores
• Prodromal phase: Constitutional symptoms, non-productive cough, nausea, vomiting, hemoptysis
• Systemic phase: Lymphadenitis, mediastinitis, bacteremia à Respiratory failure, septic shock, hemorrhagic meningitis
• Acute presentation with rapid deterioration
• CXR: Widened mediastinum
Gastrointestinal Anthrax: Ingestion of contaminated meat containing spores, mucosal ulcerations, hematemesis, melena
Prevention: Post-exposure prophylaxis (Anthrax vaccination + prolonged antibiotics)
Medical Management: Ciprofloxacin, doxycycline, clindamycin, linezolid +/- Anthrax immune globulin
Microbiology: Enterococcus and Bacillus Bootcamp.com

General Principles:
• Gram positive motile bacilli
• Catalase positive
• Spore forming
• β-hemolytic
• Facultative anaerobe
• Can grow on blood agar
Pathogenesis:
• Transmission via food (improperly refrigerated) à Reheated rice is classic
• Enterotoxin I (Cereulide, pre-formed) à Emetic properties
• Enterotoxin II à Diarrheal properties
Gastroenteritis: Enterotoxin I and/or II (heat-stable), reheated rice, emesis, watery diarrhea, abdominal pain
Medical Management: Supportive
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0077

A 73-year-old male with a past medical history of hypertension, hyperlipidemia, and type II diabetes mellitus who presents to his primary care physician
with a chief complaint of painful urination over the past three days. He states he has sudden urges to urinate and has had one episode overnight when he
was almost unable to get to the bathroom in time to void. He denies any recent surgical procedures, however states that he had a colonoscopy
performed six days ago. Vital signs reveal a temperature of 37.9℃ (100.2 ℉), respiratory rate of 16 breaths/min, heart rate of 88 beats/min, and a blood
pressure of 128/68 mmHg. Physical examination is relatively unrevealing. There is no evidence of suprapubic or costovertebral angle tenderness.
Urinalysis results are shown below. Given the information provided, which of the following features are most consistent with the likely pathogen
responsible for this patient’s presentation?

Leukocyte esterase: 2+
Nitrite: Negative
Protein: 1+
Glucose: 1+
Ketones: Negative
Urobilinogen: Negative
Urine pH: 6.30
Bacteria: Many

⚪ A. Lactose-fermenting gram-negative rod

⚪ B. Catalase-positive gram-positive cocci

⚪ C. Oxidase-positive gram-negative rod

⚪ D. Catalase-negative gram-positive cocci

⚪ E. Urease-positive gram-negative rod

 OUTLINE
1. Mycobacterium Tuberculosis
A. General Principles

Microbiology: 2.
B. Pathogenesis
Pulmonary Tuberculosis
A. Pathophysiology

Mycobacteria
B. Disease Variants
C. Presentation
D. Diagnostics
E. Management
F. Considerations
3. Tuberculosis Screening
A. Tuberculin Skin Test
B. Interferon-Ɣ Release Assay
C. Bacillus-Calmette Guérin Vaccine
4. Mycobacterium Leprae and Leprosy
A. General Principles
B. Pathophysiology
C. Presentation
D. Diagnostics
E. Management
E. Considerations
5. Additional Nontuberculous Mycobacterium
A. General Principles
B. Mycobacterium Marinum
C. Mycobacterium Scrofulaceum
D. Mycobacterium Avium-intracellular complex
Microbiology: Mycobacteria Bootcamp.com
Microbiology: Mycobacteria Bootcamp.com

General Principles:
• Mycobacterium tuberculosis (MTB)
• Acid-fast, non-motile, gram neutral bacilli
• Ziehl-Neelsen stain, Auramine-rhodamine stain
• Lӧwenstein-Jensen agar, Middlebrook agar
• Catalase positive (negative in INH drug-resistance)
• Facultative intracellular
• Obligate aerobe
Pathogenesis:
• Transmitted via aerosol droplets
• Mycolic acid à Does not absorb gram stain effectively
• Cord factor (trehalose dimycolate) à “Serpentine” structure à ↑ TNF-⍺, ↑ Macrophage activation à Caseating granuloma
• Additional glycolipids (sulfatides) à ↓ Phagolysosomal vesicle fusion
• Catalase-peroxidase à ↓ ROS and H2O2
• KatG or inhA gene mutations à ↓ Catalase-peroxidase activity à ↓ Isoniazid activation à INH drug-resistance
Microbiology: Mycobacteria Bootcamp.com

Pathophysiology:
• Transmitted via air droplet nuclei à Inhaled into lungs à MTB interaction w/ alveolar macrophages
• MTB sulfatides à ↓ Phagolysosomal vesicle fusion à MTB replication within alveolar macrophages
• Dendritic cells present MTB antigens à Naïve CD4+ T-cells à ↑ IL-12 à Th1-cell differentiation à ↑ IFN-Ɣ
• Macrophage activation à Phagosome maturation, ↑ TNF-⍺, Langhan’s (multinucleated giant) cell formation
• Cord factor à ↑↑↑ TNF-⍺ à Granuloma formation
Disease Variants:
• Active Tuberculosis
• Latent Tuberculosis: MTB infection = Host immune response
• Reactivation Tuberculosis: MTB infection >> Host immune response
Active (Primary) Pulmonary Tuberculosis: Ghon complex, middle and lower lobes, symptomatic, contagious after initial exposure, TST positive, IGRA positive
Latent Pulmonary Tuberculosis: Asymptomatic, generally not contagious, TST positive, IGRA positive
Reactivation (Secondary) Pulmonary Tuberculosis: Upper lobe +/- cavitation, caseating granuloma, symptomatic, contagious, TST positive, IGRA positive
Miliary Tuberculosis: ↑ Risk in immunocompromised, Pott disease (vertebrae), hepatosplenomegaly, scrofuloderma (skin)
Gastrointestinal Tuberculosis: M. bovis, contaminated cow milk
Presentation:
• Non-productive cough à Hemoptysis, dyspnea
• Fever (low-grade), lymphadenopathy, anorexia, night sweats
• Variable pulmonary auscultation findings
Diagnostics:
• Sputum sample, NAAT, tuberculin skin test (TST), interferon-Ɣ release assay (IGRA)
• CXR: Ghon complex (1°), hilar LAD (unilateral), consolidation, pleural effusion, cavitary lesions (2°, UL)
Management:
• Active and Reactivation: Rifampin + INH + Pyrazinamide + Ethambutol x 2m à Rifampin + INH x 4m
• Latent: Isoniazid (INH), Rifampin, Rifapentine (multiple regimens exist)
Considerations:
• Immunocompromised may have negative diagnostic tests
• Patients starting immunosuppressive therapy should be screened
Microbiology: Mycobacteria Bootcamp.com

Tuberculin Skin Test (TST):

• Purified protein derivative test (PPD), Mantoux test
• Generates immune response intradermally via previously sensitized T-cells
• Requires effective cell-mediated immunity (T-cell, type IV hypersensitivity reaction)
• Does not distinguish between active and latent MTB infection
• False positive: History of BCG vaccination, nontuberculous mycobacteria infection
• False negative: Immunosuppression, sarcoidosis
• Interpreter variability and varying induration diameters for positive result
Interferon-Ɣ Release Assay (IGRA):
• Measures IFN-Ɣ released by T-cells
• Requires effective cell-mediated immunity (T-cell, type IV hypersensitivity reaction)
• Does not distinguish between active and latent MTB infection
• Preferred if prior BCG vaccination à Does not have false positives due to history of BCG vaccination
• False negative: Immunosuppression, sarcoidosis
Bacillus Calmette-Guérin (BCG) Vaccination
• Live attenuated strain of Mycobacterium bovis
• Not typically given in the U.S.
• Avoid in immunosuppressed or pregnancy
• May cause false positive TST
Microbiology: Mycobacteria Bootcamp.com

General Principles:
• Mycobacterium leprae complex = M. leprae, M. lepromatosis
• Reservoir of humans and armadillos
• Acid-fast, non-motile, gram neutral bacilli
• Ziehl-Neelsen stain
• Cannot be cultured
• Grows more readily in colder temperatures
• Obligate intracellular
• Obligate aerobe
Pathophysiology:
• M. leprae affinity for peripheral nerve tissue à Schwann cell destruction, demyelination
• Tuberculoid Leprosy: Th1 response à T-cell mediated endoneurium non-caseating granuloma formation and epineurium fibrosis; Scarce bacilli on AFB
• Lepromatous Leprosy: Th2 response à Hypergammaglobulinemia, M. leprae mediated, inadequate cell-mediated response; Numerous bacilli on AFB
Presentation:
• Tuberculoid Leprosy: Hypopigmented macules/plaques, hair loss, localized/asymmetric hyperesthesia à hypoesthesia
• Lepromatous Leprosy: “Leonine facies”, nodular lesions, symmetrical length-dependent sensorimotor neuropathy (“glove-and-stocking distribution”)
Diagnostics:
• Tuberculoid Leprosy AFB: Noncaseating granulomas surrounded by epithelioid, Langhans, and lymphocytic cells, minimal bacilli
• Lepromatous Leprosy AFB: Foamy histiocytes, minimal lymphocytes, numerous bacilli
• Lepromin test: (-) test à Lepromatous Leprosy
• PCR à Detects M. leprae DNA in tissue
Management:
• Dapsone + Rifampin +/- Clofazimine (for lepromatous)
Considerations:
• False positive VDRL or ANA
Microbiology: Mycobacteria Bootcamp.com

General Principles:
• Acid-fast, non-motile bacilli
• Ziehl-Neelsen stain
Mycobacterium Marinum:
• Fish tank granuloma, classically a hand lesion
Mycobacterium Scrofulaceum:
• Cervical lymphadenitis (children)
Mycobacterium Avium-intracellulare complex (MAC):
• Disseminated disease à CD4+ count <50 cells/μL
• Nonspecific symptom presentation (fever, lethargy, abdominal pain, diarrhea, weight loss), LAD, HSM
• Commonly MDR
• Rx: Variable, macrolide classic
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪✪ Bootcamp.com
Question ID: 0079

A 17-year-old male who recently immigrated from India presents to his primary care physician with weakness and “electric” shooting pains of the right
hand that have been progressively worsening for the past couple of years. He states that he is having greater difficulty opening jars and has been
dropping items frequently. Physical examination reveals weakness at the abductor digiti minimi muscle on the right hand. Dysesthesias are also present
to light touch over the dorsal surface of the right hand. Reflexes are present and 2+ bilaterally at the biceps tendon. There is also some evidence of
intrinsic right-hand muscle wasting with slight clawing of the fourth and fifth digits. Serum laboratory workup is shown below. MRI of the brain and cervical
spine are unremarkable. Incisional skin biopsies of the right upper extremity are performed and shown below. Sample A is stained with hematoxylin and
eosin at 100x magnification and contains an inset at 400x magnification revealing neuronal tissue. Sample B is stained with a Ziehl-Neelsen stain at 100x
magnification and contains an inset at 1000x magnification revealing neuronal tissue. Which of the following options would best explain this patient’s
presentation and diagnostic findings?

Vitamin B12 440 pg/mL (reference: 160-950 pg/mL)

Thyroid stimulating hormone: 1.1 μU/mL
IgG: 2750 mg/dL (reference: 650-1,500 mg/dL)
IgM: 370 μg/dL (reference: 40-345 mg/dL)
VDRL: Positive
ANA: Elevated titer

⚪ A. Anti-GM1 ganglioside autoantibodies

⚪ B. Anti-GQ1b autoantibodies

⚪ C. Anterior horn cell motor neuron degeneration

⚪ D. Robust Th1-mediated cellular immune response

⚪ E. Enveloped RNA retrovirus

 OUTLINE
1. Corynebacterium Diphtheriae
A. General Principles

Microbiology: B. Pathogenesis
C. Presentation
D. Diagnostics

Non-Spore
E. Management
F. Complications
G. Prevention

Forming Gram
2. Listeria Monocytogenes
A. General Principles
B. Pathogenesis

Positive Bacilli
C. Disease Variants
D. Diagnostics
E. Management
3. Nocardia
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Diagnostics
E. Management
4. Actinomyces Israelii
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Diagnostics
E. Management
Microbiology: Non-Spore Forming Gram Positive Bacilli Bootcamp.com
Microbiology: Non-Spore Forming Gram Positive Bacilli Bootcamp.com

General Principles:
• Gram positive, non-motile, “club-shaped” bacilli
• Methylene blue used to stain (aniline dye)
• Lӧeffler agar à Metachromatic granules
• Cystine-tellurite blood agar à Forms black colonies in angular arrangements (“halo”)
• Elek test: Directly tests for diphtheria exotoxin
• Catalase positive
• Facultative anaerobe
Pathogenesis:
• Transmitted via respiratory droplets à Colonizes upper respiratory tract
• Diphtheria toxin: Inactivation of EF2 via ADP-ribosylation à ↓ Protein synthesis
• β-Prophage codes for diphtheria exotoxin (Tox gene)
Presentation:
• Pseudomembranous pharyngitis: Gray-white pseudomembrane, bleeds easily
• Cervical lymphadenopathy à “Bull neck”, upper airway obstruction
• Halitosis, sore throat, fever
Diagnostics:
• Pharyngeal swab à Culture
• PCR à tox gene
Management:
• Diphtheria antitoxin
• Penicillin G
Complications: Systemic dissemination: Peripheral polyneuropathy, myocarditis (arrhythmias, dilated cardiomyopathy), airway compromise
Prevention: Toxoid vaccine (DTaP, Tdap, Td)
Microbiology: Non-Spore Forming Gram Positive Bacilli Bootcamp.com

General Principles:
• Gram positive motile (”tumbling”) bacilli
• Catalase positive
• Facultative anaerobe
• Facultative intracellular
• ↑ Growth in cold temperatures
• β-hemolytic (very narrow zone of hemolysis)
• CAMP factor à ↑ S. aureus hemolysis area on culture
Pathogenesis:
• Transmitted by unpasteurized dairy products and cold deli meats, transplacental and vaginal transmission during birth
• “Rocket tails” via actin polymerization à ↑ Intracellular movement à Tumbling motility à ↓ Ab interactions
• Listeriolysin O à Creates pores in phagosomes and ↓ T-cell activation from antigen presenting cells
Gastroenteritis:
• Immunocompetent: Watery diarrhea, fever, self-limited
• Immunocompromised: Watery diarrhea, fever, systemic symptoms, nausea, emesis à ↑ Risk of meningitis and sepsis
Listeriosis of Pregnancy: Risk of transmission to fetus (transplacental, vaginal) à Chorioamnionitis, spontaneous abortion, granulomatosis infantiseptica in neonate
Granulomatosis Infantiseptica: Disseminated abscesses, respiratory distress, dermatologic lesions +/- meningeal signs
Meningoencephalitis:
• Neonates, elderly, and immunocompromised
• Meningeal signs (nuchal rigidity, photophobia, + Kernig sign, + Brudzinski sign)
Diagnostics:
• Pregnant à Blood cultures +/- cold enrichment
• Suspected meningitis à Lumbar puncture
Management:
• Ampicillin
Microbiology: Non-Spore Forming Gram Positive Bacilli Bootcamp.com

General Principles:
• Nocardia asteroides complex, Nocardia brasiliensis
• Gram positive with branching filaments
• Partial acid-fast (Ziehl-Neelsen stain)
• Catalase positive
• Urease
• Aerobe
Pathogenesis:
• Ubiquitous in soil
Pulmonary Nocardiosis:
• Immunocompromised patient
• Presentation: Productive cough, dyspnea, weight loss, night sweats, fever, chills
• TST test negative
• ↑ Risk of CNS spread
Disseminated Nocardiosis:
• Multiple sites affected (lungs, CNS)
• Neurologic à Lethargy, confusion, seizures, focal neurologic deficits
• Dermatologic à Abscesses, cellulitis, subcutaneous mycetoma, painful LAD
Diagnostics:
• Sputum culture, chest X-ray
• Skin biopsy
• Lumbar puncture, MRI brain
Management:
• Trimethoprim-Sulfamethoxazole
Microbiology: Non-Spore Forming Gram Positive Bacilli Bootcamp.com

General Principles:
• Gram positive with branching filaments
• Yellow sulfur granules
• Not acid-fast
• Anaerobic
Pathogenesis:
• Oral (most common), intestinal, and female genital flora
Cervicofacial Actinomycosis:
• ↑ Risk with poor dental hygiene, oral or maxillofacial trauma, diabetes mellitus
• Insidiously progressive painless mass +/- induration, purulent discharge, fistulae, draining sinus tracts
• Perimandibular masses are classic
• Sulfur granules within purulent discharge
Abdominal and Pelvic Actinomycosis:
• ↑ Risk in females with IUD
• Pelvic inflammatory disease à Ascending infection to gastrointestinal system
• Abdominal pain, fever, ↑ vaginal bleeding +/- discharge
Diagnostics:
• Identification of sulfur granules
• Culture à Slow growth
Management:
• Penicillin G +/- Surgical debridement
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0080

A 54-year-old male with an unknown past medical history presents to the emergency department for progressively worsening fatigue and
lightheadedness over the past 4 days. He states that he lives in China and is currently visiting North America for business meetings. When asked about
his underlying conditions he states that he has a history of hypertension, malaria and syphilis. He states that he also has a kidney problem for which he
takes prednisone and tacrolimus daily. His blood pressure on arrival is 74/50 mmHg and his temperature is 38.1℃ (100.6℉). Physical examination
reveals multiple areas of soft tissue swelling on his neck and left gluteal region that are tender to touch without evidence of discharge. He denies any
recent injury. The patient also has 2+ pitting edema in the bilateral lower extremities up to the distal thigh. During the encounter, the patient is observed to
be coughing up yellow sputum. Laboratory evaluation and advanced imaging of the chest are shown below. Bronchial washings reveal gram positive
bacilli in branching filaments. Which of the following most likely describes a distinguishing characteristic of the pathogen causing this patient’s illness?

Leukocyte count: 17,200/mm3

Hemoglobin: 9.5 g/dL
Platelets: 108,000/mm3
Creatinine: 2.1 mg/dL
Serum albumin: 2.2 g/dL
Urine dipstick: 3+ protein

⚪ A. Urease positive

⚪ B. Weakly β-hemolytic

⚪ C. Yellow microscopic granules

⚪ D. Polypeptide capsule

⚪ E. Absent cell wall

 OUTLINE
1. Escherichia Coli
A. General Principles

Microbiology: B. Pathogenesis
C. LPS Endotoxin
D. Extended-spectrum β-lactamase-producing E. coli

Lactose
2. Variant Strains of Escherichia Coli
A. Enterohemorrhagic
B. Enterotoxigenic

Fermenting Gram
C. Enteroinvasive
D. Enteropathogenic
E. Enteroaggregative

Negative Bacilli
F. Uropathogenic
G. Neonatal Meningitis
3. Klebsiella
A. General Principles
B. Pathogenesis
C. Disease Variants
E. Management
4. Additional Pathogens
A. Serratia Marcescens
B. Citrobacter
C. Enterobacter
Microbiology: Lactose Fermenting Gram Negative Bacilli Bootcamp.com
Microbiology: Lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Gram negative motile bacilli
• Non-spore forming, encapsulated
• Lactose, glucose, and sorbitol fermenter
• β-galactosidase
• MacConkey agar à Pink colonies
• Eosin-Methylene blue agar à Green metallic sheen
• Sorbitol-MacConkey Agar à Selective for E. coli O157:H7 (does not turn medium pink)
• Facultative anaerobe
• Catalase positive, indole positive, oxidase negative, urease negative, bile resistant
Pathogenesis:
• Intestinal flora
• LPS endotoxin à Bacteremia and septic shock
• Heat-labile, heat-stable enterotoxins (ETEC) à ↑ Electrolyte and fluid secretion into intestinal lumen à Watery diarrhea
• Shiga-like toxin (EHEC) à Inactivation of 60S ribosomal subunit à Gastroenteritis à ↓ Protein formation à Enterocyte necrosis à Bloody diarrhea
• P fimbriae à ↑ Adhesion to uroepithelium à Cystitis, pyelonephritis
• K antigen (capsule): K1 capsule à ↓ Phagocytosis and complement activation à Neonatal meningitis
• H antigen (flagella)
LPS Endotoxin:
• O-antigen: Outer domain, target for host antibodies (TLR4, CD14)
• Core domain: Linked between O-antigen and lipid A
• Lipid A: Toxicity to host à Septic shock
Extended-spectrum β-lactamase-producing E. coli (ESBL):
• Resistance to β-lactamase antibiotics (Cephalosporins)
 Microbiology: Lactose Fermenting Gram Negative Bacilli Bootcamp.com

Enterohemorrhagic (EHEC):
• Transmitted via undercooked meat, raw leafy vegetables, and unpasteurized dairy products
• Does not ferment sorbitol
• O157:H7
• Shiga-like toxin à Inactivation of 60S ribosomal subunit à ↓ Protein formation à Enterocyte necrosis à Bloody diarrhea
• Hemolytic Uremic Syndrome: Hemolytic anemia, thrombocytopenia, acute renal failure
• Supportive management (Antibiotics may ↑ risk of development of HUS)
Enterotoxigenic (ETEC):
• Traveler’s diarrhea
• Heat-labile (LT) enterotoxin à ↑ Gs à ↑↑↑ Adenylate cyclase activation à ↑ Intracellular cAMP à ↑ Cl- ion secretion into lumen
• Heat-stable (ST) enterotoxin à ↑↑↑ Guanylate cyclase à ↑ Intracellular cGMP à ↑ Cl- ion secretion into lumen
• Watery diarrhea, abdominal pain, nausea, emesis
• Supportive management
Enteroinvasive (EIEC):
• Enterotoxin à Watery diarrhea
• Enterocyte invasion à Enterocyte necrosis à Bloody diarrhea
• Supportive management
Enteropathogenic (EPEC):
• Effacement and destruction of microvilli of enterocytes à ↓ Absorption, ↑ Permeability of tight junctions
• Does not produce toxin
• Children
Enteroaggregative (EAEC):
• Aggregation and adherence to enterocytes (“Stacked brick” pattern) à ↑ Inflammation à Persistent diarrhea (watery à bloody +/- pus)
Uropathogenic (UPEC):
• MCC of cystitis/UTI
• P fimbriae (pili) à Pyelonephritis
• Dysuria, urinary frequency/urgency, +/- costovertebral tenderness
• Trimethoprim-sulfamethoxazole, fosfomycin, nitrofurantoin
Neonatal Meningitis (NMEC):
• K1 capsular polysaccharide à ↓ Phagocytosis and complement activation
• Hypotonia, neck stiffness, lethargy, bulging fontanelle, hyperthermia/hypothermia, Kernig sign, Brudzinski sign
• Lumbar puncture
• Ampicillin
Microbiology: Lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Klebsiella pneumoniae, Klebsiella granulomatis, Klebsiella oxytoca
• Gram negative non-motile bacilli
• Non-spore forming, encapsulated (large mucoid capsule)
• Lactose and glucose fermenter
• MacConkey agar à Mucoid pink colonies
• Eosin-Methylene blue agar à Purple-black colonies
• Catalase positive, indole negative, oxidase negative, urease positive
• Facultative anaerobe
Pathogenesis:
• Intestinal flora (K. pneumoniae), genital flora (K. granulomatis)
• Large polysaccharide capsule à↓ Phagocytosis and complement activation
• LPS endotoxin à Septic shock
Nosocomial UTI:
• Indwelling catheter
• Struvite (magnesium ammonium phosphate) nephrolithiasis: ↑ Risk with urease-producing bacteria à Staghorn calculi (weakly radiopaque)
Pneumonia:
• Classically aspiration, consider CAP, lobar distribution, destructive process
• Immunocompromised, alcohol use disorder, diabetics
• Dark red “currant jelly” sputum
Invasive Abscesses:
• Pulmonary
• Hepatic à RUQ pain
Granuloma Inguinale (Donovanosis): K. granulomatis, STI, chronic ulcerative genital disease, “beefy-red” ulcer, Donovan bodies
Neonatal bacteriemia: K. oxytoca, premature infants
Management:
• Multi-drug resistance (ESBL)
• Ceftriaxone (3rd generation cephalosporins)
Microbiology: Lactose Fermenting Gram Negative Bacilli Bootcamp.com

Serratia Marcescens:
• Gram negative motile bacilli
• Reservoir: Water, starchy foods, soil
• Weak/slow lactose fermenter
• Prodigiosin (pink-red pigment)
• Catalase positive, oxidase negative, indole negative
• Facultative anaerobe
• Multi-drug resistance
• Nosocomial (PNA, UTI, wound), ocular infections, endocarditis, and meningitis
Citrobacter:
• Gram negative motile bacilli
• Weak/slow lactose fermenter
• Catalase positive, oxidase negative, indole positive
• Neonatal meningitis, UTI
Enterobacter:
• E. aerogenes, E. cloacae à Lactose fermenters
• Gram negative motile bacilli
• Catalase positive, oxidase negative, indole negative
• Facultative anaerobe
• Immunocompromised (hospitalized, mechanical ventilation)
• Nosocomial (PNA, UTI)
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0081

A 3-year-old female is admitted to a Children’s Hospital for epistaxis. The patient’s mother states that she “can’t get her daughter’s nose to stop bleeding”.
She denies any significant birth, medical, and family history. She reports that the patient has progressively become more lethargic over the past several
days. The patient has also reportedly had three days of loose, dark color stools per her mother. Physical examination reveals a temperature of 36.7℃
(98℉), blood pressure of 78/40 mmHg, heart rate 130/min, and oxygen saturation of 95% on room air. The patient’s skin is pale with decreased skin
turgor. Kernig and Brudzinski signs are negative. The epistaxis subsequently resolves with head elevation and local pressure over the course of one hour.

Serum laboratory workup is shown below. Stool culture later demonstrates growth of E. coli. Administration of which of the following would have been
most appropriate for this patient?

Leukocyte count: 28,200/mm 3

Hemoglobin: 8.1 g/dL
Platelets: 37,000/mm 3
Creatinine: 1.5 mg/dL
Urea nitrogen: 62 mg/dL
Lactate dehydrogenase 1630 U/L
Aspartate aminotransferase 60 U/L
Alanine aminotransferase 10 U/L
C-reactive protein 9.2 mg/L
⚪ A. Empiric antibiotic therapy with ampicillin and gentamycin Peripheral blood smear: Poikilocytes and fragmented erythrocytes.

⚪ B. Empiric antibiotic therapy with trimethoprim/sulfamethoxazole

⚪ C. Platelet transfusion

⚪ D. Bismuth subsalicylate

⚪ E. Intravenous fluids
 OUTLINE
1. Shigella 6. Proteus
A. General Principles A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Management and Complications
B. Pathogenesis
C. Disease Variants
D. Management

Non-lactose
2. Non-typhoidal Salmonella 7. Pseudomonas Aeruginosa
A. General Principles A. General Principles
B. Pathogenesis B. Pathogenesis

Fermenting Gram
C. Disease Variants C. Disease Variants
D. Management and Complications D. Management
3. Salmonella Typhi 8. Legionella Pneumophila

Negative Bacilli
A. General Principles A. General Principles
B. Pathogenesis B. Pathogenesis
C. Disease Variants C. Disease Variants
E. Management and Complications E. Management
4. Yersinia Enterocolitica
A. General Principles
B. Pathogenesis
C. Disease Variants
E. Management and Complications
5. Yersinia Pestis
A. General Principles
B. Pathogenesis
C. Disease Variants
E. Management and Complications
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com
Microbiology Non-Lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• S. dysenteriae, S. flexneri, S. boydii, S. sonnei
• Gram negative non-motile bacilli
• Non-lactose fermenter
• Glucose fermenter
• Does not produce H2S
• MacConkey agar à Colorless colonies
• Triple sugar iron test à Yellow base, red slant
• Facultative anaerobe
• Catalase positive (except S. dysenteriae type 1), oxidase negative, urease negative
Pathogenesis:
• Food contamination (undercooked meat)
• Fecal-oral transmission à Invasion of Peyer’s patches and M-cells à Cell to cell transmission à Phagosome evasion à Bloody, mucous diarrhea
• Resistance to gastric acid, no hematogenous dissemination (no flagella)
• Shiga-toxin à Inactivation of 60S ribosomal subunit (minor pathogenicity vs EHEC)
• LPS endotoxin à Septic shock
Gastroenteritis, Dysentery:
• ↑ Risk in children, ↓ ID50
• Watery à Bloody and mucoid diarrhea
• Nausea, emesis, abdominal pain/cramping, malaise
Management:
• Hydration, correct electrolyte derangements
• Ceftriaxone, ciprofloxacin, trimethoprim-sulfamethoxazole
Complications:
• Reactive arthritis (Reiter syndrome) à Conjunctivitis, urethritis, oligoarthritis (lower extremities)
• Hemolytic uremic syndrome (similar to EHEC)
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• S. enterica serotype Enteritidis, S. enterica serotype Typhimurium
• Gram negative motile bacilli
• Non-lactose fermenter
• Glucose fermenter
• Produces H2S
• MacConkey agar à Colorless colonies
• Triple sugar iron test à Yellow base, black color above base, red slant
• Facultative anaerobe
• Catalase positive, oxidase negative, urease negative
Pathogenesis:
• Reservoir: Humans and animals
• Food contamination (undercooked poultry, eggs), reptile pets (turtles)
• Fecal-oral transmission à Bacteria destroyed in stomach à Surviving bacteria multiply in intestine à Endotoxin release à Watery +/- Bloody diarrhea
• ↑↑↑ Neutrophil inflammatory response
• Not resistant to gastric acid, hematogenous dissemination
• Flagella
• LPS endotoxin à Septic shock
Gastroenteritis, Dysentery:
• ↑ Risk in children, ↑ ID50
• Watery +/- Bloody diarrhea
• Nausea, emesis, abdominal pain/cramping, malaise
Management:
• Hydration, correct electrolyte derangements
• Typically self-limited
Complications:
• Reactive arthritis (Reiter syndrome) à Conjunctivitis, urethritis, oligoarthritis (lower extremities)
 Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• S. enterica serotype Typhi, S. enterica serotype Paratyphi
• Gram negative motile bacilli
• Encapsulated
• Non-lactose fermenter
• Glucose fermenter
• Produces H2S
• MacConkey agar à Colorless colonies
• Triple sugar iron test à Yellow base, black color above base, red slant
• Facultative anaerobe
• Catalase positive, oxidase negative, urease negative
Pathogenesis:
• Reservoir: GI tract
• Travelers to resource-limited regions and areas of poor sanitation
• Fecal-oral transmission à Bacteria destroyed in stomach à Surviving bacteria invade Peyer’s patches and M-cells à Hematogenous spread
• +/- Gallbladder colonization in chronic carriers
• Not resistant to gastric acid, hematogenous dissemination
• Flagella
• LPS endotoxin à Septic shock
• Vi capsule (vaccine target) à ↓ Phagocytosis à ↓↓↓ Neutrophil response à ↑ Intracellular replication à Spread to reticuloendothelial system à Monocyte-mediated response
Gastroenteritis, Typhoidal Fever:
• ↑ Risk in children, ↑ ID50
• Progressively worsening fever over several days, high fever, pulse-temperature dissociation
• Faint erythematous maculopapular lesions (“Rose spots), chest and abdomen are classic, trunk à extremities
• Nausea, emesis, abdominal pain/cramping, malaise
• Constipation à Watery (“pea-soup”) diarrhea
• Hepatosplenomegaly, anemia, leukopenia
• Osteomyelitis in sickle cell disease
Management:
• Hydration, correct electrolyte derangements
• Ceftriaxone, ciprofloxacin, azithromycin
• Oral vaccine: Live-attenuated S. typhi
• IM vaccine: Vi capsular polysaccharide
Complications: Ulceration, hemorrhage à Bowel perforation
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Y. enterocolitica, Y. pseudotuberculosis
• Gram negative non-motile coccobacilli (pleomorphic)
• Bipolar staining (“closed safety pin”)
• Non-lactose fermenter
• Glucose fermenter
• Iron and cold enrichment ↑ growth (siderophilic)
• Does not produce H2S
• MacConkey agar à Colorless colonies
• Facultative anaerobe
• Catalase positive, oxidase negative, urease positive
Pathogenesis:
• Food contamination (undercooked pork, unpasteurized milk), pet feces
• Fecal-oral transmission à Bacteria proliferate in terminal ileum and invade Peyer’s patches and M-cells à Enterotoxin release à Bloody diarrhea
• Migration to mesenteric lymph nodes à Lymphadenopathy
• Enterotoxin à ↑↑↑ Guanylate cyclase à ↑ Intracellular cGMP à ↑ Cl- ion secretion into lumen à Watery diarrhea
• Type III secretion system à Inject Yops à Forms pores in host cell membranes, ↓ phagocytosis, ↓ host cytokine production
• LPS endotoxin à Septic shock
Gastroenteritis:
• ↑ Risk in children, day-care centers, and iron-overload states (hemochromatosis)
• Watery +/- bloody diarrhea
• Nausea, emesis, abdominal pain/cramping, malaise
• Pseudoappendicitis: RLQ abdominal pain + mesenteric lymphadenitis
• Abdominal CT: No imaging evidence of appendicitis
Management:
• Hydration, correct electrolyte derangements
• Typically self-limited
• Severe cases à Gentamycin, doxycycline, ceftriaxone, trimethoprim-sulfamethoxazole
Complications:
• Reactive arthritis (Reiter syndrome) à Conjunctivitis, urethritis, oligoarthritis (lower extremities)
• Intussusception à Bowel ischemia
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Gram negative non-motile coccobacilli (pleomorphic)
• Bipolar staining (“closed safety pin”)
• Non-lactose fermenter
• Iron and cold enrichment ↑ growth (siderophilic)
• Does not produce H2S
• MacConkey agar à Colorless colonies
• Facultative anaerobe
• Catalase positive, oxidase negative, urease negative
Pathogenesis:
• Reservoir: Rats/rodents and prairie dogs
• Flea bite transmission à Bacteria migrate to local lymph nodes à F1 and V capsular antigen ↓ phagocytosis à Bacteria survive within macrophages
• Type III secretion system à Inject Yops à Forms pores in host cell membranes, ↓ phagocytosis, ↓ host cytokine production
• LPS endotoxin à Septic shock
Plague:
• Very rare incidence (Southwest U.S.)
• ↑ Risk in young patients with exposure to small rodents or occupational exposure
• High fever, chills, myalgias, fatigue, lymphedema
• Bubonic: Regional tender, swollen lymph nodes (“buboes”) à May rupture with purulent discharge
• Pneumonic: Hemoptysis, chest pain, dyspnea, cough
Management:
• Hydration, correct electrolyte derangements, respiratory and hemodynamic support
• Gentamycin, doxycycline, ciprofloxacin
• Untreated disease à High mortality
• Inactivated vaccine à High risk populations
Complications:
• Acute respiratory distress syndrome
• Disseminated intravascular coagulopathy
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• P. mirabilis, P. vulgaris
• Gram negative motile (“swarming”) bacilli
• Non-lactose fermenter
• Produces H2S
• MacConkey agar à Colorless colonies
• Triple sugar iron test à Yellow base, black color above base, red slant
• Facultative anaerobe
• Catalase positive, oxidase negative, urease positive
Pathogenesis:
• Reservoir: Gastrointestinal tract
• ↑ Fimbriae and flagella à Rapid motility
• LPS endotoxin à Septic shock
Urinary Tract Infection:
• Nosocomial UTI: Indwelling catheter
• Dysuria, ↑ urinary frequency +/- costovertebral tenderness
• Nitrite positive
• Struvite (magnesium ammonium phosphate) nephrolithiasis: ↑ Risk with urease-producing bacteria à Staghorn calculi (weakly radiopaque)
Management:
• Trimethoprim-sulfamethoxazole
• Nitrofurantoin, ceftriaxone (pregnancy)
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Gram negative motile bacilli
• Non-lactose fermenter
• Non-glucose fermenter
• Does not produce H2S
• MacConkey agar à Colorless colonies
• Triple sugar iron test à Red base and slant (appears the same as control)
• Facultative anaerobe (prefers aerobic conditions)
• “Grape-like” or “sweet” odor
• Encapsulated (mucoid polysaccharide)
• Biofilm
• Catalase positive, oxidase positive
Pathogenesis:
• Exotoxin A: Inactivation of EF2 via ADP-ribosylation à ↓ Protein synthesis
• Pyoverdine and pyocyanin: blue-green pigments à blue-green pus,↑ reactive oxygen species
• Phospholipase C: Degrades phospholipids in cell membranes
• Elastase: Degrades elastin à Connective tissue destruction
• β-lactamase, antibiotic-modifying enzymes, efflux pumps
• LPS endotoxin à Septic shock
Ventilator-associated Pneumonia: Nosocomial infection, classic in immunocompromised or prior chronic pulmonary disease
Recurrent Pneumonia: Cystic fibrosis à Hyperviscous mucous à ↓ Mucociliary clearance (MCC in adulthood= Pseudomonas)
“Hot-tub” Folliculitis: Contaminated water exposure à Pruritis, pustular rash on trunk and extremities
Otitis Externa (“Swimmer’s Ear”): Contaminated water exposure à Outer ear infection à Tenderness palpating tragus +/- otorrhea
Malignant Otitis Externa: Elderly, T2DM, immunocompromised à Severe pain and otorrhea à ↑ Risk of cranial osteomyelitis
Ecthyma Gangrenosum: Bacteremia à Exotoxin-mediated tissue necrosis à Rapidly progressive necrotic lesion
Corneal Ulcers: Contact lens wearers
Osteomyelitis: IVDU, diabetes (puncture foot wounds)
Urinary Tract Infection: Indwelling/frequent catheterization, nosocomial infection, ↑ multidrug resistance
Management:
• Piperacillin-tazobactam, ticarcillin-clavulanate
• Ceftazidime, cefepime
Microbiology Non-lactose Fermenting Gram Negative Bacilli Bootcamp.com

General Principles:
• Gram negative motile facultative intracellular bacilli
• Poorly visualized on gram stain
• Silver stain
• Charcoal yeast extract agar: Buffered with cysteine and iron
• MacConkey agar à Colorless colonies
• Obligate aerobe
• Catalase positive, oxidase positive
Pathogenesis:
• Aerosol transmission from contaminated water (air conditioning, water tanks, cruise ships)
• Rare person-to-person transmission
• β-lactamase
• LPS endotoxin à Septic shock
Legionnaire’s Disease:
• ↑ Risk with chronic pulmonary disease (COPD), immunocompromised
• Unilateral atypical pneumonia (classically), dry à productive cough
• Fever, pulse-temperature dissociation, watery diarrhea, nausea, emesis
• Neurologic symptoms: Confusion, encephalopathy, seizures
• Diagnostics: Hyponatremia, urine antigen testing
Pontiac Fever:
• Healthy patient (usually)
• Mild variant, constitutional symptoms, self-limited
Management:
• Levofloxacin, moxifloxacin
• Erythromycin, azithromycin
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0082

A 55-year-old female is transferred to a tertiary care hospital for of sepsis of unknown etiology and had been treated with various antibiotics. She has a
past medical history of chronic obstructive pulmonary disease and had been lost to follow up for many years prior to admission. Her symptoms initially
started 3-weeks earlier with lethargy and abdominal pain. On examination her temperature is 39.4℃ (102.9℉), blood pressure of 110/80mmHg, heart rate
68/min. The patient has a grey-bronzed complexion diffusely, including over areas of unexposed skin. Scleral icterus and palmar erythema are also
present. The patient has abdominal tenderness to palpation in the right upper and lower quadrants with evidence of hepatomegaly. Relevant laboratory
investigations are shown below. Abdominal ultrasounds reveals an enlarged liver with increased echogenicity and irregular contour. A CT scan of the
abdomen and pelvis is performed demonstrating a heterogenous liver with numerous hypodense lesions and mesenteric lymphadenopathy. A gram stain
of tissue isolated from one of the lesions reveals numerous gram-negative bacteria with dense staining of the pathogen peripherally and poor staining
centrally.

Which of the following features are most consistent with the pathogen isolated from this patient?

Leukocyte count: 18,400/mm 3

Erythrocyte sedimentation rate: 140 mm/h (ref: 0-20 mm/h)
Alanine aminotransferase (ALT): 380 U/L (ref: 8-20 U/L)
Aspartate aminotransferase (AST): 390 U/L (ref: 8-20 U/L)
Total bilirubin: 3.4 mg/dL (ref: 0.1-1.0 mg/dL)
Alkaline phosphatase (ALP): 370 U/L (20-70 U/L)
⚪ A. Produces green color colonies on thiosulfate citrate bile salts sucrose agar Gamma glutamyl transferase (GGT): 450 U/L (ref: 5-40 U/L)
Albumin: 1.8 g/dL (ref: 3.5-5.5 g/dL)
⚪ B. Produces black-purple color colonies on eosin methylene blue agar Ferritin: 1,670 ng/mL (ref: 15-150 ng/mL)
Transferrin saturation: 98% (ref: 15-45%)
⚪ C. Produces colorless colonies on MacConkey agar

⚪ D. Produces a narrow zone of hemolysis on blood agar

⚪ E. Produces a black color within the medium on the triple sugar iron test
 OUTLINE
1. Campylobacter Jejuni
A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Management and Complications

Gram Negative
2. Helicobacter Pylori
A. General Principles
B. Pathogenesis

Curved Rods
C. Disease Variants
D. Diagnostics
E. Management and Complications
3. Vibrio
A. General Principles
B. Pathogenesis
C. Disease Variants and Management
Microbiology: Gram Negative Curved Rods Bootcamp.com
Microbiology: Gram Negative Curved Rods Bootcamp.com

General Principles:
• Gram negative motile “corkscrew-shaped” bacilli
• “Darting” motility
• Growth at high temperatures (37-42℃, thermophilic)
• Microaerophile
• Catalase positive, oxidase positive, urease negative
Pathogenesis:
• Food contamination (undercooked poultry or meat, unpasteurized dairy), contact with infected domestic animals, travel to resource-limited regions
• Fecal-oral transmission à Invasion of intestinal mucosa à Watery diarrhea à Bloody diarrhea
• Cytolysins
• Polar flagella (amphitrichous)
• LOS endotoxin à Septic shock
Gastroenteritis, Dysentery:
• ↑ Risk in children, ↓ ID50
• Bloody, mucoid diarrhea
• Fever, nausea, emesis, abdominal pain/cramping, malaise
Management:
• Hydration, correct electrolyte derangements
• Azithromycin (severe infections)
Complications:
• Reactive arthritis (Reiter syndrome) à Conjunctivitis, urethritis, oligoarthritis (lower extremities)
• Guillain-Barre syndrome à Ascending muscle weakness, ↓ DTRs
Microbiology: Gram Negative Curved Rods Bootcamp.com

General Principles:
• Gram negative motile “spiral-shaped” bacilli
• Silver stain
• Microaerophile
• Catalase positive, oxidase positive, urease positive
Pathogenesis:
• Antrum à Body of stomach
• Urease hydrolyzes urea to form ammonia à Ammonia neutralizes gastric acid à H. pylori attaches to epithelial cells à Destroys somatostatin-producing D-cells
• ↓ Somatostatin release à ↑ Gastrin, ↑ HCl à ↑ Risk of PUD
• Flagella (lophotrichous)
• LPS endotoxin à Septic shock
Gastroenteritis, Peptic Ulcer Disease:
• ↑ Risk with smoking and NSAID use
• Epigastric pain/cramping, bloating, GERD
• Gastric or duodenal ulcers
Diagnostics:
• Urea breath test
• Fecal antigen test
• Endoscopy à Gastric biopsy
Management:
• Triple therapy: Amoxicillin + Clarithromycin + PPI (omeprazole)
• Quadruple therapy: Metronidazole + Tetracycline + Bismuth subcitrate + PPI (omeprazole)
• Antacid for symptomatic treatment
• Avoid NSAID, tobacco, caffeine, alcohol
Complications:
• Gastric adenocarcinoma
• MALT Lymphoma
• Iron deficiency anemia
Microbiology: Gram Negative Curved Rods Bootcamp.com

General Principles:
• V. cholerae, V. vulnificus, V. parahaemolyticus
• Gram negative motile “comma-shaped” bacilli
• V. cholerae: Growth in alkaline media. (acid labile)
• Thiosulfate citrate bile salts sucrose agar: V. cholerae à yellow colonies, V. parahaemolyticus and V. vulnificus à green colonies
• Nonlactose fermenter (exception: V. vulnificus)
• Nonsucrose fermenter (exception: V. cholerae)
• Iron enrichment ↑ growth
• Facultative anaerobe
• Catalase positive, oxidase positive, urease negative
Pathogenesis:
• Saltwater, brackish marine waters
• Water contamination or raw shellfish (oysters), travel to resource-limited regions
• V. cholera à Cholera toxin: ↑ Gs à ↑↑↑ Adenylate cyclase activation à ↑ Intracellular cAMP à ↑ Cl- and H2O secretion into the lumen
• V. vulnificus à Hemolysins, cytolysins, and metalloproteases à Invasive
• V. vulnificus à Polysaccharide capsule
• Polar flagella: V. cholerae, V. vulnificus (monotrichous), V. parahaemolyticus (peritrichous)
• LPS endotoxin
Cholera:
• ↑ ID50
• Cholera-toxin mediated disease à Profuse “rice-water” diarrhea, dehydration (“sunken” eyes)
• Non-inflammatory
• Isonatremic hypovolemia, hypokalemia, lactic acidosis
• Rx: Aggressive rehydration, correct electrolyte derangements
Dysentery, Necrotizing Wound Infections, Septic Shock:
• V. vulnificus, V. parahaemolyticus
• ↑ Risk of V. vulnificus infection in cirrhosis, pre-existing wounds, handling shellfish, and ↑ serum iron levels (hemochromatosis)
• High mortality rate
• Cellulitis àBullous lesions à Necrotizing fasciitis
• Rx: Third generation cephalosporin (cefotaxime or ceftriaxone) + Doxycycline + Ciprofloxacin +/- surgical wound debridement
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0083

A researcher is attempting to study the effects of a toxigenic strain of Vibrio cholerae serogroup O139. The researcher reviews a prior study of which
patients with known V. cholerae serogroup O139 infection were placed into asymptomatic and symptomatic groups based on their clinical presentation.
The duration and number of bacteria shed in the stool were measured with mean data shown below. The researcher notes that the study does not
account for possible antibiotic, proton pump inhibitor, or antacid medication use in either group.

If curve “X” represents symptomatic patients that have not taken any medications in the past year, which of the following curves is most consistent with
symptomatic patients on chronic proton pump inhibitor therapy?
Patient Group Mean Pathogen Shed Quantity Mean Pathogen Shed Duration
(Vibrios/L of stool) (Days)

Asymptomatic 103 1.2

Symptomatic 1011 12.4

% infected
by V. cholerae A C D E
Serogroup O139 B X
⚪ A. Curve A

⚪ B. Curve B
50

⚪ C. Curve C

⚪ D. Curve D

⚪ E. Curve E

102 106 1010 Bacterial

inoculum
 OUTLINE
1. Neisseria Gonorrhoeae
A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Diagnostics

Gram Negative
E. Management
F. Complications
2. Neisseria Meningitidis

Diplococci
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Diagnostics
E. Management
F. Complications
3. Moraxella Catarrhalis
A. General Principles
B. Pathogenesis
C. Disease Variants
Microbiology: Gram Negative Diplococci Bootcamp.com
Microbiology: Gram Negative Diplococci Bootcamp.com

General Principles:
• Gram negative “kidney-shaped” diplococci
• Thayer-Martin media: Chocolate blood agar selective for Neisseria (Vancomycin, Trimethoprim, Colistin, Nystatin)
• Glucose fermenter
• Non-maltose fermenter
• Facultative intracellular (neutrophils)
• Aerobic, oxidase positive
Pathogenesis:
• Transmitted sexually or perinatally
• ↑ Risk w/ multiple sexual partners, lack of barrier protection
• Type IV Pilus (Adhesin) à ↑ Mucosal attachment to host (vaginal and urethral tissue)
• IgA1 protease à Cleaves serum and secretory IgA à ↑ Mucosal adherence to host
• Does not contain polysaccharide capsule
• LOS endotoxin à Septic shock
• Antigenic and phase variation à Pili, LOS
Cervicitis, Urethritis (Gonorrhea):
• Can be asymptomatic
• Dysuria, urinary urgency, mucopurulent urethral discharge, pruritis
• Friable cervical mucosa
Diagnostics:
• Nucleic acid amplification testing (NAAT)
Management:
• Ceftriaxone (1 dose IM) + Doxycycline or Azithromycin (unless Chlamydial infection ruled out)
• Avoid doxycycline in pregnancy
• Sexual partners should be treated
• No vaccination available (Pili antigenic variation)
Complications:
• Pelvic Inflammatory Disease: Abdominal/pelvic pain, cervical motion tenderness, purulent cervical/vaginal discharge, ↑ Risk of infertility and ectopic pregnancy
• Fitz-Hugh-Curtis Syndrome (Perihepatitis): Pleuritic RUQ pain, Violin-string-like adhesions
• Epididymitis: Acute onset, unilateral (usually) testicular pain and edema, classically < 35y
• Disseminated Gonococcal Infection: Asymmetric migratory polyarthralgias +/- tenosynovitis, dermatitis
• Neonatal Gonococcal Conjunctivitis: Rare in U.S., ↑ Risk of keratitis à Blindness
Microbiology: Gram Negative Diplococci Bootcamp.com

General Principles:
• Gram negative “kidney-shaped” diplococci
• Thayer-Martin media: Chocolate blood agar selective for Neisseria (Vancomycin, Trimethoprim, Colistin, Nystatin)
• Glucose fermenter
• Maltose fermenter
• Facultative intracellular
• Aerobic, oxidase positive
Pathogenesis:
• Colonization of nasopharynx à Transmitted via respiratory droplets
• ↑ Risk in college students, military and those with underlying terminal complement deficiencies
• Nasopharynx à Hematogenous spread à Choroid plexus à Meninges
• Type IV Pilus (Adhesin) à ↑ Mucosal attachment to host (epithelial tissue in nasopharynx)
• IgA1 protease à Cleaves serum and secretory IgA à ↑ Mucosal adherence to host
• Polysaccharide capsule à ↓ Phagocytosis, ↓ Complement-mediated destruction
• LOS endotoxin à Petechial rash, Septic shock
• Antigenic and phase variation à Pili, LOS
Bacterial Meningitis, Meningococcemia:
• Acute onset headache, nuchal rigidity, photophobia, nausea, emesis, fever, chills, myalgias
• Petechiae, purpura ecchymoses, Brudzinski’s and Kernig sign
Diagnostics:
• Lumbar puncture à CSF gram stain and/or culture à Pleocytosis
• Leukocytosis, bandemia
• Blood cultures
Management:
• Ceftriaxone (Empiric)
• Rifampin, ciprofloxacin, or ceftriaxone for chemoprophylaxis in close contacts
• Vaccination with MenACWY (Quadrivalent conjugate) (2 doses); MenB for high risk
Complications:
• Waterhouse-Friderichsen Syndrome (Adrenal infarction/hemorrhage) à Adrenal insufficiency, circulatory collapse, fever, DIC
Microbiology: Gram Negative Diplococci Bootcamp.com

General Principles:
• Gram negative diplococci
• Non-glucose fermenter
• Non-maltose fermenter
• Obligate aerobe, oxidase positive
Pathogenesis:
• Colonization of nasopharynx
• ↑ Risk in infants and children, COPD
Acute Otitis Media:
• Fever, bulging tympanic membrane, otalgia, loss of light reflex
Additional Disease Variants:
• Acute COPD exacerbation
• Rhinosinusitis
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪ Bootcamp.com
Question ID: 0084

A 33-year-old male with a past medical history of asthma presents to the emergency room for acute onset “stabbing” abdominal pain. He states that he
consumed a tuna sandwich with a glass of milk for lunch earlier in the day. He also reports that his urine has been dark red for the past several hours.
Physical examination reveals jaundice of the skin, scleral icterus, and right upper quadrant tenderness to light palpation with a palpable liver border.
Doppler ultrasound reveals a thrombotic occlusion of a hepatic vein. Urine dipstick is positive for heme. The patient undergoes localized thrombolysis and
is later started on ravulizumab for his underlying condition. Primary prevention from which pathogen is most likely indicated in this patient?

⚪ A. Neisseria gonorrhoeae

⚪ B. Neisseria meningitidis

⚪ C. Human herpesvirus type 3

⚪ D. Mycobacterium tuberculosis

⚪ E. Bacillus anthracis
 OUTLINE
1. Haemophilus
A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Diagnostics

Gram Negative
E. Management
2. Bordetella Pertussis
A. General Principles

Coccobacilli
B. Pathogenesis
C. Disease Variants
D. Diagnostics
E. Management
F. Complications
3. Additional Pathogens
A. Pasteurella Multocida
B. Francisella Tularensis
C. Acinetobacter Baumannii
D. Brucella
Microbiology: Gram Negative Coccobacilli Bootcamp.com
Microbiology: Gram Negative Coccobacilli Bootcamp.com

General Principles:
• H. influenzae, H. ducreyi
• Gram negative non-motile coccobacilli
• Chocolate agar: Growth requires factor V (NAD+) and X (hematin)
• Satellite growth on blood agar when plated with hemolytic pathogen (S. aureus)
• Facultative anaerobe
• Catalase positive, oxidase positive
Pathogenesis:
• Colonization nasopharynx à Aerosol transmission
• IgA protease à Cleaves serum and secretory IgA à ↑ Mucosal adherence to host
• Nontypeable = Unencapsulated
• Polysaccharide polyribosylribitiol phosphate capsule (Type B) à ↓ Phagocytosis, ↓ Complement-mediated destruction
• LOS endotoxin
Acute Otitis Media: H. influenzae nontypeable; Fever, bulging tympanic membrane, otalgia, loss of light reflex
Mucosal Infections (Sinusitis, bronchitis, conjunctivitis): H. influenzae nontypeable
Bacterial Meningitis: H. influenzae type B (Hib)
• Acute onset headache, nuchal rigidity, photophobia, nausea, emesis, fever, chills, myalgias
• Brudzinski’s and Kernig sign
Epiglottitis: H. influenzae type B (Hib)
• Dysphagia, sore throat, muffled voice, drooling, inspiratory stridor, tripod position, high fever, “thumbprint” sign, “cherry red” epiglottis
Endocarditis: Culture negative
• HACEK organisms: Haemophilus, Actinobacillus, Cardiobacter, Eikenella, Kingella
Chancroid: H. ducreyi
• Transmitted via sexual intercourse
• Deep painful ulcers with ragged borders and grey exudate, painful regional LAD
Asplenia: ↑ Risk of infection w/ encapsulated pathogens (Streptococcus pneumoniae, Haemophilus)
Management:
• Mucosal Infection (Non-typeable): Amoxicillin + clavulanate
• Meningitis (Hib): Ceftriaxone, Prophylaxis with Rifampin
• Chancroid: Azithromycin or ceftriaxone
• Vaccination with Hib vaccine
Microbiology: Gram Negative Coccobacilli Bootcamp.com

General Principles:
• Gram negative motile coccobacilli
• Bordet-Gengou agar
• Regan-Lowe medium (Modified to be selective)
• Obligate aerobe
• Oxidase positive
Pathogenesis:
• Transmitted via respiratory droplets
• ↑ Risk in infants
• Pertussis toxin à ADP ribosylation of Gi à ↓ Gi à ↑ Adenylate cyclase activation à ↑ Intracellular cAMP à ↑ Na+ , Cl-, H2O à ↓ Phagocytosis
• Tracheal cytotoxin à Targets respiratory epithelial tissue à ↓ Mucociliary clearance
• Filamentous hemagglutinin (FHA) à ↑ Attachment to ciliated respiratory epithelia
• LOS endotoxin
Pertussis (Whooping Cough):
• 3 stages: Catarrhal à Paroxysmal à Convalescent
• Catarrhal: Low fever, coryza, mild cough
• Paroxysmal: Paroxysms of intense dry cough (expiration) à Inspiratory “whoop” (“Whooping cough”) à Posttussive emesis
• Convalescent: Gradual recovery
• Lymphocytosis (more classically observed in viral infections)
Management:
• Azithromycin
• Vaccination with DTaP or Tdap
Complications: Respiratory failure, apnea failure to thrive (infants)
 Microbiology: Gram Negative Coccobacilli Bootcamp.com

Pasteurella Multocida:
• Charcoal yeast extract buffered with cysteine and iron
• Bipolar staining (similar to Yersinia)
• Facultative anaerobe
• Catalase positive, oxidase positive, urease negative
• Reservoir: Oropharynx of dogs and cats à Animal bite inoculation à Cellulitis à Osteomyelitis
Francisella Tularensis:
• Cultured on charcoal yeast extract buffered with cysteine and iron
• Facultative intracellular, obligate aerobe
• Catalase weakly positive, oxidase negative
• Transmission via ticks (Amblyomma Americanum, Dermacentor spp.), deer flies (Chrysops spp.), and contaminated dust, aerosols, food, and water, ↓ ID50
• Reservoir: Rabbits, rodents
• Systemic involvement: High fever, painful LAD, can affect any organ system
• Ulceroglandular tularemia à Painful maculopapular rash à Ulcerates with raised border
• Pulmonary tularemia à ↑ Mortality, pneumonia, pleuritic chest pain, dyspnea
• Typhoidal tularemia à Nausea, emesis, HSM
• Transaminitis, ↑ CPK, hyponatremia, thrombocytopenia
• Tissue biopsy: Granulomas
• Gentamicin, streptomycin, doxycycline, ciprofloxacin
Acinetobacter Baumannii:
• Obligate aerobe
• Catalase positive, oxidase negative, urease negative
• Hospital-acquired MDR infections: Ventilator-associated pneumonia
Brucella:
• B. melitensis, B. abortus, B. suis
• Charcoal yeast extract buffered with cysteine and iron
• Facultative intracellular, facultative anaerobe
• Catalase positive, oxidase positive, urease positive
• Cattle, goats, sheep, camels à ↑ Risk in farmers and veterinarians
• Transmitted via contact w/ infected animals or consumption of raw meat and/or unpasteurized dairy products, ↓ ID50
• Systemic involvement: Undulant fever, constitutional symptoms, chills, night sweats, painful LAD, HSM
• Localized involvement: Arthralgias, endocarditis, encephalopathy
• Tissue biopsy: Noncaseating granulomas
• Doxycycline + Rifampin or Doxycycline + Streptomycin
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪ Bootcamp.com
Question ID: 0085

A pathologist attempts to isolate an unknown pathogen likely involved in a systemic infection from a patient admitted in the hospital. The sample was
collected from an upper extremity wound. A gram stain from the tissue revealed numerous gram-negative coccobacilli. Cultures of the bacteria are
pending. Additional laboratory testing data of the unknown pathogen is shown below. Which of the following bacteria are most likely the cause of this
patient’s illness?

Experimental Test Result Additional Comment

Addition of hydrogen Production of bubbles Very few bubbles produced

peroxide to sample
pathogen
⚪ A. Helicobacter pylori Oxidase test (Wet Filter No color change n/a
Paper)
⚪ B. Vibrio vulnificus
Urease test (Test tube) pH prior to addition of sample: 6.8 Medium color was orange prior to and
pH after addition of sample: 6.7 after addition of sample
⚪ C. Pseudomonas aeruginosa

⚪ D. Brucella

⚪ E. Francisella tularensis

⚪ F. Pasteurella multocida
 OUTLINE
1. Treponema Pallidum
A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Diagnostics

Spirochetes
E. Complications
F. Management
G. Additional Species
2. Borrelia Burgdorferi
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Management
3. Borrelia Recurrentis
A. General Principles
B. Disease Variants
4. Leptospira
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Diagnostics
 Microbiology: Spirochetes Bootcamp.com

General Principles: Gram negative motile “helical” spirochete

Pathogenesis:
• Transmission via sexual/direct contact and transplacental
• ↑ Risk in HIV positive patients
Primary Syphilis (Localized):
• Painless chancre (ulcer w/ raised red borders), localized
• +/- painless inguinal LAD
Secondary Syphilis (Disseminated):
• Fever, fatigue, myalgias, alopecia (“moth-eaten”)
• Condyloma lata: Painless “wart-like” grey/white genital lesions
• Nonpruritic maculopapular rash (palms and soles)
• Painless generalized LAD
• Latent Syphilis: Positive serology, asymptomatic
Tertiary Syphilis (Disseminated):
• Type IV hypersensitivity reaction
• Gummas (chronic necrotizing granulomas), painless
• Endarteritis (vasa vasorum) à Inflammation and ischemia à ↓ Integrity of large vessel walls à Aneurysmal dilation
Congenital Syphilis:
• Early: Hepatomegaly, jaundice, rhinorrhea, maculopapular rash (palms and soles), painless generalized LAD
• Late: Saddle nose, notched “Hutchinson” teeth, rhagades, rhinorrhea, short maxilla, “saber” shins, CN VIII deafness
• Prevention: Mother receives penicillin early in pregnancy (transmission ~ 1st trimester)
Diagnostics:
• Dark-field microscopy
• Nontreponemal tests: VDRL, RPR à Screening tests, false positive in SLE (anti-cardiolipin)
• Treponemal test: Fluorescent treponemal antibody-absorption (FTA-ABS) à Confirmation test
Complications:
• Neurosyphilis: Tabes Dorsalis à Posterior column (DCML) à ↓ Proprioception, ↓ Vibration, Hyporeflexia, Sensory ataxia
• Argyll Robertson pupils: Light-near-dissociation
Management: Penicillin G à Jarisch-Herxheimer reaction, treat sexual partners
Additional Species: Treponema vincentii à Acute necrotizing ulcerative gingivitis
 Microbiology: Spirochetes Bootcamp.com

General Principles: Gram negative motile spirochete

Pathogenesis:
• Transmission via ticks (Ixodes scalpularis) and mice (”white-foot” mouse)
• Northeastern and north Midwest U.S. (outdoor activities)
Lyme Disease, Stage 1 (Localized):
• Erythema migrans (“bulls-eye”, “target” lesion)
• Fever, fatigue, myalgias
Lyme Disease, Stage 2 (Disseminated):
• Facial nerve palsy (Bell’s palsy), polyneuropathy
• Multiple erythema migrans
• Arthralgias (Migratory)
• Cardiac AV block (arrhythmias)
Lyme Disease, Stage 3 (Disseminated):
• Aseptic meningitis à Progressive encephalomyelitis
• Chronic arthritis (“Lyme arthritis”)
Management: Doxycycline (Localized), Ceftriaxone (Disseminated)
 Microbiology: Spirochetes Bootcamp.com

General Principles: Gram negative motile spirochete

Relapsing Fever:
• Tick-borne: Zoonosis in U.S., Borrelia spp.
• Louse-borne: Transmitted via human body louse (Pediculus spp.), Borrelia recurrentis
• Days of fever à Afebrile period à Relapse into another fever
• Headache, arthralgia, chills, abdominal pain (systemic)
• Hepatosplenomegaly
• Thrombocytopenia
• Multiphasic antigenic variation
• Doxycycline or penicillin G
 Microbiology: Spirochetes Bootcamp.com

General Principles:
• Leptospira interrogans, Leptospira kirschneri
• Gram negative motile spirochete, “hook-shaped” terminal ends, thin wall
Pathogenesis:
• Transmission via contaminated water w/ animal urine (Rodents, sheep, cattle, dogs)
• ↑ Risk in freshwater sport athletes and tropical areas (Hawaii)
Leptospirosis:
• Fever, myalgias (calf muscles), non-productive cough
• Conjunctival suffusion, photophobia
• Rx: Doxycycline, Azithromycin
Icterohemorrhagic Leptospirosis (Weil’s Disease):
• Hepatitis: Jaundice, scleral icterus/conjunctival suffusion, transaminitis, acute liver failure
• Acute kidney injury: Oliguria, hematuria, azotemia
• Anemia, hemorrhagic diathesis (purpura, hemoptysis)
• Myocarditis, pericarditis à Arrhythmia
• Rx: Penicillin G (IV)
Diagnostics: Dark-field microscopy, PCR
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0086

A 29-year-old male with a past medical history of asthma presents to his primary care physician for a new painless ulcer that was first noticed one day
prior at the base of the penile shaft. He reports that he has had unprotected sexual intercourse with twelve new partners in the past two months. He is
particularly concerned because a new sexual partner contacted him a few weeks ago to report that she had acquired a sexually transmitted infection.
Shortly thereafter, he received a one-time dose of intramuscular penicillin as prophylaxis. During the encounter he denies any urethral discharge or
dysuria. There is no evidence of other dermatologic lesions, and the patient is otherwise asymptomatic and afebrile. Examination reveals a hard,
indurated 2-centimeter erythematous lesion with mild ulcerative erosion centrally and a minor degree of exudation. HIV immunoassay is negative. Nucleic
acid amplification testing of a urine sample is negative for Chlamydia trachomatis and Neisseria gonorrhoeae. A rapid plasmin regain test is also
negative. Given the information above, which of the following would be the most appropriate empiric antimicrobial therapy for this patient at this time?

⚪ A. 5-fluorouracil

⚪ B. Metronidazole

⚪ C. Penicillin

⚪ D. Ceftriaxone

⚪ E. Dolutegravir, tenofovir, emtricitabine

⚪ F. Acyclovir
 OUTLINE
1. Chlamydia Trachomatis 7. Coxiella Burnetti
A. General Principles A. General Principles

Microbiology: B. Pathogenesis
C. Disease Variants
D. Diagnostics
B. Disease Variants

Atypical Bacteria
E. Management
F. Complications
2. Chlamydia Pneumoniae and Psittaci
A. General Principles
B. Pathogenesis
C. Disease Variants
D. Management
3. Gardnerella Vaginalis
A. General Principles
B. Disease Variants
C. Diagnostics
D. Management
4. Rickettsia
A. General Principles
B. Pathogenesis
C. Disease Variants
5. Ehrlichia and Anaplasma
A. General Principles
B. Disease Variants
6. Mycoplasma and Ureaplasma
A. General Principles
B. Disease Variants
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Gram negative à Stains poorly
• ↓ Muramic acid in cell wall à ↓ Peptidoglycans
• Obligate intracellular
• Serotypes: A-C, D-K, L1-L3
Pathogenesis:
• Phase 1: Elementary bodies à Attach à Endocytosis à Transformation
• Elementary bodies: Stable within extracellular environment, ↓ Metabolic activity
• Phase 2: Reticulate bodies à Replication à Transformation à Lysis
• Reticulate bodies: Obligate intracellular, ↑ Metabolic activity
Trachoma (Follicular Conjunctivitis):
• Serotypes A-C
• Transmitted via direct contact or insects (flies in developing countries)
• Active phase: Mucopurulent discharge, conjunctival follicles
• Cicatricial phase à Entropion, trichiasis, neovascularization à Conjunctival scarring à Blindness
Urethritis, Cervicitis (Chlamydia):
• Serotypes D-K
• Dysuria +/- purulent urethral/cervical/vaginal discharge
• Pelvic Inflammatory Disease: Abdominal/pelvic pain, cervical motion tenderness, purulent cervical/vaginal discharge, ↑ Risk of infertility and ectopic pregnancy
• Fitz-Hugh-Curtis Syndrome (Perihepatitis): Pleuritic RUQ pain, Violin-string-like adhesions
• Neonatal transmission perinatally à Neonatal conjunctivitis (1-2 weeks after birth), neonatal pneumonia (staccato cough, eosinophilia)
Lymphogranuloma Venereum:
• Serotypes L1-L3
• Small painless genital ulcers à Painful inguinal lymphadenopathy (buboes) à Abscesses à Fibrosis
Diagnostics:
• Nucleic acid amplification testing (NAAT)
• Giemsa stain: Cytoplasmic inclusion (reticulate) bodies
Management:
• Azithromycin or doxycycline + Ceftriaxone (1 dose IM) (unless Neisseria infection ruled out)
• Sexual partners should be treated
Complications: Reactive arthritis (Reiter syndrome) à Conjunctivitis, urethritis, oligoarthritis (lower extremities)
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Gram negative à Stain poorly
• ↓ Muramic acid in cell wall à ↓ Peptidoglycans
• Obligate intracellular
Atypical Pneumonia:
• Likely transmitted via aerosols
• Insidious onset of symptoms
• Dry cough or minimal sputum, dyspnea
• Myalgias, sore throat, headaches, +/- low grade fever
Psittacosis:
• Ornithosis: Chlamydia psittaci, parrots and other birds
• Abrupt onset of symptoms
• Likely transmitted via aerosols
• High grade fever, dyspnea
• Myalgias, sore throat, headaches
Diagnostics:
• General Atypical PNA CXR: Diffuse patchy infiltrates in interstitial areas (>1 lobe, usually)
• Psittacosis CXR: Lower lobe consolidation
Management:
• C. pneumoniae: Azithromycin
• C. psittaci: Doxycycline
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Pleomorphic gram-variable rod
• Facultative anaerobe
• Normal vaginal flora
Bacterial Vaginosis:
• Vaginal irrigation, recent use of antibiotics, immunosuppression
• Association with ↑ sexual activity (not sexually transmitted)
• Dysbiosis: ↓ Lactobacilli, ↑ G. vaginalis and other anaerobes
• Thin gray vaginal discharge, vaginal “fishy” odor
• Nonpainful, many cases asymptomatic
Diagnostics:
• Clue cells (vaginal epithelial cells) covered with Gardnerella on wet mount microscopy
• Vaginal pH > 4.5
• Amine (“Whiff”) test: Vaginal discharge + KOH à ↑ Characteristic amine (“fishy”) odor
Management:
• Metronidazole or clindamycin
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Gram negative non-motile coccobacilli
• Obligate intracellular
Pathogenesis:
• Tropism for vascular endothelial cells à Small vessel vasculitis
Rocky Mountain Spotted Fever:
• Rickettsia rickettsii
• Transmitted via ticks (Dermacentor spp.), Eastern and midwestern U.S. (North Carolina)
• Headache, fever
• Centripetally spreading maculopapular rash, begins on wrists and ankles (includes palms and soles)
• Thrombocytopenia
• Complicated by systemic involvement à Multiorgan dysfunction, DIC, shock
• Rx: Doxycycline
Typhus:
• Rickettsia typhi (Endemic), Rickettsia prowazekii (Epidemic)
• Transmitted via rat and cat fleas (R. typhi) and human body louse (R. prowazekii)
• Fever, myalgias, headache (more severe symptoms with R. prowazekii)
• Centrifugal spreading rash (spares palms and soles)
• Rx: Doxycycline
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Gram negative
• Obligate intracellular (Ehrlichia à monocytes/macrophages, Anaplasma à neutrophils)
Ehrlichiosis:
• Ehrlichia chaffeensis, Ehrlichia ewingii, Ehrlichia muris
• Transmitted via ticks (Amblyomma americanum, Ixodes scapularis)
• Fever, myalgias, headache +/- maculopapular/petechial rash
• Hepatomegaly
• Pancytopenia (lymphopenia), transaminitis
• PBS: Morulae within monocytes (E. chaffeensis)
• Rx: Doxycycline
Anaplasmosis:
• Anaplasma phagocytophilum
• Transmitted via ticks (Ixodes scapularis, Ixodes pacificus)
• Fever, myalgias, headache
• No rash (usually)
• Pancytopenia, transaminitis
• PBS: Morulae within neutrophils (or other granulocytes)
• Rx: Doxycycline
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Incomplete cell wall (not visible on gram stain)
• Cholesterol-stabilized membrane
• Pleomorphic
• I-antigen (binding site)
• Eaton agar (Mycoplasma pneumoniae)
Atypical Pneumonia, Tracheobronchitis:
• Mycoplasma pneumoniae
• Classically younger patients, close contact
• Insidious onset of symptoms
• Dry cough or minimal sputum, dyspnea
• Myalgias, sore throat, headaches, +/- low grade fever
• CXR: Diffuse patchy infiltrates in interstitial areas (>1 lobe, usually)
• Rx: Macrolides or doxycycline or respiratory fluoroquinolones (levofloxacin, moxifloxacin)
Autoimmune Hemolytic Anemia (Cold Agglutinin):
• Mycoplasma pneumoniae
• Other classic causes: EBV, Waldenstrom macroglobulinemia, CLL
• General anemia features: Fatigue, conjunctival pallor, dyspnea
• Painful acrocyanosis of distal extremities, livedo reticularis, Raynaud phenomena
• Direct Coombs: Positive (Anti-C3b), ↓ Serum C3 and C4, ↑ LDH, ↓ Haptoglobin
• Rx: Avoid cold exposure and triggers, maintenance w/ Rituximab
Erythema Multiforme:
• Mycoplasma pneumoniae
• Other classic causes: HSV, β-lactam antibiotics, phenytoin
• Symmetric and centripetally spreading maculopapular rash à Target lesions (can include palms and soles)
• Nikolsky negative, no mucous membrane involvement unless major form
• Rx: Symptomatic treatment in most cases
Steven -Johnson Syndrome:
• Mycoplasma pneumoniae
• Other classic causes: Allopurinol, TMP/SMX, HIV, piroxicam, antiepileptics (phenytoin)
• Painful erythematous/purpuric macules +/- targetoid appearance à Full-thickness epidermal necrosis, sloughing of tissue
• Nikolsky positive, mucous membrane involvement
• Rx: Fluid resuscitation, wound management +/- antibiotic therapy
UTI: Ureaplasma urealyticum
 Microbiology: Atypical Bacteria Bootcamp.com

General Principles:
• Gram negative coccobacilli
• Obligate intracellular
• Reservoir: Farm animals, animal hides (cattle, goats, and sheep)
• Endospore à Survival in harsh environments
Q Fever:
• Transmitted via inhalation of aerosol
• ↓ ID50
• Fever, headache
• Mild pneumonia
• Transaminitis
• Rx: Doxycycline
Endocarditis: Culture negative
• Other à HACEK organisms: Haemophilus, Actinobacillus, Cardiobacter, Eikenella, Kingella
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0087

A 63-year-old previously healthy male presents to the emergency department for worsening chills and nausea over the past three days. He states that he
believes this all started after a “bug bite” on a camping trip recently. Vital signs reveal a temperature of 101℉ (38.3℃), blood pressure of 94/54mmHg,
heart rate of 108/bpm, and oxygen saturation of 97% on room air. Physical examination reveals conjunctival pallor and is otherwise relatively
unremarkable. Serum laboratory studies are shown below including a peripheral blood smear sample. Which of the following vectors would be most
consistent with the underlying disease process?

Laboratory Marker Result

Leukocyte count 1,800/mm3
⚪ A. Amblyomma americanum
Hemoglobin 9.8 g/dL
⚪ B. Ixodes pacificus Platelet count 84,000/mm3

⚪ C. Dermacentor andersoni Glucose 122 mg/dL

Sodium 138 mEq/L
⚪ D. Musca sorbens
Potassium 3.7 mEq/L
⚪ E. Dermacentor variabilis Magnesium 1.8 mEq/L
Creatinine 1.4 mg/dL
Alanine aminotransferase 176 U/L
Aspartate aminotransferase 224 U/L
PCR Ehrlichia DNA Undetectable
Reverse transcriptase PCR viral RNA Undetectable
 OUTLINE
1. Histoplasma 5. Sporothrix
A. General Principles A. General Principles

Microbiology: B. Pathogenesis
C. Histoplasmosis
D. Diagnostics
B. Pathogenesis
C. Lymphocutaneous Sporotrichosis
D. Diagnostics

Dimorphic
E. Management E. Management
2. Blastomyces
A. General Principles

Mycosis
B. Pathogenesis
C. Blastomycosis
D. Diagnostics
E. Management
3. Coccidioides
A. General Principles
B. Pathogenesis
C. Coccidioidomycosis
D. Diagnostics
E. Management
4. Paracoccidioides
A. General Principles
B. Pathogenesis
C. Paracoccidioidomycosis
D. Diagnostics
E. Management
 Microbiology: Dimorphic Mycosis Bootcamp.com

General Principles:
• Histoplasma capsulatum
• Dimorphic fungi à Temperature dependent (mold – cold, yeast – heat)
Pathogenesis:
• Mold form à Growth in environment (Sabouraud agar)
• Yeast form à Growth in tissues (blood agar)
• Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised)
• Not transmitted person to person
Histoplasmosis:
• Mississippi and Ohio river valley (Ohio, Indiana, Illinois, Iowa, Michigan, Nebraska)
• Bat or bird droppings, immunosuppressed patient
• Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia
• Immunosuppressed: Disseminated disease à AIDS-defining illness
• Fever, chills, headache, myalgias, chest pain, cough, and hemoptysis
• Weight loss, hepatosplenomegaly, LAD, oral ulcerative lesions (palate, tongue)
Diagnostics:
• Positive polysaccharide antigen test (urine or serum)
• Pancytopenia
• CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation, hilar/mediastinal lymphadenopathy
• Silver stain, PAS stain, KOH wet prep: Yeast within macrophages (narrow-based budding, oval-shape)
• Granulomas may be present
• Sabouraud agar: Fungal culture
• Yeast < RBC (size)
Management:
• Mild disease: Itraconazole, may be self limiting if immunocompetent
• Severe disseminated disease: Amphotericin B
 Microbiology: Dimorphic Mycosis Bootcamp.com

General Principles:
• Blastomyces dermatitidis
• Dimorphic fungi à Temperature dependent (mold – cold, yeast – heat)
Pathogenesis:
• Thick cell wall à ↓ Phagocytosis
• Mold form à Growth in environment (Sabouraud agar)
• Yeast form à Growth in tissues (blood agar)
• Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised)
• Not transmitted person to person
Blastomycosis:
• Eastern and Midwestern U.S.
• Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia
• Immunosuppressed: Disseminated disease
• Fever, chills, chest pain, myalgias, cough, and hemoptysis
• Verrucous skin lesions with irregular borders
• No LAD (usually)
• Osteolytic bone lesions à Osteomyelitis
Diagnostics:
• CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation
• Silver stain, PAS stain, KOH wet prep: Yeast within macrophages (broad-based budding, thick walls)
• Sabouraud agar: Fungal culture
• Granulomas may be present
• Yeast = RBC (size)
Management:
• Mild disease: Itraconazole, may be self limiting if immunocompetent
• Severe disseminated disease: Amphotericin B
 Microbiology: Dimorphic Mycosis Bootcamp.com

General Principles:
• Coccidioides immitis, Coccidioides posadasii
• Dimorphic fungi
Pathogenesis:
• Giant spherules containing endospores
• Mold form à Growth in environment
• Endospore/spherule form à Growth in tissues
• Inhalation of arthroconidia à Endospores replicate in spherules in tissue à Rupture of endospore from spherule
• Not transmitted person to person
Coccidioidomycosis (“Valley Fever”):
• Southwestern U.S., dust exposure
• Immunocompetent: Often asymptomatic or flu-like symptoms +/- pneumonia
• Immunosuppressed: Disseminated disease à AIDS-defining illness
• Fever, chills, chest pain, myalgias, cough, and hemoptysis
• "Desert Rheumatism”: Erythema nodosum (“desert bumps”), arthralgias, fever
• Meningitis
Diagnostics:
• Eosinophilia
• CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation
• Silver stain, PAS stain, KOH wet prep: Large spherules containing endospores
• Sabouraud agar: Fungal culture
• Spherules > RBC (size)
Management:
• Mild disease: Self-limited in many immunocompetent, fluconazole, itraconazole
• Severe disseminated disease: Amphotericin B
 Microbiology: Dimorphic Mycosis Bootcamp.com

General Principles:
• Paracoccidioides brasiliensis, Paracoccidioides lutzii
• Dimorphic fungi
Pathogenesis:
• Inhalation of spores à Evasion of pulmonary defenses à Phagocytic infection à Dissemination (immunocompromised)
• Not transmitted person to person
Paracoccidioidomycosis:
• South America, Central America
• ↑ Risk in men, soil exposure (agricultural occupational exposure)
• Immunocompetent: Often asymptomatic or flu-like symptoms
• Immunosuppressed: Disseminated disease
• Fever, chills, weight loss
• Oral and mucosal ulcerative lesions, LAD (cervical is classic)
• Verrucous skin lesions with irregular borders
Diagnostics:
• Anemia, eosinophilia
• CXR: Variable; diffuse patchy/nodular infiltrates vs focal consolidation
• Silver stain, PAS stain, KOH wet prep: Budding yeast with “captain’s wheel” formation
• Sabouraud agar: Fungal culture
• Yeast > RBC (size)
Management:
• Mild disease: Self-limited in many immunocompetent, itraconazole
• Severe disseminated disease: Amphotericin B
 Microbiology: Dimorphic Mycosis Bootcamp.com

General Principles:
• Sporothrix schenckii
• Dimorphic fungi
Pathogenesis:
• Mold form à Growth in soil (Sabouraud agar)
• Yeast form à Growth in tissues (blood agar)
• Survives on vegetation à Traumatic inoculation (thorn prick)
• Not transmitted person to person
Lymphocutaneous Sporotrichosis (“Rose Gardener’s Disease”):
• ↑ Risk in gardeners
• Generally immunocompetent patient
• Ulcerative, pustular lesions à Nodular ascending lymphangitis
• Immunosuppressed: Disseminated disease
Diagnostics:
• Silver stain, PAS stain: Often negative, oval or “cigar-shaped” yeast
• Sabouraud agar: Fungal culture
Management:
• Mild disease: Itraconazole or KI
• Severe disseminated disease: Amphotericin B
 Microbiology: Dimorphic Mycosis Bootcamp.com

*Not to scale

Disease Location Key Association/Feature Histopathology Size vs RBC*

Histoplasmosis Mississippi and Ohio river valley Bat droppings, caves Oval
Narrow-based budding

Blastomycosis Eastern and Midwestern U.S. No lymphadenopathy Thick walls

Verrucous cutaneous lesions Broad-based budding

Coccidioidomycosis Southwestern U.S. Dust exposure Spherules w/ endospores

“Desert Rheumatism”

Paracoccidioidomycosis South and Central America Agricultural/soil exposure Budding yeast

Verrucous cutaneous lesions “Captain’s wheel”

Sporotrichosis N/a Gardening, landscaping “Cigar-shaped” yeast

(Lymphocutaneous) Skin inoculation (vs inhalation)
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0088

A 27-year-old male presents to his primary care physician with a dry cough that “hasn’t gone away”. The Figure 1
patient reports that he recently went to an urgent care and received antibiotics for pneumonia. He also
endorses significant unintentional weight loss over the past several weeks. He is afebrile and his vital signs are
within normal limits. A painless skin lesion is identified on the dorsal right hand (figure 1). Similar skin lesions
are identified on the left thigh and dorsum of the right foot. A chest x-ray reveals a large right-sided pleural
effusion and poorly defined soft tissue nodules throughout both lung fields. No significant hilar or mediastinal
lymphadenopathy was observed.

The patient is subsequently taken for pleurocentesis, and pleural fluid analysis is shown in the table below. A
biopsy taken from the right hand is also performed and shown under high magnification (figure 2). Which of
following would risk factors is most significantly correlated to the underlying pathology in this patient?

Pleural Fluid Result

Appearance Straw color
pH 8 (ref: 7.6-7.64) Figure 2

Glucose 110 mg/dL

⚪ A. History of Crohn’s disease LDH 205 U/L

⚪ B. Archeological exploration Gram stain Negative

Acid fast stain Negative
⚪ C. Rose gardening

⚪ D. Employment as a healthcare worker

⚪ E. Frequent cave exploration

 OUTLINE
1. Aspergillus 4. Mucor and Rhizopus
A. General Principles A. General Principles

Microbiology: B. Pathogenesis
C. Aspergillosis
D. ABPA
B. Pathogenesis
C. Mucormycosis
D. Diagnostics

Opportunistic
E. Diagnostics E. Management
F. Management F. Complications
G. Complications 5. Pneumocystis

Mycosis
2. Candida A. General Principles
A. General Principles B. Pathogenesis
B. Pathogenesis C. Pneumocystis Pneumonia
C. Oropharyngeal Candidiasis D. Diagnostics
D. Esophageal Candidiasis E. Management
E. Vulvovaginal Candidiasis F. Complications
F. Cutaneous Candidiasis
G. Candidemia
H. Diagnostics
I. Management
3. Cryptococcus
A. General Principles
B. Pathogenesis
C. Cryptococcosis
D. Diagnostics
E. Management
F. Complications
 Microbiology: Opportunistic Mycosis Bootcamp.com

General Principles:
• Aspergillus fumigatus, Aspergillus flavus
• Monomorphic mold
• Catalase positive
Pathogenesis:
• Inhalation of spores à Evasion of pulmonary defenses à Local invasion à Dissemination (immunocompromised)
Aspergillosis:
• ↑ Risk in immunocompromised à Chemotherapy, transplant recipient, chronic granulomatous disease (catalase +)
• ↑ Risk in pulmonary disease à COPD, prior pulmonary infection (TB, PJP)
• General symptoms: Fever, weight loss, night sweats, chills, dry cough
• Pulmonary: Dyspnea, hemoptysis, pleuritic chest pain
• Invasive disease: Hypotension, tachycardia, tachypnea à Septic shock
• Aspergilloma: Pre-existing cavitary lesions (TB) à Mycetoma formation (mobile)

Allergic Bronchopulmonary Aspergillosis (ABPA):

• Hypersensitivity reaction to Aspergillus
• ↑ Risk in bronchopulmonary disease à Asthma, cystic fibrosis
• Dyspnea, wheezing, exacerbations of underlying pulmonary disease (asthma)
• Bronchiectasis, productive cough (brown-black mucous casts)
Diagnostics:
• Invasive Disease: Positive galactomannan enzyme assay
• Chest CT: Bronchiectasis (ABPA), Nodules +/- cavitation and consolidation (Invasive), mobile mycetoma (Aspergilloma)
• Silver stain, PAS stain: Mold with septate hyphae branching dichotomously at 45° (acute) angles (Invasive)
• ABPA: ↑ IgE, eosinophilia, Aspergillus IgG, Positive Aspergillus skin test
• Serum 1,3-β-D-glucan (non-specific)
Management:
• Prophylaxis: Posaconazole
• Invasive: Voriconazole or Posaconazole (1st line), Echinocandins (Caspofungin, anidulafungin, micafungin) (2nd line)
• Aspergilloma: Surgical resection
• ABPA: Prednisone
Complications:
• Invasive disease: Hemorrhagic dermatologic lesions, endocarditis, brain abscesses, meningitis, venous sinus thrombosis
• Aflatoxin (A. flavus) à ↑ Risk of hepatocellular carcinoma
 Microbiology: Opportunistic Mycosis Bootcamp.com

General Principles:
• Candida albicans
• Dimorphic fungi à Temperature dependent (pseudohyphae and budding yeast – cold, germ tubes – heat)
• Catalase positive
Pathogenesis:
• Local Disease: Imbalance in flora à ↑ C. albicans à Local infection
• Disseminated Disease: Local infection à Hematogenous spread à Multi-organ involvement (Immunocompromised)
• ↑ Risk in immunocompromised à Chemotherapy, transplant recipient, HIV, chronic granulomatous disease (catalase +)
• ↑ Risk in obesity, diabetes, neonates, pregnancy, recent antibiotics (vulvovaginitis) or steroid use (inhaled à oral)
Oropharyngeal Candidiasis: Pseudomembrane candidiasis, “oral thrush”, can be scraped off
Esophageal Candidiasis: AIDS-defining illness, odynophagia
Vulvovaginal Candidiasis:
• Thick white vaginal discharge, “cottage cheese” appearance, odorless
• Local erythema, pruritis, dysuria, dyspareunia, burning sensation
• Vaginal pH ~4-4.5, vaginal discharge + KOH à Pseudohyphae on wet mount
Cutaneous Candidiasis:
• Erythematous patches, satellite lesions
• Intertriginous areas, skin folds (axilla, groin, beneath breasts)
• Diaper dermatitis (infants)
Candidemia:
• Classically immunocompromised patient, IVDU, vascular catheters (parenteral nutrition)
• Systemic symptoms (fever, chills, myalgias) à End organ damage
• Endocarditis with IVDU
Chronic Mucocutaneous Candidiasis:
• ↓ T-cell response to Candida antigens: ↓ IL-17 response
• AIRE protein deficiency
• Refractory and recurring candida infections
• No induration on Candida skin test
Diagnostics:
• KOH wet prep, silver stain: Yeasts, hyphae, and pseudohyphae
• Endoscopy (esophagitis)
• Blood culture (candidemia) à Germ tubes produced in serum
• Serum 1,3-β-D-glucan (non-specific)
Management:
• Clotrimazole, miconazole, ketoconazole, nystatin (Local disease, usually topical)
• Fluconazole (Esophageal)
• Caspofungin or Amphotericin B (Systemic, intravenous)
 Microbiology: Opportunistic Mycosis Bootcamp.com

General Principles:
• Cryptococcus neoformans, Cryptococcus gatti
• Monomorphic yeast
• Urease positive
Pathogenesis:
• Thick polysaccharide capsule à ↓ Phagocytosis
• Phenol oxidase
• Inhalation of spores à Evasion of pulmonary defenses à Hematogenous dissemination (Immunocompromised) à Meninges
• ↑ Risk in immunocompromised (Disseminated disease is AIDS-defining condition, CD4+ <100)
Cryptococcosis:
• Bird (pigeon) droppings
• Meningoencephalitis: Fever, chills, refractory headache, malaise, photophobia, + Kernig and Brudzinski signs
• Cranial abscess: Signs of ↑ ICP (papilledema, abducens nerve palsy, Cushing triad)
• Pneumonia: Fever, cough, dyspnea (MC site of infection)
Diagnostics:
• Silver stain, PAS stain: 5-10µm narrow unequal budding, thick capsule
• India ink stain: Clear halo, light on a dark background (polysaccharide capsule)
• Mucicarmine stain: Stains capsule bright red
• Fontana-Masson stain: Stains for melanin
• Latex agglutination test: Detects capsular protein
• MRI Brain: ”Soap bubble” lesions (Pseudocysts)
• Lumbar puncture
• Sabouraud agar: Fungal culture
Management:
• Amphotericin B + flucytosine (Induction) à Fluconazole (Maintenance)
Complications:
• Seizure, hydrocephalus, CVA
 Microbiology: Opportunistic Mycosis Bootcamp.com

General Principles:
• Mucor and Rhizopus spp.
• Monomorphic mold
Pathogenesis:
• Inhalation of spores à Evasion of pulmonary defenses à Proliferation in blood vessel walls à Contiguous spread
• ↑ Risk in immunocompromised à Classically, poorly controlled diabetes or DKA
Mucormycosis:
• Soil and decomposed material
• Invasive, necrotic infection with contiguous spread à Paranasal sinuses à Orbit à Cranial
• Severe pain, vision loss, headache
• Black eschar in paranasal region or palate
• Cranial abscess: Signs of ↑ ICP (papilledema, abducens nerve palsy, Cushing triad)
Diagnostics:
• Silver stain, PAS stain: Mold with non-septate, irregular, hyphae broad, “ribbon-like”, branching at 90° (wide, right) angles
• CT of sinuses: Air-fluid levels in sinuses +/- bony destruction
Management:
• Emergent surgical debridement + Amphotericin B
• Isavuconazole (second line)
Complications:
• Cavernous sinus thrombosis
 Microbiology: Opportunistic Mycosis Bootcamp.com

General Principles:
• Pneumocystis jirovecii
• Yeast-like fungi
Pathogenesis:
• Inhalation of spores
• ↑ Risk in immunocompromised (AIDS-defining condition)
Pneumocystis Pneumonia:
• Progressive exertional dyspnea, fever, chills, weight loss
Diagnostics:
• Serum 1,3-β-D-glucan (non-specific)
• Silver stain: Disc-shaped yeast
• Fluorescent antibody stain
• CXR: Bilateral interstitial opacities
• CT Chest: Diffuse bilateral, patchy ground-glass opacities +/- pneumatoceles
Management:
• Trimethoprim-Sulfamethoxazole
• Dapsone
• Pentamidine
• Prednisone for hypoxemia
• Prophylaxis for CD4+ < 200
Complications:
• Acute respiratory distress syndrome
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0089

A 57-year-old male presents to the emergency department with acute onset of severe, “stabbing”, left-sided chest
pain that is worse with deep inspiration. The pain started approximately 2 hours earlier when the patient reports that
he had a particularly severe coughing episode. He states that the coughing episodes have progressively worsened
over the past two months. The patient has no known history of coronary artery disease or tobacco use. A review of
the patient’s medication list shows that the patient is taking mycophenolate mofetil, tacrolimus, omeprazole, and Lab Test Result
prednisolone. The patient reportedly had a liver transplantation 2 years ago due to an underlying diagnosis of primary
biliary cirrhosis. Vital signs reveal a temperature of 38.5℃ (101.4℉), blood pressure of 122/88mmHg, heart rate of Leukocyte count 4,500/mm3
110/min, respiratory rate of 24/min with shallow breathing, and an oxygen saturation of 90% on room air. On Hemoglobin 11.1 g/dL
auscultation of the lungs the patient has absent breath sounds on the right. There is no evidence of any dermatologic
or mucocutaneous lesions, the liver is not palpable, and cardiac auscultation shows slightly decreased heart sounds Platelet count 178,000/mm3
in the retrosternal region. Electrocardiogram shows sinus tachycardia without additional abnormalities. A CT scan of Creatinine 2.8 mg/dL
the chest is also obtained and shown.
Troponin I 0.01 ng/mL
The patient is hemodynamically stabilized and started on empiric antibiotic therapy without improvement. A lung
BNP 30 pg/mL
biopsy is later performed revealing yeast on a methenamine silver stain. Which of the following mechanisms of
antimicrobial therapy would likely be most effective in this patient? Sputum culture Growth: Candida
albicans

Latex Agglutination Negative

⚪ A. Binding to the 50S ribosomal subunit Cryptococcal Ag

⚪ B. Inhibition of microbial dihydrofolate reductase

Serum CMV Ag Negative

⚪ C. Binding to ergosterol and membrane pore formation Serum 1,3-β-D- Positive

glucan

⚪ D. Inhibition of ergosterol synthesis Galactomannan Negative

assay
⚪ E. Inhibition of squalene epoxidase
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0089

A 57-year-old male presents to the emergency department with acute onset of severe, “stabbing”, left-sided chest
pain that is worse with deep inspiration. The pain started approximately 2 hours earlier when the patient reports that
he had a particularly severe coughing episode. He states that the coughing episodes have progressively worsened
over the past two months. The patient has no known history of coronary artery disease or tobacco use. A review of
the patient’s medication list shows that the patient is taking mycophenolate mofetil, tacrolimus, omeprazole, and Lab Test Result
prednisolone. The patient reportedly had a liver transplantation 2 years ago due to an underlying diagnosis of primary
biliary cirrhosis. Vital signs reveal a temperature of 38.5℃ (101.4℉), blood pressure of 122/88mmHg, heart rate of Leukocyte count 4,500/mm3
110/min, respiratory rate of 24/min with shallow breathing, and an oxygen saturation of 90% on room air. On Hemoglobin 11.1 g/dL
auscultation of the lungs the patient has absent breath sounds on the right. There is no evidence of any dermatologic
or mucocutaneous lesions, the liver is not palpable, and cardiac auscultation shows slightly decreased heart sounds Platelet count 178,000/mm3
in the retrosternal region. Electrocardiogram shows sinus tachycardia without additional abnormalities. A CT scan of Creatinine 2.8 mg/dL
the chest is also obtained and shown.
Troponin I 0.01 ng/mL
The patient is hemodynamically stabilized and started on empiric antibiotic therapy without improvement. A lung
BNP 30 pg/mL
biopsy is later performed revealing yeast on a methenamine silver stain. Which of the following mechanisms of
antimicrobial therapy would likely be most effective in this patient? Sputum culture Growth: Candida
albicans

Latex Agglutination Negative

⚪ A. Binding to the 50S ribosomal subunit Cryptococcal Ag

" B. Inhibition of microbial dihydrofolate reductase

Serum CMV Ag Negative

⚪ C. Binding to ergosterol and membrane pore formation Serum 1,3-β-D- Positive

glucan

⚪ D. Inhibition of ergosterol synthesis Galactomannan Negative

assay
⚪ E. Inhibition of squalene epoxidase
 OUTLINE
1. Toxoplasma 5. Plasmodium
A. General Principles A. General Principles

Microbiology:
B. Pathophysiology B. Pathophysiology
C. Toxoplasmosis C. Malaria
D. Diagnostics D. Diagnostics

Systemic
E. Management E. Management
2. Naegleria 6. Babesia
A. General Principles A. General Principles

Protozoa
B. Pathophysiology B. Pathophysiology
C. Primary Amebic Meningoencephalitis C. Babesiosis
D. Diagnostics D. Diagnostics
E. Management E. Management
3. Trypanosoma brucei 7. Leishmania
A. General Principles A. General Principles
B. Pathophysiology B. Pathophysiology
C. African Trypanosomiasis C. Visceral Leishmaniasis
D. Diagnostics D. Cutaneous Leishmaniasis
E. Management E. Diagnostics
4. Trypanosoma cruzi F. Management
A. General Principles 8. Trichomonas vaginalis
B. Pathophysiology A. General Principles
C. Chagas Disease B. Pathophysiology
D. Diagnostics C. Trichomoniasis
E. Management D. Diagnostics
E. Management
Microbiology: Systemic Protozoa Bootcamp.com

Toxoplasma
General Principles:
• Toxoplasma gondii
• Single-celled obligate intracellular protozoan
• Four life cycle stages: Oocysts (infectious), sporozoites, tachyzoites (active), bradyzoites (latent)
• Oocysts ingested from cat feces
• Cysts (bradyzoites) contained in undercooked infected meat
• Vertical transmission from mother to fetus
Pathophysiology:
• Ingestion of oocyst → Excyst in SI as sporozoites → Invade intestinal epithelium
• Sporozoites → Tachyzoites → Rapid replication → Disseminate through blood and lymphatics
• Tachyzoites form cysts in the brain and muscle → Remain latent
• Ingestion of cysts → Bradyzoite release in SI → Differentiate into tachyzoites
• Infection incites strong Th1 reaction → IFNγ, IL-12 and TNFɑ
Toxoplasmosis:
• High risk in immunocompromised and pregnancy (HIV CD4+ T cell count <100)
• Fever, fatigue, myalgia, cervical or occipital lymphadenopathy
• Congenital toxoplasmosis: Chorioretinitis, hydrocephalus, intracranial calcifications
• Brain abscesses: Headache, confusion, loss of vision, seizures, aphasia
Diagnostics:
• Brain abscesses → Multiple ring enhancing lesions on MRI, surrounding mass edema
• Serological detection of IgM and IgG antibodies
• Identification of tachyzoites on microscopy, culture, PCR or biopsy
• Fundoscopic exam showing white focal lesion and vitreous inflammation
Management:
• Treatment not necessary in nonpregnant, immunocompetent patients
• Pyrimethamine + Sulfadiazine + Leucovorin
• TMP-SMX for prophylaxis for HIV
Microbiology: Systemic Protozoa Bootcamp.com

Naegleria
General Principles:
• Naegleria fowleri
• Three life cycle stages: Trophozoite (invasive), flagellate (transitory), cyst (dormant)
Pathophysiology:
• Trophozoites in warm freshwater enter nasal cavity → Flagellates invade olfactory mucosa
• Ascend along the olfactory nerve through the cribriform plate → Olfactory bulb
• Amoeba consume and destroy cells → Inflammatory response → Necrosis and hemorrhage
Primary Amebic Meningoencephalitis:
• Freshwater swimming, hot springs, water sports
• Nasal irrigation and contact lens
• Headache, fever, nuchal rigidity → AMS, seizures, coma, death
• Rapidly progressive (<1 week), high mortality
Diagnostics:
• Lumbar puncture → Amoeba visualized on microscopy, ↑ WBC and CSF pressure
• Brain biopsy and culture → Amoeba visualized in trophozoite form
Management:
• Amphotericin B
• Early detection and treatment critical for survival
• Prevention → Chlorination, monitoring recreational water, nose plugs
 Microbiology: Systemic Protozoa Bootcamp.com

Trypanosoma Brucei
General Principles:
• T. brucei rhodesiense and T. brucei gambiense
• Single celled, single flagella
• Two main lifecycle stages: Metacyclic + Bloodstream trypomastigotes
Pathophysiology:
• Tsetse fly releases metacyclic trypomastigote during a blood meal → Host bloodstream
• Bloodstream trypomastigote rapidly divides → Local inflammation and organ damage
• Migration to CSF → Inflammation and damage to brain tissue
• Antigenic variation of glycoprotein coats → Evasion of host immune response
• May cause host immunosuppression → Inhibit macrophage, T cell, and B cell responses
African Trypanosomiasis:
• “Sleeping sickness”
• Endemic to sub-Saharan Africa
• Painful bite, inoculation chancre may be present 2-15 days post-bite
• Hemolymphatic stage → Recurrent fevers, posterior cervical and axillary lymphadenopathy
• Meningoencephalitic stage → Nighttime insomnia, daytime somnolence, visual problems, sensory disorder
Diagnostics:
• Screening: Card agglutination test for trypanosomiasis (CATT)
• Diagnosis: Blood smear → Visualize trypomastigotes
• Staging: Lumbar puncture → Detection of WBC and trypomastigotes in CSF
• Follow up: Serological and lumbar puncture every 6 months for 2 years
Management:
• Hemolymphatic stage → Pentamidine OR Suramin
• Menigoencephalitic stage → Nifurtimox-eflornithine OR Melarsoprol
• Disease is typically fatal without treatment
 Microbiology: Systemic Protozoa Bootcamp.com

Trypanosoma Cruzi
General Principles:
• Transmitted by Reduviid or “kissing” bug
• Main life cycle stage is trypomastigote
Pathophysiology:
• Reduviid bug takes blood meal → Defecates trypomastigote near host wound
• Trypomastigotes enter blood supply → Invade, replicate in and lyse nucleated cells
• Dissemination through blood and lymphatics → Target muscle and ganglion cells
• Chronic infection → Chronic inflammation → Destruction of muscle fibers and nerves, fibrosis
• Th1 response crucial for parasitic clearance
Chagas Disease:
• Endemic to Central and South America
• Primary infection: Asymptomatic OR fever, malaise, Romaña’s sign, Chagoma
• Chronic infection: Asymptomatic OR Dilated cardiomyopathy, Megacolon, Megaesophagus
• Dilated cardiomyopathy: JVD, S3 gallop, pitting edema, arrhythmia
• Megacolon: Prolonged constipation, abdominal pain, bloating
• Megaesophagus: Dysphagia, odynophagia, regurgitation of food
• Reactivation in immunocompromised → Acute myocarditis, brain abscess
Diagnostics:
• Primary infection: Blood smear → Motile, flagellated trypomastigotes, PCR
• Chronic infection: Serology, history and PE
• 12 lead ECG → Atrial fibrillation, LVH, ↓ EF
• CXR: Cardiomegaly
• Echo and MRI: Thinned ventricular walls
Management:
• Benznidazole OR Nifurtimox
Microbiology: Systemic Protozoa Bootcamp.com

Plasmodium
General Principles:
• P. falciparum → Irregular fever patterns, malignant tertian
• P. vivax and P. ovale → 48 hour fever cycles, tertian, dormant schizonts (hypnozoites)
• P. malariae → 72 hour fever cycles, quartan
Pathophysiology:
• Female Anopheles mosquito injects sporozoite into bloodstream during blood meal
• Sporozoite → Liver → Schizonts → Release merozoites → Infect RBCs → Trophozoites
• Infected RBCs can become gametophytes OR schizonts → RBC lysis → Merozoites
• Gametophytes ingested by different mosquito → Sexual reproduction → Sporozoites
• P. falciparum infected RBCs can occlude capillaries in brain, lungs, kidneys
Malaria:
• Recent travel or living in malaria endemic areas (Sub-Saharan Africa)
• Cyclic fever, headache, anemia, hepatosplenomegaly
• Severe malaria: Coma, prostration, seizures, significant bleeding
• Sickle cell trait, G6PD deficiency: ↓ Transmission, morbidity and mortality
• Chronic liver infection from hypnozoites
Diagnostics:
• Peripheral blood smear with Giemsa stain → Trophozoite rings, Schuffner stippling, crescent gametophytes
• Rapid antigen detection tests, PCR
• Hypoglycemia, thrombocytopenia and hemolytic anemia → ↑ LDH, indirect bilirubin, reticulocytes ↓ Haptoglobin
Management:
• Chloroquine → Useful in areas with ↓ Chloroquine resistance
• Mefloquine → Useful in areas with ↑ Chloroquine resistance
• Atovaquone/proguanil OR Artemether/lumefantrine → Chloroquine resistant P. falciparum
• Primaquine → Elimination of hypnozoites in P. vivax and P. ovale
• IV Artesunate + Artemether/lumefantrine OR quinine → Severe, life-threatening infections
Microbiology: Systemic Protozoa Bootcamp.com

Babesia
General Principles:
• Main species: B. microti, B. duncani, B. divergens
• Coinfection with Borrelia burgdorferi (Lyme) and Anaplasma (Anaplasmosis)
Pathophysiology:
• Ixodes tick bite → Sporozoites released → Attach to and invade RBCs
• Sporozoites mature → Trophozoites → 4 merozoites
• RBC lysis → Merozoites release → Invade other RBCs
• Instigates host inflammatory response
Babesiosis:
• Outdoor activities in northeastern United States
• Severe in asplenic, sickle cell trait, immunocompromised, elderly
• Commonly asymptomatic
• Fever, fatigue, dark urine
• Jaundice, petechiae, ecchymosis, splenomegaly
Diagnostics:
• Peripheral blood smear → RBCs with rings + central pallor or Maltese cross
• Hemolytic anemia, thrombocytopenia
• ↓ Hb, haptoglobin, platelets
• ↑ Reticulocytes, LDH, bilirubin
• DIC: ↓ Platelets, fibrinogen, ↑ D-dimer, bleeding times (PT, PTT)
Management:
• Atovaquone + Azithromycin
Microbiology: Systemic Protozoa Bootcamp.com

Leishmania
General Principles:
• L. donovani → Visceral leishmania or “Kala-azar”
• L. braziliensis → Cutaneous leishmania
• Two life cycle stages: Promastigote (infectious), Amastigote (active)
• Vector: Phlebotomus papatasi sandfly
Pathophysiology:
• Sandfly injects promastigote during blood meal → Phagocytized by macrophages
• Promastigote differentiates into amastigote → Rapid replication
• Macrophage lysis → Amastigote release
• Visceral: Macrophages in bone marrow, liver, spleen
• Accelerates progression of HIV → AIDS due to bone marrow suppression
• Cutaneous: Macrophages in dermis
Visceral Leishmaniasis:
• Endemic to tropical and subtropical areas (Africa, South America)
• Fever, weakness, hyperpigmented lesions, hepatosplenomegaly
• Untreated visceral infections → Anemia, jaundice, wasting, multiorgan failure and death
Cutaneous Leishmaniasis:
• Nonpruritic, nontender ulcerations → Diffuse plaques, ulcers, nodules in immunocompromised
Diagnostics:
• Amastigotes in macrophages: Skin biopsy, dermal scraping, bone marrow or spleen aspiration
• Serology, culture (Novy-Nicolle-McNeal medium) and PCR
• Visceral: Pancytopenia and hemolytic anemia findings in CBC
Management:
• Visceral: Amphotericin B
• Cutaneous: Observation, topical paromomycin, oral pentamidine, sodium stibogluconate injection
Microbiology: Systemic Protozoa Bootcamp.com

Trichomonas
General Principles:
• Trichomonas vaginalis
• Associated with increased risk of HIV, pregnancy complications, cervical and prostate cancer
• Main life cycle stage is trophozoite, inability to form cysts
• Anaerobic flagellated protozoan (motile)
Pathophysiology:
• Transferred through sexual contact
• T. vaginalis cells attach to genital epithelial cells → Form aggregates of ameboid cells
• Adherence is cytotoxic → Lysis of host cell, erosion of epithelium
• Parasite-mediated apoptosis
Trichomoniasis:
• Female: Vulvar pruritus, burning, frothy foul smelling green discharge, postcoital bleeding
• Pelvic exam → Punctate hemorrhages on cervix or “strawberry cervix”
• Male: Mostly asymptomatic → Urethritis, epididymitis, or prostatitis
Diagnostics:
• Wet mount of vaginal swab + Saline → Motile trophozoites under microscopy
• pH > 4.5, Whiff test negative
• Rapid antigen detection test, culture
• Urethral swab, urine, or semen in male patients
Management:
• Metronidazole for patient and partner(s)
• Test for other STIs
 OUTLINE

1. Enterobius 5. Trichuris 9. Loa Loa

Microbiology:
A. General Principles A. General Principles A. General Principles
B. Pathophysiology B. Pathophysiology B. Pathophysiology
C. Enterobiasis C. Trichuriasis C. Loiasis
D. Diagnostics D. Diagnostics

Nematodes
D. Diagnostics
E. Management E. Management E. Management
2. Ascaris 6. Trichinella 10. Wuchereria and Brugia
A. General Principles A. General Principles A. General Principles
B. Pathophysiology B. Pathophysiology B. Pathophysiology
C. Ascariasis C. Trichinellosis C. Lymphatic Filariasis
D. Diagnostics D. Diagnostics D. Diagnostics
E. Management E. Management E. Management
3. Strongyloides 7. Toxocara
A. General Principles A. General Principles
B. Pathophysiology B. Pathophysiology
C. Strongyloidiasis C. Toxocariasis
D. Diagnostics D. Diagnostics
E. Management E. Management
4. Hookworms 8. Onchocerca
A. General Principles A. General Principles
B. Pathophysiology B. Pathophysiology
C. Hookworm Infection C. Onchocerciasis
D. Diagnostics D. Diagnostics
E. Management E. Management
Microbiology: Nematodes Bootcamp.com

Enterobius
General Principles:
• Enterobius vermicularis or “pinworm”
• Three life cycle stages: Eggs (infectious), larvae, and adult worms (active)
Pathophysiology:
• Fecal-oral transmission
• Gravid female worms migrate out of rectum at night → Deposit eggs in perianal region
• Eggs become infective 4-6 hours later → Irritate the perianal region
• If eggs ingested by another host → Hatch in SI → Larvae → Adult worms in colon
Enterobiasis:
• Most common helminth infection in the US
• Children and those around children (families, daycare)
• Perianal pruritus and/or scratching at night
• Migration of worms → Vulvovaginitis, dysuria, abdominal pain
Diagnostics:
• Scotch tape test → Eggs visualized on microscopy
• Microscopy of samples from under the fingernails
• Oval eggs, flattened on one side
Management:
• 2 single doses of oral treatment, given two weeks apart to prevent reinfection
• Albendazole OR Mebendazole
• Pyrantel pamoate
• Prevent transmission → Hand hygiene, avoid itching and nail biting
Microbiology: Nematodes Bootcamp.com

Ascaris
General Principles:
• Ascaris lumbricoides or “giant roundworm”
• Three life cycle stages: Egg (infectious), larvae, and adult worms
Pathophysiology:
• Fecal-oral transmission
• Ingestion of eggs → Larvae in duodenum → Invade mesenteric wall → Blood and lymph supply
• Liver → IVC → R Heart → Pulmonary arteries → Lungs
• Larvae coughed up through trachea → Swallowed → Mature and live in the SI
• Local inflammation and eosinophilia in the liver and lungs from larvae migration
• ↑ Adult worm load → Nutrient malabsorption, biliary and intestinal obstruction or perforation
Ascariasis:
• Most common helminth infection worldwide, endemic to tropical areas
• Asymptomatic with low parasitic load
• Löeffler's Syndrome: Difficulty breathing, wheezing, fever, cough
• Intestinal infection: Abdominal distension and pain, nausea, vomiting, unintentional weight loss
• Intestinal perforation: Severe abdominal pain, inability to pass stool or gas, fever
• Hepatobiliary ascariasis: Cholestasis and pancreatitis
Diagnostics:
• Detection of eggs in feces → Thick, knobby coated oval-shaped eggs
• Detection of eggs or larvae in sputum or vomitus
• CBC: Eosinophilia
Management:
• Albendazole OR Mebendazole OR Ivermectin
• Pregnancy: Pyrantel pamoate
• Surgery indicated to treat intestinal perforation
 Microbiology: Nematodes Bootcamp.com

Strongyloides
General Principles:
• Strongyloides stercoralis or “threadworm”
• Four lifecycle stages: Infectious larvae, adult worm, egg, rhabditiform larvae
Pathophysiology:
• Fecal-soil transmission through exposed skin
• Larvae penetrate skin → Bloodstream or lymphatics → Lungs → Eosinophilic infiltration
• Larvae are coughed up and swallowed → SI → Adult worms → Parthenogenesis → Eggs
• Eggs → Rhabditiform larvae → Pass in stool OR become infective larvae
• Autoinfection: Infective larvae penetrate intestinal wall → Bloodstream → Lungs
• Hyperinfection: ↑ Worm burden due to ↑ Autoinfection, seen in immunocompromised
Strongyloidiasis:
• ↑ Risk with frequent exposure to soil, severe in immunocompromised
• Larva currens: Rapid development of pruritic, serpiginous and erythematous rash
• Pulmonary: Dry cough, irritated trachea, hemoptysis → Löffler’s Syndrome
• Gastrointestinal: Diarrhea, constipation, nausea, abdominal pain and bloating
• Disseminated disease: Other organ involvement and complicated by bacterial infection → Sepsis
Diagnostics:
• Rhabditiform larvae under microscopy of stool sample
• CBC: Eosinophilia
• Serology, stool culture, PCR
• Endoscopy or colonoscopy with biopsy: Adults in gastric crypts or duodenal glands, eosinophilia
Management:
• Ivermectin
• Thiabendazole, albendazole or mebendazole
• Avoid immunosuppressive agents
Microbiology: Nematodes Bootcamp.com

Hookworm
General Principles:
• Ancylostoma duodenale and Necator americanus
• Three life cycle stages: Egg, larvae (infectious), adult worm (active)
• Eggs require warmth, moisture and shade to survive in environment
Pathophysiology:
• Fecal-soil transmission through exposed skin
• Larvae penetrate skin → Blood supply or lymphatics → Lungs
• Larvae coughed up and swallowed → Mature in SI → Adult worms attach to intestinal wall
• Female adult worms lay thousands of eggs daily → Eggs pass in stool
• Adult worms damage intestinal wall while ingesting host blood → Intestinal blood and protein loss
• Virulence factors: Hydrolytic enzymes and anticoagulants → Promote more damage and blood loss
• Th2 mediated response: IL-5, IL-10, IL-13, IgE and eosinophils
Hookworm Infection:
• ↑ Risk with exposure to infected beaches or soil, endemic to tropical areas
• Acute infection includes cutaneous, pulmonary and gastrointestinal symptoms
• Cutaneous larva migrans: Pruritic, papular and serpiginous rash at site of invasion
• Pulmonary: Cough, sore throat
• Gastrointestinal: Nausea, vomiting, diarrhea, abdominal pain
• Chronic infection: Fatigue, dyspnea on exertion, pica, edema and ascites
Diagnostics:
• Iron deficiency anemia: Hypochromic, microcytic, ↓ Ferritin ↓ Iron ↓ Hb ↓ MCV and ↑ TIBC
• Stool sample: Detection of eggs or larvae under microscopy
• CBC: Eosinophilia
Management:
• Albendazole or mebendazole
• Pyrantel pamoate
• Iron repletion as needed
Microbiology: Nematodes Bootcamp.com

Trichuris
General Principles:
• Trichuris trichiura or “whipworm”
• Three lifecycle stages: Eggs (infectious), larvae, and adult worms (active)
Pathophysiology:
• Fecal-oral transmission
• Eggs ingested from contaminated food, water or soil → Hatch in SI as larvae
• Larvae travel to cecum → Multiple molts → Adult worm
• Adult worms burrow into colon epithelium → Intestinal blood loss and inflammation
• Female adult worms lay eggs → Eggs pass in stool
• Th2 mediated response: IL-5, IL-10, IL-13, IgE and eosinophils
Trichuriasis:
• Tropical and subtropical environments, disease more commonly seen in children
• ↓ Parasitic load: Asymptomatic
• Moderate parasitic load: Abdominal pain, diarrhea, vomiting, weight loss
• ↑ Parasitic load: Dysentery, abdominal pain, tenesmus, rectal prolapse, fatigue, impaired growth
Diagnostics:
• Stool sample → Visualize barrel-shaped eggs on microscopy
• Serology: Iron deficiency anemia and eosinophilia
• Charcot-Leyden crystals under microscopy due to eosinophil breakdown
Management:
• Albendazole OR mebendazole
Microbiology: Nematodes Bootcamp.com

Trichinella
General Principles:
• Trichinella spiralis
• Two life cycle stages: Larvae (infectious AND active), adult worms
• Enteral and parenteral phases
Pathophysiology:
• Consumption of encysted larvae from infected undercooked meat
• Encysted larvae exposed to gastric acid → Free larvae → SI
• Larvae mature into adult worms → Sexual reproduction → Release larvae into blood and lymph
• Newborn larvae circulate → Penetrate skeletal muscle cells → Myofibril breakdown
• Encapsulation of larvae → Angiogenesis → Collagen deposition → Calcification
Trichinellosis:
• Commonly due to ingestion of undercooked pork or game meat
• Asymptomatic if low parasitic load
• Enteral: Diarrhea, nausea, vomiting, abdominal pain
• Parenteral: Myalgia, facial and periorbital edema, fever
Diagnostics:
• Muscle biopsy with encysted larvae
• Anti-Trichinella antibody detection, PCR
• Eosinophilia, leukocytosis and ↑ CK ↑ AST ↑ ALT ↑ LDH
Management:
• Albendazole OR mebendazole
Microbiology: Nematodes Bootcamp.com

Toxocara
General Principles:
• Toxocara canis and Toxocara cati
• Three life cycle stages: Eggs (infectious), larvae (active), adult worms
• Toxocara species cannot complete their life cycle in a human host
Pathophysiology:
• Fecal-oral transmission
• Infected animal passes eggs with stool → Eggs embryonated in soil → Infective eggs
• Eggs ingested by host → Hatch in SI → Larvae perforate intestinal wall → Bloodstream
• Larvae disseminate → Inflammation, hemorrhage and necrosis → Organ damage
• Larvae can be encapsulated within granulomas → Destroyed by macrophages
Toxocariasis:
• ↑ Risk with exposure to dogs, cats or areas contaminated by their excrement
• Children are most commonly affected
• Visceral larva migrans: Abdominal pain, cough, myocarditis, pruritus, hepatomegaly
• Ocular toxocariasis: Uniocular uveitis → Visual impairment, blindness
• Neurotoxocariasis: Fever, headache → Seizures, coma, neurodegenerative diseases
Diagnostics:
• Eosinophilia and serological detection of larval antigens
• Biopsy: Detection of larvae with inflammation or granulomas
• CT: Hypodense lesions in the liver or brain
• MRI: Multifocal, well circumscribed T2 enhancing lesions in the brain
Management:
• Albendazole OR mebendazole
Microbiology: Nematodes Bootcamp.com

Onchocerca
General Principles:
• Onchocerca volvulus
• Two life cycle stages: Microfilariae (infectious AND active), adult worms
• Symbiotic relationship with Wolbachia
Pathophysiology:
• Simulium black flies inject larvae into host during blood meal → Larvae under the skin
• Stimulates formation of fibrous nodules → Larvae mature to adult worms inside nodules
• Female adult worms produce larvae → Migrate through blood and lymph → Black fly
• Th2 response: IL-5, IL-10, IL-13, IgE and eosinophils → Larval death → Release of Wolbachia
• Neutrophil activation → Inflammation in the skin and eye
Onchocerciasis:
• Endemic to sub-Saharan Africa, black flies near rivers and streams
• Typically asymptomatic
• Cutaneous: Pruritic eczematous rash, scaly plaques with hyperpigmentation
• Subcutaneous nodules, ↓ Skin elasticity, changes in vision
• Non-fatal +/- ↓ Vision
• Depigmentation and skin atrophy
Diagnostics:
• Skin snips: Detection of free microfilariae under microscopy
• Skin biopsy of nodules: Detection of adult worms
• Serological testing and PCR
• CBC: Eosinophilia
Management:
• Ivermectin
Microbiology: Nematodes Bootcamp.com

Loa Loa
General Principles:
• Transmitted by Chrysops fly, also known as deer, horse, or mango fly
• Multiple bites before infection
• Three life cycle stages: Larvae (infectious), adult worm and microfilariae (active)
Pathophysiology:
• Multiple Chrysops fly blood meals → Larvae in subcutaneous tissue → Mature to adult worms
• Female adult worms produce microfilariae → Disseminate through lymphatics
• Microfilariae accumulate in lungs → Peripheral blood → Migrate through host body
• Chrysops fly takes a blood meal containing microfilariae
• Activation of immune system during migration → Localized inflammation in hosts
Loiasis:
• Endemic to Western and Central Africa
• Most infections are asymptomatic
• Calabar swelling: Non-tender, non-pitting swelling +/- Pruritus, resolve spontaneously
• Migration of adult worm across conjunctiva → Pruritus, congestion, photophobia
Diagnostics:
• Blood smear: Detection and quantification of microfilariae
• Presence of eye worm on physical exam
• Excision: Detection of adult worm
• CBC: Eosinophilia
Management:
• Diethylcarbamazine for ↓ Parasite load → Neurologic effects and fatal encephalopathy
• Albendazole or apheresis for ↑ Parasite load
 Microbiology: Nematodes Bootcamp.com

Wuchereria and Brugia

General Principles:
• Wuchereria bancrofti, Brugia malayi and Brugia timori
• Mosquito: Microfilariae → Larvae
• Human: Adult worms → Microfilariae
Pathophysiology:
• Female mosquito takes blood meal → Injects larvae into host skin → Lymphatics
• Larvae mature into adult worms → Produce microfilariae → Lymphatics and blood supply
• Mosquito takes a blood meal including microfilariae
• Inflammation due to allergens, toxins, secondary bacterial infections and death of worms
• Chronic inflammation → Dilation of lymph vessels → Lymphedema → Elephantiasis
• Th2 mediated response: IL-5, IL-10, IL-13, IgE and eosinophils
Lymphatic Filariasis:
• Endemic to tropical and subtropical areas
• Most infections are asymptomatic
• Lymphedema: Painful swelling typically in lower limbs → Thickened skin and functional deformity
• Filarial fever, painful lymphadenopathy, and hydrocoele
Diagnostics:
• Blood smear: Visualize microfilariae under microscopy
• Rapid antigen test, PCR
• CBC: Eosinophilia
Management:
• Diethylcarbamazine
• Albendazole, ivermectin or doxycycline as alternative therapies
• Limb elevation and hygiene for lymphedema
 OUTLINE

1. Taenia
A. General Principles

Microbiology: B. Pathophysiology
C. Taeniasis
D. Diagnostics

Cestodes 2.
E. Management
Diphyllobothriid
A. General Principles
B. Pathophysiology
C. Diphyllobothriasis
D. Diagnostics
E. Management
3. Echinococcus
A. General Principles
B. Pathophysiology
C. Echinococcosis
D. Complications
E. Diagnostics
F. Management
Microbiology: Cestodes Bootcamp.com

Taenia
General Principles:
• Taenia solium (pork tapeworm) or Taenia saginata (beef tapeworm)
• Three life cycle stages: Adult worm (active), egg (infectious), and larva (active)
Pathophysiology:
• Consumption of undercooked meat with larval cysticerci OR fecal-oral transmission of eggs
• Larvae → SI → Adult worms → Attach to mucosa of SI using scolex
• Adult worms release proglottids → Proglottids and eggs in feces
• Consumption of eggs → Larvae released when exposed to gastric acid → Invade intestinal wall
• Larvae in host blood supply → Muscle, eye, heart, CNS → Encyst as cysticerci
• Death of larvae or degeneration of cysts → Inflammation → Fibrosis → Calcification
Taeniasis:
• Endemic to Latin America, Asia and Africa
• Most cases are asymptomatic
• Intestinal taeniasis: Abdominal pain, loss of appetite, weight loss, nausea, diarrhea, bloating
• Neurocysticercosis: Headache, intracranial hypertension, cognitive dysfunction → Seizures
• Ocular cysticercosis: Visual disturbances, limited eye movement, uveitis, chorioretinitis
Diagnostics:
• Stool sample: Eggs or proglottids visualized on microscopy
• Cerebral MRI/CT: Brain cysts +/- Dot sign, hyperdense cyst fluid, surrounding edema, calcifications
• CBC: Eosinophilia
Management:
• Praziquantel
• Albendazole and corticosteroids for neurocysticercosis
• Antiseizure medication and surgical removal of cysterci if severe
 Microbiology: Cestodes Bootcamp.com

References
• Histology of subcutaneous T. solium cysticercus:
• https://www.pathologyoutlines.com/topic/skinnontumorcysticercosis.html
• Courtesy: Thiriveni Balajji, M.D., M. Kavitha, M.D. via PathologyOutlines.com
• MRI of Neurocysticercosis:
• Courtesy of Living Art Enterprises/Science Photo Library
• Taenia emplumada.jpg:
• https://commons.wikimedia.org/wiki/File:Taenia_emplumada.jpg
• Peones45aire, CC BY-SA 4.0, via Wikimedia Commons
• Taenia species egg.JPG:
• https://commons.wikimedia.org/wiki/File:Taenia_species_egg.JPG
• Riddlemaster, CC BY-SA 4.0, via Wikimedia Commons
• Taenia solium Pathophysiology:
• Created with BioRender.com
Microbiology: Cestodes Bootcamp.com

Diphyllobothriid
General Principles:
• Dibothriocephalus latus or “fish tapeworm”
• Three lifecycle stages: Adult worm (active), egg, larva (infectious)
Pathophysiology:
• Consumption of undercooked or raw fish that are infected with larvae
• Larvae → SI → Adult worms → Attach to intestinal mucosa with scolex
• Adult worms feed off chyme and Vitamin B12 → Megaloblastic anemia
• Adult worms release eggs that pass in feces
Diphyllobothriasis:
• ↓ Worm burden: Asymptomatic → Weight loss, loss of appetite
• ↑ Worm burden: Diarrhea, abdominal pain, vomiting → Intestinal obstruction, cholecystitis
• Vitamin B12 deficiency: Fatigue, subacute combined degeneration, glossitis
Diagnostics:
• Stool ova and para test → Visualize eggs or proglottids underneath microscopy
• Vitamin B12 deficiency: ↓ Serum Vitamin B12, ↓ Hb, ↑ MCV, Hypersegmented neutrophils
• Adult worms seen on colonoscopy, endoscopy or in feces
• CBC: Eosinophilia
• Cholecystitis: ↑ ALP ↑ AST ↑ ALT ↑ Bilirubin
Management:
• Praziquantel
• Niclosamide
Microbiology: Cestodes Bootcamp.com

Echinococcus
General Principles:
• Echinococcus granulosus
• Four life cycle stages: Eggs (infectious), Oncospheres (active), larvae and adult worms
Pathophysiology:
• Fecal-oral transmission of eggs
• Cysts in sheep are consumed by canines → Larvae in SI of canine → Adult worms → Eggs in feces
• Eggs contaminate food and water → Eggs consumed by human host → Hatch as oncospheres
• Oncosphere penetrates gut wall → Blood supply → Liver → Cyst formation
Echinococcosis:
• ↑ Risk with exposure to infected dogs and/or sheep
• Slow growing cysts → Asymptomatic for years
• Hydatid cysts: Hepatomegaly, palpable mass, RUQ pain, weight loss, cough, chest pain, dyspnea
Complications:
• Rupture of cyst → Antigenic fluid released → Increased IgE & Eosinophils → Anaphylactic shock
• Fever, urticaria, chest tightness, dysphagia, syncope
• Cyst rupture can occur during surgical drainage or removal
• Large hydatid cysts → Budd-Chiari Syndrome → Jaundice, ascites, hepatomegaly
Diagnostics:
• CT of liver: Cysts with eggshell calcifications, typically in R lobe
• US of liver: Well-defined anechoic cysts with eggshell calcifications
• Biopsy + PCR: Detection of antigens
• CBC: Eosinophilia
Management:
• Albendazole
• Surgical removal for complicated cysts
 OUTLINE

1. Schistosoma
A. General Principles

Microbiology: B. Pathophysiology
C. Schistosomiasis
D. Complications

Trematodes E. Diagnostics
F. Management
2. Clonorchis
A. General Principles
B. Pathophysiology
C. Clonorchiasis
D. Complications
E. Diagnostics
F. Management
Microbiology: Trematodes Bootcamp.com

Schistosoma
General Principles:
• Schistosoma mansoni, Schistosoma japonicum, Schistosoma haematobium
• Four life cycle stages: Eggs (active), miracidia, cercariae (infectious), adults
Pathophysiology:
• Eggs in water hatch into miracidia → Penetrate snail tissue → Release cercariae
• Cercariae penetrate skin of host → Enter venous supply → Mature into adults → Target organs
• Female adult flukes lay eggs in blood supply → Inflammation and capillary blockage
• Eggs penetrate SI or bladder → Eggs pass in stool or urine
• Acute infection → Immune complex formation from egg or adult worm antigens
• Chronic infection → Chronic inflammation → Granuloma formation
Schistosomiasis:
• Endemic to South America, Caribbean, Africa, Middle East, China, and Southeast Asia
• Cercarial dermatitis: Pruritic maculopapular rash at penetration site
• Katayama fever: Fever, myalgia, angioedema, fatigue, cough
• Intestinal: Abdominal pain, diarrhea, intestinal bleeding → Iron deficiency anemia
• Hepatosplenic: Hepatosplenomegaly, periportal fibrosis and portal hypertension
• Genitourinary: Hematuria, dysuria → Painless hematuria
Complications:
• Inflammation of urothelium → Squamous metaplasia→ Squamous cell carcinoma of the bladder
Diagnostics:
• CBC: Eosinophilia
• Stool or urine sample: Visualize eggs underneath microscopy
Management:
• Praziquantel
• Acute infection: Corticosteroids for symptomatic management
Microbiology: Trematodes Bootcamp.com

Clonorchis
General Principles:
• Clonorchis sinensis
• Three lifecycle stages: Egg, cercariae (infectious) and adult worms (active)
Pathophysiology:
• Eggs contaminate water supply → Ingested by snails → Larvae released by snails → Penetrate fish
• Consumption of undercooked or raw fish infected with larvae → Migrate to biliary tract
• Larvae mature → Adult worms → Release eggs in bile tract → Eggs released in feces
• Adult flukes obstruct bile tract and ↑ Inflammatory response
Clonorchiasis:
• Endemic to Asia
• Asymptomatic for most infections
• Migration of flukes (Acute): RUQ pain, diarrhea, fatigue, fever, cholangitis
• Obstruction and inflammation of bile tract (Chronic): Malnutrition, weight loss, jaundice
Complications:
• Chronic inflammation → Biliary tract fibrosis
• Brown pigmented gallstone formation → Cholelithiasis → Postprandial biliary colic
• ↑ Risk of cholangiocarcinoma
Diagnostics:
• Stool ova and para test → Visualize operculated eggs underneath microscopy
• ↑ Eosinophilia and ↑ ALP
Management:
• Praziquantel
 OUTLINE

1. Sarcoptes
A. General Principles

Microbiology: B. Pathophysiology
C. Scabies
D. Complications

Ectoparasites E. Diagnostics
F. Management
2. Pediculus & Pthirus
A. General Principles
B. Pathophysiology
C. Pediculosis
D. Complications
E. Diagnostics
F. Management
3. Cimex
A. General Principles
B. Pathophysiology
C. Bed Bug Bites
D. Diagnostics
E. Management
Microbiology: Ectoparasites Bootcamp.com

Sarcoptes
General Principles:
• Sarcoptes scabiei
• Arthropod → Arachnid
• Three life cycle stages: Adults (infectious), Eggs, Larvae
Pathophysiology:
• Adult female mite burrows into stratum corneum → Lays eggs + Deposits scybala
• Eggs hatch → Larvae mature over 3 weeks → Adult mites → More eggs + Burrowing
• Decomposing adult mites + Scybala → Release antigens → T-cell sensitization
• Type IV immune reaction: Cell-mediated memory response → ↑ Inflammation + Cell death
Scabies:
• Highly contagious, skin-to-skin contact → ↑ Risk in children, crowded living conditions
• Intense pruritus (↑ at night), erythematous papules, vesicles, burrows, burning sensation
• Most common sites of invasion: Interdigital folds, flexor surface of wrist, medial surface of fingers
Complications:
• Secondary bacterial infection → Impetigo → PSGN (GAS), Sepsis (S. aureus)
• Eczema, delusion of parasitosis
Diagnostics:
• Detection of adult mites, larvae, eggs or scybala on demascopy, microscopy, histology
• Direct contact with other infected person
Management:
• Permethrin lotion applied a week apart for every member of the household
• Oral ivermectin in severe cases
• Wash all bedding and clothing during treatment
 Microbiology: Ectoparasites Bootcamp.com

Pediculus & Pthirus

General Principles:
• Pediculus humanis capitis, Pediculus humanis corporis, Pthirus pubis
• Commonly referred to as “lice”
• Three life cycle stages: Adult louse (infectious and active), egg (nits), nymph
Pathophysiology:
• Direct physical contact OR sharing bedding, clothes, hair accessories
• Adult louse lay eggs at hair shaft → Eggs hatch to nymphs → Mature to adults in 3 weeks
• Adults feed on host blood by injecting saliva into skin → Inflammation of the infected area
Pediculosis:
• More commonly seen in children, teenagers and young adults
• ↑ Risk with limited access to bathing or washing clothes
• Asymptomatic in mild infections
• Pruritus, excoriations, post-inflammatory hyperpigmentation
Complications:
• Rickettsia prowazekii → Epidemic typhus → Fever, HA, maculopapular rash
• Borrelia recurrentis → Relapsing fever → Cycle between days of febrile and afebrile
• Bartonella quintana → Trench fever → Five day fever, malaise, headache, nausea, vomiting
Diagnostics:
• Direct visualization of louse or nits with naked eye or microscopy
• Wood lamp examination: UV light to detect skin lesions
Management:
• Topical pediculicides: Permethrin, pyrethrin, malathion
• Remove nits with a fine-tooth comb
• Wash bedding, clothes, combs and brushes
• Pthirus pubis: Screen for other STIs and treat partners
 Microbiology: Ectoparasites Bootcamp.com

Cimex
General Principles:
• Cimex lectularius
• Commonly referred to as “bed bugs”
• Three lifecycle stages: Egg, nymph (active) and adult (active)
Pathophysiology:
• Passive transmission: Adults and eggs live on clothes, luggage, mattresses and furniture
• Adults and nymphs feed on blood at night → Hypersensitivity response to saliva
• Saliva contains anticoagulants, vasodilation factors and proteolytic enzymes
Bed Bug Bites:
• ↑ Risk in high-turnover, crowded or unsanitary living conditions
• Initial bite is typically asymptomatic
• Pruritic, linear, erythematous papules with central hemorrhagic punctum, resolve spontaneously
• Typically notice bites after sleeping
• Secondary bacterial infection can occur → Cellulitis or impetigo
Diagnostics:
• Detection of bed bugs in environment
Management:
• Symptomatic management: Antihistamines and/or topical corticosteroids
• Insecticides or heat treatment from pest control
• Antibiotic therapy if needed
 OUTLINE
1. Approach to Virology
A. Virology Format

Microbiology: B. Viral Structure and Organization

C. Viral Replication and Function
D. Host Defense

Approach to 2. Comprehensive Virus Diagrams

A. Structural Approach
B. Systems Approach

Virology
 Microbiology: Approach to Virology Bootcamp.com

• Virology Format:
• General virology
• Specific virology
• Derivative answer choices
• Viral Structure and Organization:
• Composition à RNA vs DNA, SS vs DS, (+) vs (-) sense
• Components à Genome, capsid, envelope, antigens
• Viral families
• Viral Replication and Function:
• Transmission and host cell entry
• Cell location à Nucleus vs cytosol
• Nucleic acid replication mechanisms à Polymerase, transcriptase
• Course of infection à Acute, chronic, latent
• Cellular changes à Inclusions, cell structure, malignancy
• Viral disease à Varies by organ system
• Host Defense:
• Host cell
• Immune system
• External defenses à Vaccines, pharmacotherapies
Microbiology: Approach to Virology Bootcamp.com
Microbiology: Approach to Virology Bootcamp.com
 OUTLINE
1. Viral Organization
A. Nucleic Acids

Microbiology:
B. Viral Proteins
C. Envelope
D. Replication

Basics of 2.
E. Morphologies
Mechanisms of Viral
infectivity

Virology
A. Transmission
B. Attachment
C. Entry
D. Replication
E. Release
F. Characteristics of
Infection
3. Viral Genetics
A. Reassortment
B. Recombination
C. Phenotypic Mixing
D. Complementation
4. Host Defense
A. Host Cell Defense
B. Immune System Defense
C. Vaccines
D. Pharmacotherapy
 Microbiology: Basics of Virology Bootcamp.com

(+) sense SS RNA

Viral Organization
Viral RNA polymerase
• Nucleic Acids: (-) sense SS RNA
• RNA single stranded (SS) (+) sense viruses à mRNA
• RNA single stranded (SS) (-) sense viruses à Carry RdR polymerase and envelope
• RNA double stranded (DS) viruses (Rota virus)
• DNA viruses à Double stranded (ex. Parvovirus)
• Reverse transcriptase (HIV, HBV) à RNA to DNA
• Linear vs circular (Papilloma, HBV, Polyoma) genomes
• Mutations à RdR polymerase (no proof reading), segmented genomes à Antigenic variation
• Viral Proteins:
• Made from viral genes
• Protein capsid à Encapsulates genetic material
• Replicative proteins à Polymerase, transcriptase
• Protein antigens à Bind antibodies and receptors
• Envelope:
DNA à mRNA Segmented genome Reverse transcriptase
• Protective membrane
• Cell entry à Fusion
• Morphologies: Virus Protein antigen
• Naked icosahedral
• Enveloped icosahedral Influenza Hemagglutinin, Neuraminidase
• Enveloped helical
Epstein Barr virus EBNA, VCA
• Bacteriophage
HIV Gp120, Gp41, p24, p17
Paramyxoviridae Fusion protein
SARS-CoV2 Spike protein
Naked Enveloped Enveloped Bacteriophage
icosahedral icosahedral helical
HBV HBsAg
 Microbiology: Basics of Virology Bootcamp.com

Virus Host Receptor

Mechanisms of Viral Infectivity Rhinovirus ICAM1
Influenza virus Sialic acid
• Transmission: SARS-CoV-2 ACE-2
• Virus enters host body
Rabies Nicotinic ACh
• Airborne: TB, Varicella, SARS, Measles (Rubeola)
• Droplet: Rubella, Adenovirus, Influenza, Neisseria meningitidis Parvovirus B19 P antigen on RBC
• Fecal-oral: Polio, HAV, Rota HIV CD4, CCXCR4, CCR5
• Contact: HSV, HPV
EBV CD21
• Blood contamination: HBV, HCV, HIV
• Attachment:
Virus Host Cell Histology
• Virus binds host receptor
• Tropism à Tendency to bind specific tissue receptors (HIV) Rabies Negri bodies
• Entry: HSV, VZV, CMV Cowdry type A bodies
• Genetic material enters host cell CMV Owl-eye nuclear bodies
• Endocytosis
HSV and Syncytia formation
• Bacteriophage genetic injection (bacteria only) Paramyxoviridae
• Replication:
• RNA viruses replicate in cytoplasm (ex. Orthomyxovirus) HPV Koilocytosis
• DNA viruses replicate in nucleus (ex. Pox virus)
• Utilize host machinery to replicate
• Release: Virus Related Malignancy
• Cell lysis or budding à Virion particle release EBV Burkitt’s and Hodgkin’s lymphoma, nasopharyngeal
• Characteristics of Infection: carcinoma, TALP disorder
• Incubation period à Time of exposure to onset of symptoms HHV8 Kaposi’s sarcoma
• Cytolysis and other cellular changes (bodies, syncytia)
• Chronic infection (HBV, HCV, HIV) HPV Cervical/penile/anal carcinoma, laryngeal papilloma
• Latency (HSV, VZV, HIV) HTLV1 T-cell leukemia
• Retrograde axonal transport (HSV, VZV, Rabies, Polio)
• Oncogenesis HCV, HBV Hepatocellular carcinoma
 Microbiology: Basics of Virology Bootcamp.com

Viral Genetics
Reassortment Exchange of gene segments from viruses with
segmented genomes.
• Bunyavirus (3)
• Orthomyxovirus (8) + à
• Arenavirus (2)
• Rota virus (10-12)

Recombination Exchange of genes between two chromosomes that

involves crossing-over.

+ à

Phenotypic New virion formation composed of genome from virus A

Mixing and surface proteins from virus B when both viruses
simultaneously co-infect a host.
• Surface proteins of second generation progeny will + à à
be original to virus A as genome is unchanged.
A B Progeny Progeny
1 2

Complementation Nonfunctional Virus A utilizes surface proteins of virus

B to infect host.
• Hepatitis D and B + à
Functional Nonfunctional Functional
 Microbiology: Basics of Virology Bootcamp.com

Host Defense
• Host Cell Defense:
• Infected cell releases IFN-ɑ and IFN-βà Paracrine signal to neighboring cells à ↓ protein synthesis à ↓ viral replication in nearby cells
• Immune System Defense:
• Cell-mediated defense à CD8 cytotoxic T cell direct destruction of virally infected cells via MHC1 presentation
• Antibody-mediated defense à Neutralizing antibodies and ADCC
• NK cell-mediated defense à Direct destruction of virally infected cells via nonspecific signals, MHC1 absence, or ADCC
• Vaccines:
• Antibody and memory cell production toward viral antigens à Viral interception and faster immune responses upon next exposure
• Live attenuated vaccine à Carries non-pathogenic virus à Strong immune response à CI in pregnant and immunocompromised
• Inactive vaccine à Carries killed virus with intact structural proteins à Weak immune response à Safer than live-attenuated
• Subunit vaccine à Carries only viral proteins
• Immunity à Pre-existing antibodies and memory cells à Interception of microbe à ↓ attachment and replication à ↓ transmission and symptoms
• Pharmacotherapy:
• Interfere with entry, replication, production and release of viruses

↓ protein synthesis

Vaccine Related Malignancy Mnemonic

Live- BCG, Influenza (intranasal), Varicella, MMR, Bioengineered Influenza
IFN-ɑ / IFN-β
↓ viral transmission
attenuated Smallpox, Polio (oral), Rota, Adenovirus, Vaccine Membrane SPRAY
Yellow fever
à
Inactivated Influenza (IM), Hepatitis A, Polio (IM), Rabies Inactivated Agent Prevents
Replication
Subunit HBV, HPV
 OUTLINE
1. Infectious Meningoencephalitis
A. General Principles

Microbiology:
B. Pathophysiology
C. Bacterial Meningoencephalitis
D. Viral (Aseptic) Meningoencephalitis

Infectious
E. Atypical Meningoencephalitis
F. Neonatal Meningoencephalitis
G. Adult Pharmacologic Management

Neuropathology
H. Neonatal Pharmacologic Management
2. Infectious Cerebral Lesions
A. General Principles
B. Pathophysiology
C. Typical Abscess Pathogens
D. Atypical Abscess/Cyst-forming Pathogens
E. Neurotoxic Pathogens
3. Infectious Spinal Cord Disease
A. Tetanus
B. Botulism
C. Poliomyelitis
D. Rabies
E. Tabes Dorsalis (Syphilitic Myelopathy)
F. Subacute Combined Degeneration
 Microbiology: Infectious Neuropathology Bootcamp.com

Infectious Meningoencephalitis
General Principles: ↑ Risk in neonates, elderly, immunocompromised, pregnancy, crowded environments
Pathophysiology: Hematogenous dissemination, direct trauma, contiguous spread 🡪 CNS
Bacterial Meningoencephalitis:
• Rapid onset fever, nuchal rigidity, headache or altered mentation
• Hypotension, tachycardia, photophobia, emesis, altered mentation, seizures
• Kernig and Brudzinski sign, papilledema, Cushing reflex
• Lumbar puncture: ↑ Opening pressure, cloudy fluid, pleocytosis (>1,000/mm3, granulocytosis), ↑ protein, ↓ glucose
• Meningococcemia: Purpura/petechiae, Waterhouse-Friderichsen syndrome
• Typical Pathogens: S. pneumoniae, N. meningitidis, H. influenzae type b, Listeria
• Atypical Pathogens: S. aureus (direct trauma, VP shunt)
Viral (Aseptic) Meningoencephalitis:
• Non-specific signs/symptoms: Low grade fever, malaise, myalgia, maculopapular rash +/- less severe meningeal signs
• Lumbar puncture: ↑/- Opening pressure, clear fluid, pleocytosis (10-500/mm3, lymphocytosis), ↑/- protein, normal glucose
• Typical Pathogens: Enteroviruses (MCC), HSV, VZV, West Nile virus, St. Louis encephalitis virus, HIV
• Subacute Sclerosing Panencephalitis: Persistent measles infection 🡪 Inflammatory demyelinating, ↑ Anti-measles IgG in CSF
• Kluver-Bucy Syndrome: Bilateral temporal lobe lesions 🡪 HSV-1 encephalitis
Atypical Meningoencephalitis:
• Tuberculous: Mycobacterium tuberculosis, immunocompromised, insidious onset, AFB, ADA activity
• Lyme: Borrelia burgdorferi, late stage neuroborreliosis, CN VII palsy, nocturnal paresthesias, mononeuritis multiplex
• Cryptococcal: Cryptococcus neoformans, immunocompromised (CD4+ <100), India ink, Latex agglutination test, narrow-based budding yeast
• Rickettsial: Rickettsia spp., petechiae, tick exposure, non-classic bacterial LP results
• Primary Amebic: Naegleria fowleri, warm freshwater ponds, rapid onset fulminant disease, hemorrhagic (RBC in LP), fatal
• Lumbar puncture: ↑ Opening pressure, pleocytosis (lymphocytes), ↑ protein, ↓ glucose
Neonatal Meningoencephalitis:
• Lethargy, emesis, hypotonia, fever (or hypothermia), bulging fontanelle, high pitched crying, seizures
• Typical pathogens: Streptococcus agalactiae (Group B), E. coli, Listeria, Enteroviruses (Coxsackie virus)
Adult Pharmacologic Management:
• Empiric: Ceftriaxone + Vancomycin + Dexamethasone +/- Ampicillin
• Fungal: Amphotericin B
• Tuberculous: RIPE variants
• Cryptococcal: Amphotericin B + Flucytosine
• Lyme: Ceftriaxone
• HSV: Acyclovir
Neonatal Pharmacologic Management: Empiric: Cefotaxime + Ampicillin + Gentamicin
Microbiology: Infectious Neuropathology Bootcamp.com

Meningitis Lumbar Puncture Table Review

Etiology WBC Predominant Glucose Protein Gram stain

G(-) Diplococci: N. meningitidis

3 G(+) Diplococci: S. pneumoniae
Bacterial >1000/mm Neutrophil <40 mg/dL >250 mg/dL
Gen G(+) Bacilli: Listeria 🡪 Ampicillin
eral G(-) Coccobacilli: H. influenzae

Viral 100-1000/mm3 Lymphocyte 40-70 mg/dL <100 mg/dL No result

No result
Fungal <500/mm3 Lymphocyte Variable >250 mg/dL

Etiology WBC Predominant Glucose Protein Additional

AFB: Acid fast bacilli

Tuberculous Lymphocyte <10 mg/dL >250 mg/dL ADA activity (CSF)
Pat RIPE therapy variants
5-1000/mm3
hog
Lymphocyte
en Lyme Variable Variable History of tick exposure
Mononuclear cell
Spe
cific India Ink
Cryptococcal 20-200/mm3 Lymphocyte <40 mg/dL <100 mg/dL
Latex agglutination (CSF)

DDx in rash/petechiae
Rickettsia 10-1000/mm3 Lymphocyte 40-70 mg/dL Variable History of tick exposure
Doxycycline

<40 mg/dL <100 mg/dL

Primary Amebic Variable +/- RBCs Neutrophil Amphotericin B
 Microbiology: Infectious Neuropathology Bootcamp.com

Infectious Cerebral Lesions

General Principles:
• Focal neurologic deficits (e.g. hemiparesis, aphasia), ↑ risk of seizures
• Avoid LP if suspect mass lesions or ↑ ICP 🡪 Risk of brain herniation
Pathophysiology: Hematogenous dissemination, direct trauma, contiguous spread 🡪 CNS
Typical Abscess Pathogens:
• Commonly polymicrobial (oral anaerobes 🡪 Bacteroides)
• Viridans streptococci (MCC)
• Staphylococcus Aureus
• Staphylococcus Epidermidis: VP shunts, neurosurgical equipment
Atypical Abscess/Cyst-forming Pathogens:
• Nocardia: Immunocompromised patient, partial acid fast, initial pulmonary disease
• Cryptococcus neoformans: Pigeons/bird droppings, immunocompromised (CD4+ <100), India ink, Latex agglutination test 🡪 “Soap bubble” lesions (Pseudocysts)
• Toxoplasma gondii: Cat feces, immunocompromised (CD4+ <100), multiple “ring-enhancing” lesions, microscopy w/ tachyzoites
• Taenia solium: Consumption of raw pork, eosinophilia, cystic lesion(s) +/- invaginated scolex
Neurotoxic Pathogens:
• JC Virus: Reactivation 🡪 PML, Immunocompromised (CD4+ <200), asymmetric T2-hyperintense lesions without mass effect
• HIV Encephalopathy: Diffuse atrophy, immunocompromised, symmetric T2-hyperintense lesions
• Primary CNS Lymphoma: Viral associations (EBV), immunocompromised (CD4+ <100), solitary variable (homogenous vs ring) enhancing lesions on CT with contrast
• Spongiform Encephalopathy: Misfolded proteins (PRPSc), startling myoclonus, rapidly progressing dementia, ↑ 14-3-3 protein (CSF), triphasic periodic sharp waves (EEG)
 Microbiology: Infectious Neuropathology Bootcamp.com

Infectious Spinal Cord Disease

Tetanus:
• Clostridium tetani 🡪 Tetanospasmin
• Tetanospasmin travels to CNS via retrograde transport 🡪 🡪 ↓ Glycine and GABA release from Renshaw cells 🡪 ↑↑↑ Activation ⍺-motor neurons (UMN)
• Penetrating trauma, wounds, burns, incomplete immunization
• Painful muscle spasms, rigidity, trismus, Risus sardonicus, opisthotonos, hyperreflexia
• Respiratory failure (laryngospasm)
• Neonatal: Umbilical stump colonization (Unvaccinated mother), ↓ Cry and suck, difficulty opening mouth and feeding (trismus), persistently clenched hands, opisthotonos
Botulism:
• Clostridium botulinum 🡪 Botulinum toxin
• Botulinum toxin travels to presynaptic cholinergic nerve terminals (nicotinic + muscarinic) 🡪 ↓ ACh exocytosis 🡪 ↓↓↓ Activation of ⍺-motor neurons (LMN)
• Descending symmetric flaccid paralysis, hyporeflexia, bulbar involvement (diplopia, dysphagia, dysarthria)
• Xerostomia, mydriasis
• Infant Botulism (“Floppy Baby” Syndrome): ↓ Cry and suck, difficulty feeding (dysphagia), ptosis, hypotonia, absent gag reflex, respiratory failure (diaphragmatic paralysis)
Poliomyelitis:
• Poliovirus: Enterovirus, Picornaviridae family, (+) ssRNA virus
• Oral ingestion of virus 🡪 Hematogenous spread 🡪 Anterior horn cell invasion 🡪 ↓↓↓ Activation of ⍺-motor neurons (LMN)
• Asymmetric acute ascending flaccid paralysis (proximal > distal), hyporeflexia, hypotonia, fasciculations, muscle atrophy, respiratory failure (diaphragmatic paralysis)
• LP: Pleocytosis, ↑ Protein, normal glucose
Rabies:
• Rabies virus: Lyssavirus, Rhabdoviridae family, (-) ssRNA virus
• Infected animal bite 🡪 Transmission of saliva containing virus 🡪 Binds to nicotinic AChR 🡪 Retrograde transport to CNS
• Hydrophobia, photophobia, autonomic dysfunction, seizures, altered mentation, paralysis, bulbar involvement, respiratory failure (diaphragmatic paralysis)
• Histopath: Eosinophilic inclusion bodies in cerebellar Purkinje and hippocampal neurons (Negri bodies)
Tabes Dorsalis (Syphilitic Myelopathy):
• Treponema pallidum
• Demyelination of dorsal root ganglia and dorsal columns 🡪 ↓ Proprioception, vibration, fine touch
• Broad-based gait, ataxia, Romberg (+), areflexia (lower extremities), paresthesias
Subacute Combined Degeneration:
• Diphyllobothrium latum (fish tapeworm) 🡪 Parasite-mediated dissociation of vitamin B12-intrinsic factor complex 🡪 ↓ Vitamin B12 availability
• Helicobacter pylori 🡪 Local destruction of gastric parietal cells 🡪 Atrophic gastritis 🡪 ↓ Intrinsic factor 🡪 ↓ Vitamin B12 availability
• Demyelination (symmetric) in dorsal columns, lateral corticospinal, and spinocerebellar tracts 🡪 ↓ Proprioception, vibration, fine touch, spastic weakness, hyperreflexia
• Additional B12 deficiency findings: Megaloblastic anemia, peripheral neuropathy, reversible dementia, glossitis
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0092

A 23-year-old male with no significant past medical history presents to the emergency department with his spouse for a continuous fever and two days of
severe headaches with one episode of non-bloody emesis. The patient’s spouse reports that his personality has seemed to change abruptly over the
past two days. Apparently, the patient had been making inappropriate remarks to strangers at the local grocery store and had calmly insisted to the store
manager that he would like to taste all packaged foods before purchasing. His spouse reports that this behavior is very abnormal for him. Vital signs
reveal a temperature of 101.4℉ (38.5℃), blood pressure of 110/68 mmHg, heart rate of 112/min, and respiratory rate of 20/min. Neurologic examination
reveals that the patient is not currently able to respond to verbal commands and is withdrawing to noxious stimuli. Pupils are normal in size and reactive.
Bilateral deep tendon reflexes are symmetrically brisk with bilateral upgoing plantar responses. There is no evidence of papilledema on fundoscopy.
Brudzinski sign is positive. An MRI of the brain is also shown below. Which of the following most likely explains the etiology of this patient’s presentation?

Lumbar Puncture

Opening pressure Normal

Fluid appearance Clear

⚪ A. Reactivation of JC virus Cell count 54/mm3

Cell predominance Lymphocytes

⚪ B. Reactivation of herpesvirus
Protein 64 mg/dL
⚪ C. Persistent measles virus
Glucose 50 mg/dL
⚪ D. Reactivation of Ebstein-Barr virus Gram stain Negative

⚪ E. Hematogenous streptococcal Acid-fast bacilli Negative

dissemination
Sabouraud culture Negative

⚪ F. Larval cyst inflammatory response Latex agglutination Negative

⚪ G. Invasive encapsulated yeast Anti-measles IgG Normal

≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0092

A 23-year-old male with no significant past medical history presents to the emergency department with his spouse for a continuous fever and two days of
severe headaches with one episode of non-bloody emesis. The patient’s spouse reports that his personality has seemed to change abruptly over the
past two days. Apparently, the patient had been making inappropriate remarks to strangers at the local grocery store and had calmly insisted to the store
manager that he would like to taste all packaged foods before purchasing. His spouse reports that this behavior is very abnormal for him. Vital signs
reveal a temperature of 101.4℉ (38.5℃), blood pressure of 110/68 mmHg, heart rate of 112/min, and respiratory rate of 20/min. Neurologic examination
reveals that the patient is not currently able to respond to verbal commands and is withdrawing to noxious stimuli. Pupils are normal in size and reactive.
Bilateral deep tendon reflexes are symmetrically brisk with bilateral upgoing plantar responses. There is no evidence of papilledema on fundoscopy.
Brudzinski sign is positive. An MRI of the brain is also shown below. Which of the following most likely explains the etiology of this patient’s presentation?

Lumbar Puncture

Opening pressure Normal

Fluid appearance Clear

⚪ A. Reactivation of JC virus Cell count 54/mm3

Cell predominance Lymphocytes

🔘 B. Reactivation of herpesvirus
Protein 64 mg/dL
⚪ C. Persistent measles virus
Glucose 50 mg/dL
⚪ D. Reactivation of Ebstein-Barr virus Gram stain Negative

⚪ E. Hematogenous streptococcal Acid-fast bacilli Negative

dissemination
Sabouraud culture Negative

⚪ F. Larval cyst inflammatory response Latex agglutination Negative

⚪ G. Invasive encapsulated yeast Anti-measles IgG Normal

 OUTLINE
1. Localized Infectious Pathology 4. Systemic Infectious Pathology
A. Erysipelas A. Staphylococcal Toxic Shock Syndrome

Microbiology: B. Cellulitis
C. Ecthyma Gangrenosum
D. Erythema Migrans
B. Staphylococcal Scalded Skin Syndrome
C. Necrotizing Fasciitis
D. Bacillary Angiomatosis

Infectious
E. Tinea Corporis E. Kaposi Sarcoma
F. Tinea Versicolor F. Herpes Zoster
G. Herpes Labialis

Dermatologic
2. Infectious Follicular Pathology
A. Acne Vulgaris
B. Folliculitis

Disease
C. Pediculosis Capitis
D. Tinea Capitis
3. Infectious Childhood Rashes
A. Impetigo
B. Molluscum Contagiosum
C. Scarlett Fever
D. Chickenpox
E. Measles (Rubeola)
F. Rubella
G. Erythema Infectiosum
H. Roseola Infantum
I. Hand Foot and Mouth Disease
 Microbiology: Infectious Dermatologic Disease Bootcamp.com

Erysipelas:
• Superficial dermis
• Raised, sharply demarcated erythema
• S. pyogenes (GAS)
Cellulitis:
• Deep dermis and subcutaneous tissue
• Poorly defined, indurated erythema
• S. pyogenes (GAS), S. aureus
• Pasteurella multocida: Cat or dog bite
Ecthyma Gangrenosum:
• Dermis
• P. aeruginosa
• Rapidly progressive, immunocompromised
• Painless erythema à Induration, pustules, bullae à Crusted ulcers, granulation tissue, pus
Erythema Migrans:
• B. burgdorferi
• Painless erythema with central clearing, “bulls-eye” rash
Tinea Corporis:
• Trichophyton rubrum, Microsporum, Epidermophyton
• Erythematous, pruritic plaques with central clearing and raised scaling borders
Tinea Versicolor:
• Malassezia furfur, Malassezia globosa
• Well-demarcated macules with variable pigmentation (hypo or hyper) +/- erythema
Herpes Labialis:
• HSV-1 (usually)
• Painful erythematous vesicular lesions à Ulcerations
 Microbiology: Infectious Dermatologic Disease Bootcamp.com

Acne Vulgaris:
• Cutibacterium (Propionibacterium) acnes
• Sebaceous gland (dermis)
• ↑ Androgens (puberty) à ↑ Sebum, Follicular hyperkeratosis à Comedone formation à Bacterial colonization
• Closed comedones: Round lesions with white color material
• Open comedones: Open lesions with oxidized sebum producing black color material
• Inflammatory/Nodular: Papular, pustular, arises from comedones, back and neck classic
• Hidradenitis suppurativa: Apocrine glands (axilla, groin, inner thigh), chronic, painful inflammatory nodular à May develop sinus tracts +/- abscess +/- comedones and scarring
Folliculitis:
• Hair follicle, Furuncle: deep to dermis, Carbuncle: confluent folliculitis: S. aureus (usually)
• Bacterial invasion of hair follicle
• Tender, pruritic papular, pustules (usually clustered)
• Hot tub folliculitis: P. aeruginosa
• DDx: Intertrigo: C. albicans
Pediculosis Capitis:
• Pediculus humanus capitis
• Children classically
• Pruritis in regions affected (scalp)
• Immature and adult lice visible on scalp or hair shaft
Tinea Capitis:
• Trichophyton tonsurans, Microsporum spp.
• Children classically
• Circular, pruritic scaly plaques
• Alopecia in affected areas, broken hair shafts
 Microbiology: Infectious Dermatologic Disease Bootcamp.com

Impetigo: S. aureus: Bullous and nonbullous, S. pyogenes (GAS): Nonbullous only

• Nonbullous: Vesicular pustules à Rupture and oozing honey-color crusting, classically on face
• Bullous: Large, flaccid bullae à Rupture to form yellow-brown crusting, classically on trunk and upper extremities
Molluscum Contagiosum: Poxvirus, Painless “pearly dome-shaped” papules with central umbilication
Scarlet Fever: S. pyogenes (GAS) à Erythrogenic exotoxin
• Tonsillopharyngitis, “strawberry tongue”, cervical LAD
• Fine, blanching, erythematous, “sandpaper” texture à Desquamation of skin
• Begins on neck, axilla, groin à Spreads to trunk, face, upper and lower extremities à Classically prominent at axilla and groin à Pastia lines
Chickenpox: Varicella Zoster Virus (HHV-3)
• Pruritic lesions in varying stages of development
• Papular à Vesicular with clear fluid on erythematous base (“dewdrop on rose petal”) à Umbilicated, crusted pustules à Scabbing
• Centrifugal spread (predominantly located on trunk)
Measles (Rubeola): Measles virus
• Prodrome with coryza, cough, and conjunctivitis +/- Koplik spots
• Erythematous, confluent, blanching maculopapular rash
• Begins on face à spreads to trunk, face, upper and lower extremities
Rubella (German Measles, Third Disease): Rubella virus
• Prodrome with post-auricular and suboccipital LAD, joint aching à polyarthritis
• Faintly erythematous, fine, non-confluent maculopapular rash
Erythema Infectiosum (Fifth Disease): Parvovirus B19
• Begins with redness of face and perioral sparing (“slapped-cheek” rash) à Rash forms on trunk, upper and lower extremities
• Erythematous, confluent, maculopapular rash à Reticular, or “lace-like”
Roseola Infantum (Exanthem Subitum, Sixth Disease): HHV-6 (usually)
• Abrupt onset of high fever à Fever resolves w/ rash formation
• Rose-pink color, nonpruritic, blanching, maculopapular rash
• Begins on trunk à Spreads to face, upper and lower extremities
Hand, Foot, Mouth Disease: Coxsackie virus
• Painful erythematous vesicular oral ulcers (buccal mucosa, tongue)
• Maculopapular +/- vesicular rash on palms of hands, soles of feet, and extremities
 Microbiology: Infectious Dermatologic Disease Bootcamp.com

Staphylococcal Toxic Shock Syndrome:

• S. aureus à TSST-1 à Superantigen
• High-absorbency tampon (prolonged use), post-surgical wound packing
• Mucosal involvement (conjunctivitis, Strawberry tongue)
• Erythematous macular rash involving the palms and soles à Desquamation of skin
Staphylococcal Scalded Skin Syndrome:
• Epidermis
• S. aureus à Exfoliative toxin A and B à Cleavage of desmoglein-1
• Infants and children
• No mucosal involvement
• Perioral erythema à Painful, diffuse blisters, easily ruptured (+ Nikolsky sign) à Widespread desquamation of epidermal tissue w/ “scalded” appearance
Necrotizing Fasciitis:
• Deep dermis, subcutaneous tissue, fascia
• Polymicrobial (E. coli, Bacteroides) vs Monomicrobial (S. pyogenes, S. aureus)
• Rapidly progressive à Septic shock
• Diffuse erythema +/- purple discoloration
• Pain out of proportion to erythema, crepitus, induration, hemorrhagic bullae à Desquamation of skin
• Gas-formation: C. perfringens, anaerobes
• Contaminated wound + marine environment à V. Vulnificus
Bacillary Angiomatosis:
• B. henselae à Cat scratch, Immunocompromised (CD4+<100)
• Red-violet, violaceous, “flesh-colored”, nodules, papules or plaques
• Neutrophilic infiltration, granulomatous inflammation
Kaposi Sarcoma:
• HHV-8, Immunocompromised (CD4+<500)
• Red-purple nodules or plaques
• Lymphocytic infiltration, granulomatous inflammation
Herpes Zoster:
• HHV-3 (Varicella Zoster Virus) reactivation
• Advancing age, immunosuppressive therapy, immunocompromised
• Painful erythematous maculopapular rash à Vesicular lesions à Crusted pustules
• Constrained to dermatomal distribution, does not cross midline
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0093

A 9-month-old female is brought to her pediatrician by her father due to multiple fluid-filled blisters observed on her face, axilla, groin, and neck. Per the
history provided, the lesions apparently first started as small macules in the periorbital region and eventually evolved into gradually enlarging bullae. Vital
signs reveal a temperature of 102.2℉ (39℃) and are otherwise within normal limits for age. On physical examination, there is evidence of large erosive
areas with shiny crusting, perioral and perianal skin detachment involving more than 50% of the total body surface area, and Nikolsky positive bullae
throughout the body. There is no mucosal involvement. Tissue cultures reveal catalase positive gram-positive cocci in clusters. A skin biopsy is also
obtained. Which of the following is most likely to be observed microscopically from this sample?

⚪ A. Epidermal detachment with full thickness keratinocyte necrosis

⚪ B. Superficial intraepidermal acantholysis

⚪ C. Neutrophilic dermal infiltrate with dermal edema

⚪ D. Subepidermal vesicles with eosinophilic spongiosis

⚪ E. Subepidermal vesicles with neutrophilic papillary microabscesses

⚪ F. Neutrophilic fascial infiltrate with extensive adipocyte necrosis

≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0093

A 9-month-old female is brought to her pediatrician by her father due to multiple fluid-filled blisters observed on her face, axilla, groin, and neck. Per the
history provided, the lesions apparently first started as small macules in the periorbital region and eventually evolved into gradually enlarging bullae. Vital
signs reveal a temperature of 102.2℉ (39℃) and are otherwise within normal limits for age. On physical examination, there is evidence of large erosive
areas with shiny crusting, perioral and perianal skin detachment involving more than 50% of the total body surface area, and Nikolsky positive bullae
throughout the body. There is no mucosal involvement. Tissue cultures reveal catalase positive gram-positive cocci in clusters. A skin biopsy is also
obtained. Which of the following is most likely to be observed microscopically from this sample?

⚪ A. Epidermal detachment with full thickness keratinocyte necrosis

" B. Superficial intraepidermal acantholysis

⚪ C. Neutrophilic dermal infiltrate with dermal edema

⚪ D. Subepidermal vesicles with eosinophilic spongiosis

⚪ E. Subepidermal vesicles with neutrophilic papillary microabscesses

⚪ F. Neutrophilic fascial infiltrate with extensive adipocyte necrosis

 OUTLINE
1. CD4+ Cell Count ≤ 500
A. Localized Cutaneous Kaposi Sarcoma

Microbiology:
B. Oropharyngeal Candidiasis
C. Oral Hairy Leukoplakia
D. HPV Carcinoma

Opportunistic
E. Reactivation (Secondary) Tuberculosis
F. Burkitt Lymphoma
2. CD4+ Cell Count ≤ 200

Infections A. Pneumocystis Pneumonia

B. Progressive Multifocal Leukoencephalopathy
C. Disseminated Kaposi Sarcoma
D. HIV-associated Dementia
E. HIV-associated Neuropathy
F. Disseminated Histoplasmosis
G. Disseminated Coccidioidomycosis
3. CD4+ Cell Count ≤ 100
A. Toxoplasmosis
B. Primary CNS Lymphoma
C. Cryptococcal Meningoencephalitis
D. Bacillary Angiomatosis
E. Infectious Esophagitis
F. Cryptosporidiosis
4. CD4+ Cell Count ≤ 50
A. Cytomegalovirus
B. Disseminated Mycobacterial Non-Tuberculous Disease
 Microbiology: Opportunistic Infections Bootcamp.com

CD4+ Cell Count ≤ 500

Localized Cutaneous Kaposi Sarcoma: HHV-8
• Red-violet, violaceous, nodules or plaques
• Histopathology: Lymphocytic infiltration, perivascular spindle-shaped cells, angiogenesis
Oropharyngeal Candidiasis: Candida albicans
• Variable CD4+
• Recent steroid use (inhaled 🡪 oral), diabetes, chronic granulomatous disease (catalase +)
• Pseudomembrane candidiasis, “oral thrush”, can be scraped off
• Histopathology: Pseudohyphae, budding yeast
Oral Hairy Leukoplakia: EBV
• White plaques (lateral tongue) of oral mucosa, cannot be scraped off
HPV Carcinoma: Oncogenic HPV subtype (16, 18, 31, 33)
• Anogenital and oropharyngeal carcinomas
Reactivation (Secondary) Tuberculosis: Mycobacterium tuberculosis
• TNF-⍺ inhibitors (Infliximab, adalimumab, golimumab, certolizumab, etanercept)
• Fever, night sweats, unintentional weight loss, hemoptysis, LAD
• Upper lobe +/- cavitation, caseating granuloma, contagious
• Miliary tuberculosis and tuberculous meningitis with worsening immunocompromised state
• Tuberculous spondylitis (Pott’s Disease): Hematogenous spread to vertebral body, TL junction
• Histopathology: Acid-fast bacilli (Ziehl-Neelsen stain, Auramine-rhodamine stain)
Burkitt Lymphoma: HIV-associated +/- EBV co-infection
• t(8:14) 🡪 C-myc (c8), heavy chain Ig (c14) 🡪 Overexpression of c-myc
• Fever, night sweats, unintentional weight loss
• Histopathology: Dense lymphocytic infiltration and macrophages with clear cytoplasm 🡪 “Starry sky” appearance
 Microbiology: Opportunistic Infections Bootcamp.com

CD4+ Cell Count ≤ 200

Pneumocystis Pneumonia: Pneumocystis jirovecii
• Nonproductive cough, progressive exertional dyspnea
• CXR, CT: Bilateral interstitial, patchy ground-glass opacities +/- pneumatoceles
• Silver stain: Disc-shaped yeast
• Prophylaxis for CD4+ <200: Trimethoprim-Sulfamethoxazole
Progressive Multifocal Leukoencephalopathy: JC virus reactivation
• Headache, confusion, seizures, FNDs
• MRI brain: Asymmetric T2-hyperintense lesions without mass effect
• Histopathology: Demyelination of axons, enlarged oligodendrocytes and astrocytes, intranuclear inclusions
Disseminated Kaposi Sarcoma: HHV-8
• Most common AIDS-associated malignancy
• Histopathology: Lymphocytic infiltration, perivascular spindle-shaped cells, angiogenesis
HIV-associated Dementia: HIV
• Significant cognitive deficits, impaired executive functioning, depression, impaired psychomotor speed and precision, bradykinesia
• MRI Brain: Diffuse cerebral atrophy out of proportion for age +/- symmetric T2-hyperintense white matter changes without mass effect
HIV-associated Neuropathy: HIV, Distal symmetric polyneuropathy, “stocking and glove” distribution
Disseminated Histoplasmosis: Histoplasma capsulatum
• Hemoptysis, LAD, oral ulcerative lesions (palate, tongue), HSM
• Pneumonia 🡪 Dissemination
• Silver stain: Yeast within macrophages (narrow-based budding, oval-shaped)
Disseminated Coccidioidomycosis: Coccidioides immitis, Coccidioides posadasii
• Hemoptysis, “Desert Rheumatism”: Erythema nodosum, arthralgias, fever
• Meningoencephalitis
• Silver stain: Large spherules containing endospores
 Microbiology: Opportunistic Infections Bootcamp.com

CD4+ Cell Count ≤ 100

Toxoplasmosis: Toxoplasma gondii
• Fever, headache, confusion, seizures, FNDs
• CT head, MRI brain: Multiple “ring-enhancing” lesions
• Microscopy: Tachyzoites
• Prophylaxis for CD4+ <100: Trimethoprim-Sulfamethoxazole
• Chorioretinitis: Visual impairment, floaters; Fundoscopy: Yellow-white “fluffy” lesions, “headlight-in-fog”
Primary CNS Lymphoma: EBV
• Headache, confusion, seizures, FNDs
• CT head, MRI brain: Multiple “ring-enhancing” lesions
• Microscopy: Atypical lymphoid cells
Cryptococcal Meningoencephalitis: Cryptococcus neoformans
• Pigeons/bird droppings
• Fever, headache, confusion, seizures, FNDs
• India ink: Encapsulated narrow-based budding yeast, Latex agglutination test
• MRI brain: “Soap bubble” lesions (pseudocysts)
Bacillary Angiomatosis: B. henselae
• Red-violet, violaceous, “flesh-colored”, nodules, papules, or plaques
• Biopsy: Benign capillary vascular proliferation, neutrophilic infiltration
Infectious Esophagitis: Candida albicans, HSV-1, CMV
• Odynophagia
• White-plaques present on endoscopy (Candida), Discrete shallow ulcers +/- vesicles (HSV-1), Deep linear ulcers (CMV)
• Histopath: Pseudohyphae, budding yeast (Candida), Eosinophilic intranuclear inclusions (HSV-1), Eosinophilic/basophilic intranuclear and cytoplasmic inclusions (CMV)
Cryptosporidiosis: Cryptosporidium spp.
• Profuse, chronic watery diarrhea, nausea, abdominal pain
• Stool microscopy: Acid fast oocysts
Invasive Aspergillosis: Aspergillus fumigatus
• Hemoptysis, nonproductive cough, B symptoms 🡪 Hypotension, tachycardia, tachypnea 🡪 Sepsis
• Disseminated disease 🡪 Invasive sinusitis, meningoencephalitis, hemorrhagic/pustular skin lesions, endocarditis
• Chest CT: Nodules +/- cavitation and consolidation +/- mycetoma
• Positive galactomannan enzyme assay
• Silver stain: Mold with septate hyphae branching dichotomously at 45° (acute) angles
 Microbiology: Opportunistic Infections Bootcamp.com

CD4+ Cell Count ≤ 50

Cytomegalovirus:
• Retinitis: Visual impairment, floaters; Fundoscopy: Retinal hemorrhages, fluffy white opacities, retinal detachment (“Pizza-pie” appearance)
• Atypical Pneumonia: Nonproductive cough, dyspnea; CXR: Diffuse bilateral interstitial infiltrates
• Esophagitis, Colitis: Odynophagia, hematochezia/melena, abdominal pain; Endoscopy: Deep linear ulcers
• Encephalitis: Headache, confusion, seizures, FNDs
• Histopathology: Atypical lymphocytes with intranuclear and cytoplasmic inclusions, Owl-eye appearance
Disseminated Mycobacterial Non-Tuberculous Disease: Mycobacterium avium-intracellulare
• Acid-fast bacilli
• Frequently drug resistant
• B symptoms, pancytopenia, hepatosplenomegaly
• Histopathology: Granulomatous inflammation +/- AFB
• Prophylaxis for CD4+ <50: Azithromycin or Clarithromycin
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0094

A 37-year-old male with poorly controlled HIV presents to the emergency department with a fever of 100.9℉ (38.3℃), respiratory rate 40/min, oxygen saturation
of 65% on room air, heart rate of 160/min, and a blood pressure of 140/90mmHg. The patient’s breathing is labored, and he reports progressively worsening
dyspnea over the course of the past week. He states that he ran out of his medication months ago and has not followed up with his primary care physician. The
patient’s cardiorespiratory status is stabilized with eventual need for endotracheal intubation and mechanical ventilator support. Initial laboratory evaluation is
significant for a C-reactive protein of 25 mg/dL (ref: <0.3 mg/dL), leukocyte count of 740/mm3, and CD4+ cell count of 86 cells/mm3. Bronchoalveolar lavage
specimen is shown below (figure 1). The patient is initiated on intravenous trimethoprim-sulfamethoxazole and methylprednisolone.

The patient initially improves and is extubated on day 5, however on hospital day 7 the patient begins to have hemoptysis and later becomes hypotensive with
increasing oxygen requirements. A STAT CT of the chest is shown below (figure 2). Based on the information provided, which of the following is the most likely
etiology of this acute decline in respiratory function?

⚪ A. Mycobacterium avium-intracellulare

⚪ B. Cytomegalovirus

⚪ C. Pneumocystis jirovecii

⚪ D. Aspergillus fumigatus

⚪ E. Toxoplasma gondii
Figure 2

Figure 1 Figure 2
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0094

A 37-year-old male with poorly controlled HIV presents to the emergency department with a fever of 100.9℉ (38.3℃), respiratory rate 40/min, oxygen saturation
of 65% on room air, heart rate of 160/min, and a blood pressure of 140/90mmHg. The patient’s breathing is labored, and he reports progressively worsening
dyspnea over the course of the past week. He states that he ran out of his medication months ago and has not followed up with his primary care physician. The
patient’s cardiorespiratory status is stabilized with eventual need for endotracheal intubation and mechanical ventilator support. Initial laboratory evaluation is
significant for a C-reactive protein of 25 mg/dL (ref: <0.3 mg/dL), leukocyte count of 740/mm3, and CD4+ cell count of 86 cells/mm3. Bronchoalveolar lavage
specimen is shown below (figure 1). The patient is initiated on intravenous trimethoprim-sulfamethoxazole and methylprednisolone.

The patient initially improves and is extubated on day 5, however on hospital day 7 the patient begins to have hemoptysis and later becomes hypotensive with
increasing oxygen requirements. A STAT CT of the chest is shown below (figure 2). Based on the information provided, which of the following is the most likely
etiology of this acute decline in respiratory function?

⚪ A. Mycobacterium avium-intracellulare

⚪ B. Cytomegalovirus

⚪ C. Pneumocystis jirovecii

🔘 D. Aspergillus fumigatus

⚪ E. Toxoplasma gondii
Figure 2

Figure 1 Figure 2
 OUTLINE
1. Antibiotics Overview 7. 50S Ribosomal Inhibitors
A. General Principles A. Macrolides

Microbiology:
B. Molecular Targets B. Lincosamides
C. Bacterial Coverage C. Streptogramins
2. β-Lactams: Penicillins D. Oxazolidinones
A. General Principles E. Amphenicols

Antibiotics B. Classic Penicillins

C. Penicillinase-Resistant Penicillins
D. Aminopenicillins
8. Disruptors of Bacterial DNA
A. Fluoroquinolones
B. Nitroimidazoles
E. Antipseudomonal Penicillins 9. Disruptors of Bacterial Metabolism
3. β-Lactams: Cephalosporins A. Diaminopyrimidines
A. General Principles B. Sulfonamides
B. 1st Generation C. Nitrofurans
C. 2nd Generation 10. Disruptors of the Bacterial Envelope
D. 3rd Generation A. Fosfomycin
E. 4th Generation B. Daptomycin
F. 5th Generation C. Polymyxins
4. β-Lactams: Additional 11. Antimycobacterial Drugs
A. Carbapenems A. Isoniazid
B. Monobactam B. Rifamycins
5. Glycopeptides C. Pyrazinamide
A. Vancomycin D. Ethambutol
B. Bacitracin E. Dapsone
6. 30S Ribosomal Inhibitors F. Clofazimine
A. Aminoglycosides 12. Empiric Antibiotic Coverage
B. Tetracyclines A. Respiratory and ENT Diseases
C. Tetracycline Derivatives B. Meningitis
C. Urinary Tract Infections
D. Gastrointestinal Infections
E. Cellulitis
F. Osteomyelitis and Septic Arthritis
G. Hematogenous Infections
 Microbiology: Antibiotics Bootcamp.com

General Principles:
• MIC = Minimum inhibitory concentration: Lowest concentration that inhibits growth of a specific microorganism
• Sigmoidal dose-response curve
• Bactericidal: Destroys bacteria; Bacteriostatic: Slows or halts bacterial growth
• Concentration-dependent killing (peak drug level); Time-dependent killing (time above MIC)
Molecular Targets:
• Cell wall: ↓ Peptidoglycan crosslinking (β-lactams); ↓ Peptidoglycan synthesis (Vancomycin, fosfomycin)
• Cell membrane: Ion leak (Daptomycin, polymyxins)
• DNA: DNA gyrase inhibitor (Fluoroquinolones); Reactive oxygen species (Metronidazole, nitrofurantoin)
• mRNA: DNA-dependent RNA polymerase inhibitor (Rifampin, rifabutin, rifaximin)
• Protein synthesis: 30S ribosome inhibitors (Aminoglycoside, tetracyclines); 50S ribosome inhibitors (Macrolides, clindamycin, linezolid, chloramphenicol)
• Metabolic: Folic acid synthesis inhibitors (Trimethoprim-Sulfamethoxazole)
Bacterial Coverage:
• Gram positive: Streptococcus, MSSA, Enterococcus
• Gram negative: Haemophilus, Enterobacter, Neisseria, E. coli, Proteus, Klebsiella, Serratia
• Atypicals: Mycoplasma, Ureaplasma, Chlamydia, Listeria, Legionella, Rickettsia, Borrelia
• Drug-resistant Gram positive: MRSA, VRE, VRSA
• Drug-resistant Gram negative: Pseudomonas, Acinetobacter, ESBL
• Anaerobes: Bacteroides, Fusobacteria, Pasteurella, Eikenella
• Mycobacterial: Mycobacterium tuberculosis, Mycobacterium leprosy, Mycobacterium Avium-Intracellulare
 Microbiology: Antibiotics Bootcamp.com

General Principles:
• Bactericidal
• Penicillin binding proteins (PBPs) catalyze peptidoglycan cross-linking
• β-lactam binds PBP catalytic site à Irreversible inactivation of PBP (inhibition of transpeptidase)
• Resistance: Penicillinase à Cleave β-lactam ring
• Resistance: mecA gene à Mutations in PBP (ex. PBP-2A in MRSA) à β-lactam unable to bind to PBP
Classic Penicillins: Medications: Penicillin G, penicillin V
• Gram positive: ★★, Gram negative: ★
• Use: Streptococcal pharyngitis, syphilis, actinomycosis
• S. pyogenes, T. pallidum, Actinomyces israelii
• Adverse effects: Hypersensitivity reactions (Immediate, delayed), hemolytic anemia, tubulointerstitial nephritis
Penicillinase-Resistant Penicillins: Medications: Nafcillin, dicloxacillin, oxacillin, floxacillin, methicillin
• Use: Cellulitis, osteomyelitis, endocarditis (MSSA)
• S. aureus (MSSA)
Aminopenicillins: Medications: Amoxicillin (+ clavulanate), ampicillin (+ sulbactam)
• Gram positive: ★★(★), Gram negative: ★★
• Use: Upper respiratory infections, otitis media, sinusitis, cellulitis, UTI
• H. influenzae, H. pylori, Listeria, E. coli, Enterococci
• Adverse effects: Pseudomembranous colitis, hypersensitivity reactions
Antipseudomonal Penicillins: Medications: Piperacillin (+ tazobactam), ticarcillin (+ clavulanate)
• Gram positive: ★★(★), Gram negative: ★★★
• Use: Hospital-acquired pneumonia, severe soft tissue infections (diabetes ulcers), intra-abdominal infections
• Additional coverage: Pseudomonas, anaerobes
• Adverse effects: Hemolytic anemia, thrombocytopenia
 Microbiology: Antibiotics Bootcamp.com

General Principles:
• Bactericidal
• Penicillin binding proteins (PBPs) catalyze peptidoglycan cross-linking
• β-lactam binds PBP catalytic site à Irreversible inactivation of PBP
• Resistance: Cephalosporinase à Cleave β-lactam ring
• Resistance: Mutations in PBP (ex. PBP-2A in MRSA) à β-lactam unable to bind to PBP
• Adverse effects: Hemolytic anemia, PCN cross-reactivity, kernicterus (ceftriaxone), disulfiram-like reaction
1st Generation: Medications: Cephalexin, cefazolin
• Use: Skin infections, UTI
• Gram positive: ★★★, Gram negative: ★
2nd Generation: Medications: Cefuroxime, cefoxitin, cefotetan, cefaclor
• Use: Intra-abdominal infections, UTI
• Gram positive: ★★, Gram negative: ★★
• Additional coverage: Anaerobes (Cefoxitin, cefotetan)
3rd Generation: Medications: Ceftriaxone, cefotaxime, ceftazidime, cefixime
• Use: Pneumonia, meningitis, meningococcal prophylaxis in pregnancy (Ceftriaxone), late Lyme disease, gonococcal infections
• Gram positive: ★, Gram negative: ★★★
• Additional coverage: Pseudomonas (Ceftazidime)
4th Generation: Medications: Cefepime
• Use: Immunocompromised, hospital-acquired pneumonia, neutropenic fever, complicated UTI
• Gram positive: ★★★, Gram negative: ★★★
• Additional coverage: Pseudomonas (Cefepime)
5th Generation: Medications: Ceftaroline, ceftolozane (+ tazobactam)
• Use: Immunocompromised, hospital-acquired pneumonia, neutropenic fever, complicated STI
• Gram positive: ★★★, Gram negative: ★★★
• Additional coverage: Anaerobes; MRSA, VRSA, Listeria, E. faecalis (Ceftaroline); Pseudomonas (Ceftolozane)
 Microbiology: Antibiotics Bootcamp.com

General Principles:
• Bactericidal
• Penicillin binding proteins (PBPs) catalyze peptidoglycan cross-linking
• β-lactam binds PBP catalytic site à Irreversible inactivation of PBP
• Resistance: Carbapenemase à Cleave β-lactam ring
• Resistance: Mutations in PBP (ex. PBP-2A in MRSA) à β-lactam unable to bind to PBP
Carbapenems: Medications: Meropenem, imipenem (+ cilastatin), ertapenem, doripenem
• Gram positive: ★★★, Gram negative: ★★★
• Additional coverage: Pseudomonas (Exception: Ertapenem), anaerobes, ESBL
• Use: Hospital-acquired infections, intra-abdominal infections, complicated soft tissue infections
• Adverse effects: Seizures (Imipenem > Meropenem), rash, acquired fungal infection
Monobactams: Medications: Aztreonam
• Gram negative: ★★★
• Use: Hospital acquired pneumonia, UTI, intra-abdominal infections (PCN allergy)
 Microbiology: Antibiotics Bootcamp.com

Vancomycin:
• Bactericidal (exception: C. difficile)
• Binds D-ala / D-ala à ↓ Peptidoglycan synthesis
• Resistance: D-ala / D-lac alteration (VRE à vanA gene)
• Use: Multi-drug resistant gram positive, pseudomembranous colitis
• Gram positive ★★★, Additional coverage: MRSA
• Adverse effects: Flushing reaction, DRESS syndrome, nephrotoxic, ototoxic, thrombophlebitis, neutropenia
Bacitracin:
• Prevent transport of peptidoglycan precursor units à ↓ Peptidoglycan synthesis
• Use: Skin infections
• Gram positive: ★★★, Additional coverage: MRSA
 Microbiology: Antibiotics Bootcamp.com

Aminoglycosides:
• Medications: Gentamicin, amikacin, neomycin, tobramycin, streptomycin
• Bactericidal
• Bind to 30S ribosomal subunit à Irreversible inhibition of initiation complex, ↓ translocation, misreading of mRNA à ↓ Protein synthesis
• Synergism: β-lactams
• Gram negative: ★★★, Additional coverage: Pseudomonas, Mycobacterium tuberculosis (Streptomycin)
• Resistance: Inactivation via acetylation, adenylation, or phosphorylation (bacterial transferases); Altered 30S ribosomal subunit structure
• Use: Severe gram negative infections, endocarditis bowel surgery preparation (Neomycin)
• Adverse effects: Nephrotoxicity, ototoxicity, neurotoxicity, teratogenicity
Tetracyclines:
• Medications: Doxycycline, tetracycline, minocycline, demeclocycline
• Bacteriostatic
• Bind to 30S ribosomal subunit à Blockade of aminoacyl-tRNA binding à ↓ Protein synthesis
• Gram positive: ★★, Gram negative: ★★
• Additional coverage: MRSA (Doxycycline), Atypicals (Mycoplasma, Ureaplasma, Rickettsia, Borrelia burgdorferi, Francisella tularensis, Chlamydia, Brucella, Coxiella)
• Resistance: Transport pumps à ↑ Tetracycline efflux or ↓ uptake within cell (Plasmid-encoded)
• Use: Acne and other skin infections, atypical pathogens, early Lyme disease and Lyme prophylaxis
• Adverse effects: Nephrotoxicity (Exception: Doxycycline), hepatotoxicity, photosensitivity, teratogenicity, tooth discoloration, GI discomfort, pill-induced esophagitis
• Avoid with divalent cation preparations (Iron, antacids)
Tetracycline Derivatives:
• Medications: Tigecycline
• Bacteriostatic
• Bind to 30S ribosomal subunit à Blockade of aminoacyl-tRNA binding à ↓ Protein synthesis
• Gram positive: ★★★, Gram negative: ★★, Additional coverage: MRSA, VRE, anaerobes, atypicals
• Use: Complicated intra-abdominal infections, soft tissue infections
• Adverse effects: Overall ↑ risk of death with severe infections, hepatotoxicity, photosensitivity, tooth discoloration, GI discomfort
• Avoid with divalent cation preparations (Iron, antacids)
Microbiology: Antibiotics Bootcamp.com
 Microbiology: Antibiotics Bootcamp.com

Macrolides: Medications: Azithromycin, clarithromycin, erythromycin

• Bacteriostatic
• Bind to 23S ribosomal RNA of 50S ribosomal subunit à ↓ Translocation à ↓ Protein synthesis
• Gram positive: ★★, Gram negative: ★★, Additional coverage: Atypicals
• Resistance: Methylation of 23S rRNA binding site
• Use: Community-acquired pneumonia (lobar/interstitial), bronchitis, COPD exacerbations, MAC prophylaxis/treatment, STI (Chlamydia), PUD (H. pylori)
• Adverse effects: QT prolongation (Erythromycin), GI discomfort (Erythromycin), hypertrophic pyloric stenosis, hepatotoxicity, +/- teratogenic (Erythromycin, clarithromycin)
• Interactions: ↑ Theophylline; CYP3A4 inhibitor (Erythromycin, clarithromycin)
Lincosamides: Medications: Clindamycin
• Bacteriostatic
• Bind to 23S ribosomal RNA of 50S ribosomal subunit à ↓ Translocation à ↓ Protein synthesis
• Gram positive: ★★★, Additional coverage: Anaerobes, MRSA
• Use: Cellulitis, sinusitis, necrotizing fasciitis, aspiration pneumonia, lung abscess
• Adverse effects: Pseudomembranous colitis, GI discomfort, teratogenicity
Streptogramins: Medications: Quinupristin-dalfopristin
• Bacteriostatic if used separately, bactericidal if used together
• Dalfopristin: Binds to 23S ribosomal RNA of 50S ribosomal subunit à ↑ Quinupristin binding, ↓ Peptidyl-transferase à ↓ Protein synthesis
• Quinupristin: Binds to 50S ribosomal subunit à ↓ Elongation
• Use: Cellulitis and soft tissue infections, poorly tolerated overall
• Adverse effects: Thrombophlebitis, pseudomembranous colitis, GI discomfort, myalgias, diarrhea, pruritis
Oxazolidinones: Medications: Linezolid
• Bacteriostatic (Bactericidal vs Streptococci)
• Binds to 23S ribosomal RNA of 50S ribosomal subunit à Inhibition of initiation complex formation à ↓ Protein synthesis
• Gram positive: ★★★, Additional coverage: MRSA, VRE, Mycobacterium tuberculosis
• Use: Skin and soft tissue infections
• Adverse effects: Myelosuppression (thrombocytopenia), sideroblastic anemia, lactic acidosis, peripheral neuropathy, optic neuritis à blindness, serotonin syndrome
• Resistance: Point mutations of 23s ribosomal RNA
Amphenicols: Medications: Chloramphenicol
• Binds to 50S ribosomal subunit à ↓ Peptidyl-transferase à ↓ Protein synthesis
• Use: Meningitis, RMSF, poorly tolerated overall
• Adverse effects: Myelosuppression, aplastic anemia, sideroblastic anemia, “Gray baby syndrome”, teratogenicity
• Resistance: Inactivation via acetyltransferase (plasmid-encoded)
 Microbiology: Antibiotics Bootcamp.com

Fluoroquinolones: Medications: Nalidixic acid, Norfloxacin, Ciprofloxacin, Ofloxacin, Enoxacin, Levofloxacin, Moxifloxacin, Gemifloxacin
• Bactericidal
• Inhibition of topoisomerase II (DNA gyrase) and IV à Double-stranded DNA breaks à ↓ DNA replication and transcription
• Resistance: Topoisomerase II and IV mutations (chromosome-encoded); ↑ Fluoroquinolone efflux (plasmid-encoded)
• Ciprofloxacin: Gram positive: ★, Gram negative: ★★★; Additional coverage: Pseudomonas; Use: UTI, intra-abdominal infections, otitis externa, anthrax
• Levofloxacin: Gram positive: ★★, Gram negative: ★★; Additional coverage: Mycobacterium tuberculosis, Pseudomonas, atypicals; Use: CAP, HAP, UTI
• Moxifloxacin: Gram positive: ★★, Gram negative: ★★; Additional coverage: Mycobacterium tuberculosis, atypicals, anaerobes; Use: CAP
• Additional coverage: Mycobacterium tuberculosis, atypicals
• Adverse effects: QT prolongation, arthropathy, tendon and cartilage damage, superinfections, GI discomfort, pseudomembranous colitis, nephrotoxicity, teratogenicity
• Avoid with divalent cation preparations (Iron, antacids)
• Avoid in pregnancy, breastfeeding, and children <18 years old
• CYP1A2 inhibitor (Ciprofloxacin)
Nitroimidazoles: Medications: Metronidazole
• Bactericidal
• Selective uptake from anaerobes à Reduced in ETC à Free radical production à DNA strand breaks à ↓ DNA replication and transcription
• Primary coverage: Anaerobes
• Use: Pseudomembranous colitis, intra-abdominal infection, giardiasis, trichomoniasis, bacterial vaginosis, peptic ulcer disease (H. pylori)
• Adverse effects: Metallic taste, peripheral neuropathy
 Microbiology: Antibiotics Bootcamp.com

Diaminopyrimidines: Medications: Trimethoprim, pyrimethamine

• Bacteriostatic if used alone, bactericidal if used with sulfonamide
• Inhibition of dihydrofolate reductase à ↓ Bacterial DNA synthesis
• Adverse effects: Megaloblastic anemia, hyperkalemia
Sulfonamides: Medications: Sulfamethoxazole, sulfadiazine, sulfisoxazole
• Bacteriostatic if used alone, bactericidal if used with diaminopyrimidine
• Inhibition of dihydropteroate synthase à ↓ Bacterial DNA synthesis
• Resistance: Mutations in dihydropteroate synthase
• TMP-SMX: Gram positive: ★★, Gram negative: ★★, Additional coverage: Pneumocystis, Toxoplasma, Nocardia, Listeria, Isospora
• TMP-SMX: Use: Pneumocystis pneumonia (prophylaxis and treatment), Toxoplasmosis (prophylaxis), Nocardiosis, Listeriosis, skin infections, AOM, UTI
• Adverse effects: Nephrotoxicity, pancytopenia, hemolytic anemia (G6PD deficiency), photosensitivity, hypersensitivity reactions (sulfa), SJS
• CYP2C9 inhibitor
• Contraindications to TMP-SMX: Pregnancy, early infancy
Nitrofurans: Medications: Nitrofurantoin
• Bactericidal
• Reactive metabolites à Bind bacterial ribosomes à ↓ Metabolism, DNA and RNA synthesis à ↓ Protein synthesis
• Gram positive: ★★★, Gram negative: ★★, Additional coverage: VRE, ESBL
• Use: UTI (pregnancy)
• Adverse effects: Hypersensitivity pneumonitis, chronic pulmonary fibrosis, hemolytic anemia (G6PD deficiency)
 Microbiology: Antibiotics Bootcamp.com

Fosfomycin:
• Bactericidal
• Binds to and irreversibly inhibits enolpyruvate transferase (MurA) à ↓ N-acetylmuramic acid à ↓ Cell wall synthesis
• Resistance: MurA mutations
• Use: UTI
• Gram positive: ★★★, Gram negative: ★★★
• Additional coverage: MRSA, VRE, Pseudomonas, some ESBL
• Adverse effects: Diarrhea
Daptomycin:
• Bactericidal
• ↑ K + channel into cell membrane à Rapid membrane depolarization à Loss of membrane potential
• Resistance: Repulsion of charge
• Use: Skin infections, endocarditis
• Gram positive: ★★★
• Additional coverage: MRSA, VRE
• Adverse effects: Myopathy, rhabdomyolysis
Polymyxins:
• Medications: Polymyxin B, polymyxin E (Colistin)
• Bactericidal
• Cationic detergent à Binds to phospholipids in cell membrane à ↑ Membrane permeability à Leakage of cell contents
• Use: Immunocompromised, severe hospital acquired multi-drug resistant infections
• Gram negative: ★★
• Additional coverage: Pseudomonas
• Adverse effects: Nephrotoxicity, neurotoxicity, respiratory insufficiency, hypersensitivity reactions
 Microbiology: Antibiotics Bootcamp.com

Isoniazid:
• Bactericidal
• ↓ Mycolic acid synthesis à ↓ Cell wall synthesis
• Prodrug à Bacterial katG gene required to activate
• Resistance: KatG gene mutations (↓ Bacterial catalase-peroxidase activity)
• Use: Tuberculosis (RIPE)
• Adverse effects: Hepatotoxicity, drug-induced lupus, seizures, neurotoxicity (Vitamin B6 deficiency)
• Variable acetylation depending on patient genetics
• CYP1A2, CYP2A6, CYP2C19, and CYP3A4 inhibitor
Rifamycins: Medications: Rifampin, rifabutin, rifapentine, rifaximin
• Bactericidal
• Inhibition of DNA-dependent RNA polymerase à ↓ Bacterial mRNA à ↓ Protein synthesis
• Resistance: Mutations in genes encoding DNA-dependent RNA polymerase
• Use: Tuberculosis (RIPE), leprosy, meningococcal prophylaxis, hepatic encephalopathy (Rifaximin)
• Adverse effects: Orange-red discoloration to body fluids, hepatotoxicity, pancytopenia
• CYP3A4 and CYP2C9 inducer (Rifampin > Rifabutin)
Pyrazinamide:
• Bactericidal
• Use: Tuberculosis (RIPE)
• Adverse effects: Hyperuricemia, hepatotoxicity
Ethambutol:
• Bacteriostatic
• Inhibition of arabinosyltransferase à ↓ Arabinogalactan à ↓ Cell wall synthesis
• Use: Tuberculosis (RIPE), MAC treatment
• Adverse effects: Optic neuropathy, red-green color blindness
Dapsone:
• Bacteriostatic
• Competitive antagonist of PABA à ↓ Bacterial DNA synthesis
• Use: Leprosy, Pneumocystis pneumonia, toxoplasmosis, malaria, dermatitis herpetiformis
• Adverse effects: Methemoglobinemia, hemolytic anemia (G6PD deficiency), agranulocytosis, peripheral neuropathy, DRESS syndrome
Clofazimine:
• Inhibition of DNA synthesis
• Use: Lepromatous leprosy
 Microbiology: Antibiotics Bootcamp.com

Respiratory and ENT Diseases:

• Community-acquired pneumonia: Ceftriaxone + Azithromycin OR Levofloxacin
• Healthcare-associated pneumonia: Vancomycin + Cefepime OR Ceftazidime OR Piperacillin-tazobactam
• Acute sinusitis: Amoxicillin +/- Clavulanate
• Pharyngitis: Penicillin
Meningitis:
• General: Ceftriaxone + Vancomycin
• Neonatal: Cefotaxime + Ampicillin + Gentamicin
• Elderly: Ceftriaxone + Vancomycin + Ampicillin
Urinary Tract Infection:
• Acute cystitis: TMP-SMX OR Nitrofurantoin OR Fosfomycin
• Pyelonephritis: Ciprofloxacin OR Ceftriaxone
• Complicated UTI: Vancomycin + Piperacillin-tazobactam OR Cefepime +/- Aminoglycoside (Various regimens)
Gastrointestinal Infections:
• Broad spectrum monotherapy: Carbapenem or piperacillin-tazobactam
• Dual therapy: Metronidazole + Ceftriaxone OR Ciprofloxacin
• Diarrhea, suspect C. difficile: Fidaxomicin OR Vancomycin (oral)
Cellulitis:
• Surgical prophylaxis: Cefazolin
• Mild: Cephalexin, nafcillin
• Moderate: TMP-SMX, Penicillin, Ceftriaxone, Clindamycin, Doxycycline (various alternatives)
• Severe: Vancomycin +/- Piperacillin-tazobactam OR Meropenem
Osteomyelitis, Septic Arthritis:
• General: Vancomycin
• Gonococcal: Ceftriaxone
• Additional co-morbidities (Severe diabetes, PVD): Vancomycin + Piperacillin-tazobactam OR Ceftriaxone (Vertebral)
Hematogenous Infections:
• Catheter: Vancomycin +/- Piperacillin-tazobactam OR Meropenem
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0095

A researcher is attempting to identify the efficacy of an unknown antibiotic known as VX-18 on Streptococcus pneumoniae isolates. The minimum inhibitory
concentration (MIC) was detected in various strains when exposed to equivalent concentrations of VX-18. Strains SP1, SP2, and SP3 contain a well-known
gene, erm(B), which encodes for a ribosomal dimethyltransferase that can dimethylate the nucleotide A2058 in 23S rRNA. To determine the contribution of
erm(B), strain SP2 includes an inserted gene, aad(9), into the erm(B) gene and strain SP3 includes a 136 base pair deletion in the leader sequence of the
erm(B) gene. Strain SP4 contains an inserted gene, pbp1a, which is known to confer high levels of β-lactam resistance in Streptococcus pneumoniae. Finally,
strain SP5 has hybrid characteristics of SP2 and SP4 as shown below.

Based on the results of this study, which of the following antibiotics would likely be most effective at eradicating strain SP5?

⚪ A. Azithromycin Strain Erm(B) Relevant Characteristics and Mutations MIC

(µg/mL)
⚪ B. Penicillin
SP0 - N/A <0.03
⚪ C. Ceftazidime

⚪ D. Aztreonam SP1 + N/A 2.03

⚪ E. Trimethoprim-Sulfamethoxazole SP2 + Aad(9) insertion into erm(B) <0.03

Figure 2
SP3 + 136-bp upstream deletion to the erm(B) gene 12.24

SP4 - Addition of the pbp1a gene <0.03

SP5 + Aad(9) insertion into erm(B) <0.03

Addition of the pbp1a gene
Figure 2
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪✪ Bootcamp.com
Question ID: 0095

A researcher is attempting to identify the efficacy of an unknown antibiotic known as VX-18 on Streptococcus pneumoniae isolates. The minimum inhibitory
concentration (MIC) was detected in various strains when exposed to equivalent concentrations of VX-18. Strains SP1, SP2, and SP3 contain a well-known
gene, erm(B), which encodes for a ribosomal dimethyltransferase that can dimethylate the nucleotide A2058 in 23S rRNA. To determine the contribution of
erm(B), strain SP2 includes an inserted gene, aad(9), into the erm(B) gene and strain SP3 includes a 136 base pair deletion in the leader sequence of the
erm(B) gene. Strain SP4 contains an inserted gene, pbp1a, which is known to confer high levels of β-lactam resistance in Streptococcus pneumoniae. Finally,
strain SP5 has hybrid characteristics of SP2 and SP4 as shown below.

Based on the results of this study, which of the following antibiotics would likely be most effective at eradicating strain SP5?

🔘 A. Azithromycin Strain Erm(B) Relevant Characteristics and Mutations MIC

(µg/mL)
⚪ B. Penicillin
SP0 - N/A <0.03
⚪ C. Ceftazidime

⚪ D. Aztreonam SP1 + N/A 2.03

⚪ E. Trimethoprim-Sulfamethoxazole SP2 + Aad(9) insertion into erm(B) <0.03

Figure 2
SP3 + 136-bp upstream deletion to the erm(B) gene 12.24

SP4 - Addition of the pbp1a gene <0.03

SP5 + Aad(9) insertion into erm(B) <0.03

Addition of the pbp1a gene
Figure 2
 OUTLINE
1. Azoles
A. General Principles

Microbiology:
B. Triazoles
C. Imidazoles
2. Allylamines, Echinocandins, and Polyenes
A. Allylamines

Antifungals B. Echinocandins
C. Polyenes
3. Additional Antifungals
A. Benzofurans
B. Antimetabolites
C. Pyridone Derivatives
D. Selenium Sulfide
4. Common Fungal Infection Management
A. Candidiasis
B. Cryptococcosis
C. Invasive Aspergillosis
D. Other Opportunistic Dimorphic Mycosis
E. Sporotrichosis
F. Mucormycosis
G. Dermatophytosis
H. Tinea Versicolor
 Microbiology: Antifungals Bootcamp.com

General Principles:
• Mechanism: Inhibition of fungal 14-𝜶-demethylase (CYP450) à Inhibition of ergosterol synthesis
• Adverse Effects: Hepatotoxicity, gynecomastia (Ketoconazole), QT prolongation, adrenal insufficiency (Ketoconazole), visual impairment (Voriconazole), teratogenic
• Contraindications: Arrhythmia, PPI use, pregnancy (1 st trimester)
• CYP2C9, CYP2C19, CYP3A4 inhibition
Triazoles:
• Fluconazole: Cryptococcal meningitis, candidiasis (all forms, including cystitis)
• Itraconazole: Sporotrichosis, ABPA, histoplasmosis, blastomycosis, coccidioidomycosis, paracoccidioidomycosis, dermatophytosis, pityriasis versicolor
• Voriconazole: Invasive aspergillosis
• Posaconazole: Mucormycosis, invasive aspergillosis (prophylaxis), candidiasis (prophylaxis)
• Isavuconazole: Invasive aspergillosis, Mucormycosis
Imidazoles:
• Ketoconazole: Pityriasis versicolor
• Clotrimazole, Miconazole: Candidiasis (oropharyngeal, vaginal), dermatophytosis
 Microbiology: Antifungals Bootcamp.com

Allylamines: Terbinafine
• Mechanism: Inhibition of fungal squalene epoxidase à ↑ Squalene à ↓ Ergosterol
• Use: Onychomycosis and other dermatophytosis
• Adverse Effects: Hepatotoxicity, GI discomfort, taste disturbances
Echinocandins: Caspofungin, Micafungin, Anidulafungin
• Mechanism: Inhibition of β-1,3-D-glucan synthesis à ↓ Cell wall synthesis
• Use: Invasive candidiasis, invasive aspergillosis
• Adverse Effects: Hepatotoxicity, flushing, GI discomfort
Polyenes: Amphotericin B, Nystatin
• Mechanism: Binds ergosterol in membrane à Forms pores in membrane
• Amphotericin B Use: Cryptococcal meningitis, invasive aspergillosis, invasive dimorphic mycosis, invasive candidiasis, mucormycosis
• Nystatin Use: Candidiasis (oropharyngeal, intertrigo, vaginal)
• Adverse Effects: Nephrotoxicity, phlebitis, anemia, arrhythmias, teratogenic
 Microbiology: Antifungals Bootcamp.com

Benzofurans: Griseofulvin
• Mechanism: Binds to β-tubulin à ↓ Microtubule function à ↓ Fungal mitosis
• Use: Dermatophytosis
• Adverse Effects: Hepatotoxicity, teratogenic, carcinogenic, disulfiram-like reaction
• CYP2C9 and CYP3A4 inducer
Antimetabolites: Flucytosine
• Mechanism: Converted to 5-fluorouracil via fungal cytosine deaminase à ↓ DNA replication and transcription
• Use: Cryptococcal meningitis
• Adverse Effects: Hepatotoxicity, nephrotoxicity, teratogenic, pancytopenia, GI discomfort
Pyridone Derivative: Ciclopirox
• Use: Pityriasis versicolor, dermatophytosis, seborrheic dermatitis
• Adverse Effects: Arrhythmias, facial edema, pruritis
Selenium Sulfide: Use: Pityriasis versicolor, seborrheic dermatitis
 Microbiology: Antifungals Bootcamp.com

Candidiasis:
• Intertriginous: Nystatin
• Oropharyngeal: Clotrimazole, miconazole, nystatin
• Esophageal: Fluconazole, itraconazole
• Vulvovaginal: Clotrimazole, miconazole, fluconazole
• Cystitis: Fluconazole
• Systemic: Echinocandin (immunosuppressed), amphotericin B
Cryptococcosis:
• Amphotericin B + Flucytosine (Induction) à Fluconazole (Maintenance)
Invasive Aspergillosis:
• Voriconazole +/- Caspofungin
Other Dimorphic Mycosis: Histoplasmosis, Blastomycosis, Coccidioidomycosis, Paracoccidioides, Sporotrichosis
• Itraconazole, fluconazole (Mild)
• Amphotericin B (Severe)
Mucormycosis:
• Emergent surgical debridement + Amphotericin B, Isavuconazole
Dermatophytosis:
• Terbinafine (topical), clotrimazole, miconazole, ciclopirox (Not for follicular involvement)
• Terbinafine (oral), fluconazole, itraconazole, griseofulvin (Extensive/refractory disease)
Pityriasis Versicolor:
• Topical selenium sulfide, terbinafine, ciclopirox, miconazole, ketoconazole (Mild)
• Fluconazole, itraconazole (Severe)
Pneumocystis Pneumonia:
• Trimethoprim-Sulfamethoxazole, Dapsone, Pentamidine
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0096

A 58-year-old male who was diagnosed with HIV approximately 6 months ago presented to the emergency department directly from his infectious disease
specialist’s office. The patient had demonstrated acutely worsening confusion, photophobia, and generalized lethargy during his outpatient appointment. His
most recent CD4+ count was <30/mm3. He had been prescribed anti-retroviral therapy around the time of his diagnosis, although he had reported poor
medication compliance overall since then. A lumbar puncture revealed an elevated opening pressure with a lymphocytic-predominant pleocytosis, elevated
protein, and low glucose. Cryptococcal antigen titer was positive in the CSF. An MRI of the brain showed leptomeningeal enhancement with diffuse
microabscesses. The patient’s treatment regimen is initiated with 2 weeks of induction therapy.

Which of the following drug combinations have the most similar mechanisms of action to the two agents likely used as induction therapy in this patient?

⚪ A. Nystatin and Griseofulvin

⚪ B. Trimethoprim and Griseofulvin

⚪ C. Nystatin and Capecitabine

⚪ D. Fluconazole and Fludarabine

Figure 2
⚪ E. Fluconazole and Penicillin

Figure 2
≣ Item 1 of 1 Test Your Knowledge
Difficulty Rating: ✪✪ Bootcamp.com
Question ID: 0096

A 58-year-old male who was diagnosed with HIV approximately 6 months ago presented to the emergency department directly from his infectious disease
specialist’s office. The patient had demonstrated acutely worsening confusion, photophobia, and generalized lethargy during his outpatient appointment. His
most recent CD4+ count was <30/mm3. He had been prescribed anti-retroviral therapy around the time of his diagnosis, although he had reported poor
medication compliance overall since then. A lumbar puncture revealed an elevated opening pressure with a lymphocytic-predominant pleocytosis, elevated
protein, and low glucose. Cryptococcal antigen titer was positive in the CSF. An MRI of the brain showed leptomeningeal enhancement with diffuse
microabscesses. The patient’s treatment regimen is initiated with 2 weeks of induction therapy.

Which of the following drug combinations have the most similar mechanisms of action to the two agents likely used as induction therapy in this patient?

⚪ A. Nystatin and Griseofulvin

⚪ B. Trimethoprim and Griseofulvin

🔘 C. Nystatin and Capecitabine

⚪ D. Fluconazole and Fludarabine

Figure 2
⚪ E. Fluconazole and Penicillin

Figure 2
 Microbiology: Spirochetes Bootcamp.com

• Darkfield Microscopy-CDC
• https://phil.cdc.gov/details.aspx?pid=10179
• Credit: W.F. Schwartz, CDC
• Chancres on the penile shaft due to a primary syphilitic infection caused by Treponema pallidum 6803 lores.jpg
• https://en.wikipedia.org/wiki/File:Chancres_on_the_penile_shaft_due_to_a_primary_syphilitic_infection_caused_by_Treponema_pallidum_6803
_lores.jpg
• Credit: M. Rein, VD
• Hutchinson’s Teeth from Syphilis
• https://phil.cdc.gov/Details.aspx?pid=2385
• Credit: CDC/ Susan Lindsley, 1971
• The face of a newborn infant displaying snuffles indicative of congenital syphilis
• https://commons.wikimedia.org/wiki/File:The_face_of_a_newborn_infant_with_Congenital_Syphilis.tif
• CDC/ Dr. Norman Cole, Public domain, via Wikimedia Commons
• Typical presentation of secondary syphilis with a rash on the palms of the hands
• https://commons.wikimedia.org/wiki/File:Secondary_Syphilis_on_palms_CDC_6809_lores.rsh.jpg
• CDC/ Robert Sumpter, Public domain, via Wikimedia Commons
• Saber Shin Deformity
• https://phil.cdc.gov/details.aspx?pid=3823
• CDC/ Dr. Peter Perine 1979
• Figure 1 (A), in: Granulome centro-facial révélant une syphilis tertiaire
• https://panafrican-med-journal.com/content/article/15/82/full/#.WZBaYlVJbIU
• Credit: Chakir K, Benchikhi
• Microscope
• Created with Biorender.com
• Diagnostic algorithm
• Created with Biorender.com
 Microbiology: Spirochetes Bootcamp.com

• Erythematous rash in the pattern of a “bull’s-eye” from Lyme disease

• https://commons.wikimedia.org/wiki/File:Bullseye_Lyme_Disease_Rash.jpg
• Hannah Garrison, CC BY-SA 2.5 <https://creativecommons.org/licenses/by-sa/2.5>, via Wikimedia Commons
• Figure 2: A Novel and Simple Method for Laboratory Diagnosis of Relapsing Fever Borreliosis
• https://openmicrobiologyjournal.com/VOLUME/2/PAGE/10/FULLTEXT/
• Christer Larsson, Sven Bergström, CC BY-SA 2.5
• White-footed Mouse (Peromyscus leucopus), Cantley, Quebec
• https://commons.wikimedia.org/wiki/File:White-footed_Mouse,_Cantley,_Quebec.jpg
• D. Gordon E. Robertson, CC BY-SA 3.0 <https://creativecommons.org/licenses/by-sa/3.0>, via Wikimedia Commons
• Adult deer tick.jpg
• https://commons.wikimedia.org/wiki/File:Adult_deer_tick.jpg
• Photo by Scott Bauer., Public domain, via Wikimedia Commons
• Microscope
• Created with Biorender.com
• Diagnostic algorithm
• Created with Biorender.com
 Microbiology: Spirochetes Bootcamp.com

• Borrelia Recurrentis CDC.png

• https://commons.wikimedia.org/wiki/File:Borrelia_recurrentis_CDC.png
• CDC, Public domain, via Wikimedia Commons
• Body lice.jpg
• https://commons.wikimedia.org/wiki/File:Body_lice.jpg
• Janice Harney Carr, Center for Disease Control, Public domain, via Wikimedia Commons
• Microscope
• Created with Biorender.com
• Diagnostic algorithm
• Created with Biorender.com
 Microbiology: Spirochetes Bootcamp.com

• Leptospira interrogans strain RGA 01.png

• https://commons.wikimedia.org/wiki/File:Leptospira_interrogans_strain_RGA_01.png
• Obtained from the CDC Public Health Image Library.Image credit: CDC/NCID/HIP/Janice Carr (PHIL #1220)., Public domain, via Wikimedia
Commons
• Conjunctival suffusion of the eyes due to leptospirosis.jpg
• https://en.wikipedia.org/wiki/Conjunctival_suffusion#/media/File:Conjunctival_suffusion_of_the_eyes_due_to_leptospirosis.jpg
• CC BY 4.0, 24 August 2013, Daniel Ostermayer: https://wikem.org/wiki/File:Conjunctivalsuffusion.jpg#filelinks
• Microscope
• Created with Biorender.com
• Diagnostic algorithm
• Created with Biorender.com
 Microbiology: Systemic Protozoa Bootcamp.com

References
• PMID20029144 02 congenital toxoplasmosis - headlight in fog.png:
• https://commons.wikimedia.org/wiki/File:PMID20029144_02_congenital_toxoplasmosis_-_headlight_in_fog.png
• S Sudharshan, Sudha K Ganesh, Jyotirmay Biswas, CC BY 2.0, via Wikimedia Commons
• Tachyzoites of Toxoplasma gondii
• https://www.pathologyoutlines.com/topic/lymphnodestoxoplasma.html
• Credit: Bobbi Pritt M.D.
• Toxoplasma gondii life cycle:
• Created with Biorender.com
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Naegleria fowleri Pathophysiology:
• Created with Biorender.com
• Naegleria trophA.JPG:
• https://commons.wikimedia.org/wiki/File:Naegleria_trophA.JPG#filelinks
• Salvadorjo~commonswiki, de.wikipedia work of US government, PD, via Wikimedia Commons
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Trypanosoma brucei gambiense - trypomastigote.jpg:
• https://commons.wikimedia.org/wiki/File:Trypanosoma_brucei_gambiense_-_trypomastigote.jpg
• Stefan Walkowski, CC BY-SA 4.0, via Wikimedia Commons
• Trypanosoma brucei Pathophysiology:
• Created with Biorender.com
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Achalasia Barium Swallow:
• Case courtesy of Jan Frank Gerstenmaier, Radiopaedia.org, rID: 24937
• Chagoma.jpg:
• https://commons.wikimedia.org/wiki/File:Chagoma.jpg
• CDC/Dr. Mae Melvin, Public domain, via Wikimedia Commons
• Dilated Cardiomyopathy CXR:
• Case courtesy of Hani Makky Al Salam, Radiopaedia.org, rID: 10283
• Toxic Megacolon XR:
• Case courtesy of Craig Hacking, Radiopaedia.org, rID: 79194
• Trypanosoma cruzi Pathogenesis:
• Created with BioRender.com
• T. cruzi trypomastigotes in peripheral blood smear.jpg:
• https://commons.wikimedia.org/wiki/File:T._cruzi_trypomastigotes_in_peripheral_blood_smear.jpg
• CDC, Public domain, via Wikimedia Commons
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Microphotographs of Plasmodium vivax in Giemsa-stained thin blood films.jpg:
• https://commons.wikimedia.org/wiki/File:Microphotographs_of_Plasmodium_vivax_in_Giemsa-stained_thin_blood_films.jpg
• Chavatte JM, Tan SB, Snounou G, Lin RT, CC BY 4.0, via Wikimedia Commons
• Plasmodium falciparum 01.png:
• https://commons.wikimedia.org/wiki/File:Plasmodium_falciparum_01.png
• CDC/Dr. Mae MelvinTranswiki approved by: w:en:User:Dmcdevit, Public domain, via Wikimedia Commons
• Plasmodium Life Cycle and Pathophysiology:
• Created with Biorender.com
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Babesia microti CDC.jpg:
• https://commons.wikimedia.org/wiki/File:Babesia_microti_CDC.jpg
• U.S. Centers for Disease Control (photographer not credited), Public domain, via Wikimedia Commons
• Babesiosis:
• Created with Biorender.com
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Leishmania Life Cycle and Pathogenesis:
• Created with Biorender.com
• Leishmania spp. - amastigota 01.jpg:
• https://commons.wikimedia.org/wiki/File:Leishmania_spp._-_amastigota_01.jpg
• Stefan Walkowski, CC BY-SA 4.0 <https://creativecommons.org/licenses/by-sa/4.0>, via Wikimedia Commons
• Leishmaniasis ulcer.jpg:
• https://commons.wikimedia.org/wiki/File:Leishmaniasis_ulcer.jpg
• Layne Harris, Public domain, via Wikimedia Commons
 Microbiology: Systemic Protozoa Bootcamp.com

References
• Trichomonas Giemsa DPDx.JPG:
• https://commons.wikimedia.org/wiki/File:Trichomonas_Giemsa_DPDx.JPG
• US Centers for Disease Control and Prevention, Public domain, via Wikimedia Commons
• Trichomonas Pathogenesis and Diagnostics:
• Created with BioRender.com
 Microbiology: Nematodes Bootcamp.com

References
• Enterobius vermicularis (01).tif:
• https://commons.wikimedia.org/wiki/File:Enterobius_vermicularis_(01).tif
• Courtesy: Public Health Image Library, Public domain, via Wikimedia Commons
• Enterobius Pathophysiology:
• Created with BioRender.com
• Tape-dispenser.jpg:
• https://commons.wikimedia.org/wiki/File:Tape-dispenser.jpg
• Evan-amos, Public domain, via Wikimedia Commons
 Microbiology: Nematodes Bootcamp.com

References
• Ascaris suum egg.jpg:
• https://commons.wikimedia.org/wiki/File:Ascaris_suum_egg.jpg
• Strongyle, CC BY-SA 3.0, via Wikimedia Commons
• Ascaris Pathophysiology
• Created with BioRender.com
• Tape-dispenser.jpg:
• https://commons.wikimedia.org/wiki/File:Tape-dispenser.jpg
• Evan-amos, Public domain, via Wikimedia Commons
 Microbiology: Nematodes Bootcamp.com

References
• Strongyloides Pathophysiology
• Created with BioRender.com
• Strongyloides stercoralis larva.jpg:
• https://commons.wikimedia.org/wiki/File:Strongyloides_stercoralis_larva.jpg#file
• Salvadorjo~commonswiki, US Federal Government public domain image. Source: CDC
• Strongyloides - high mag.jpg:
• https://commons.wikimedia.org/wiki/File:Strongyloides_-_high_mag.jpg
• Nephron, CC BY-SA 3.0, via Wikimedia Commons
 Microbiology: Nematodes Bootcamp.com

References
• Hookworm egg.png:
• https://commons.wikimedia.org/wiki/File:Hookworm_egg.png
• Division of Parasitic Diseases and Malaria (DPDM) of the Centers for Disease Control and Prevention, Public domain, via Wikimedia
Commons
• Hookworm Pathophysiology:
• Created with BioRender.com
 Microbiology: Nematodes Bootcamp.com

References
• Charcot-Leyden crystals, HE 2.jpg:
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 Microbiology: Nematodes Bootcamp.com

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 Microbiology: Nematodes Bootcamp.com

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 Microbiology: Nematodes Bootcamp.com

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 Microbiology: Nematodes Bootcamp.com

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 Virology: Strategies Bootcamp.com

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Brain
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Nerves
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 Virology: Structure, Replication and Host Defense Bootcamp.com

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DNA
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Reverse transcriptase
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 Virology: Structure, Replication and Host Defense Bootcamp.com

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 Virology: Structure, Replication and Host Defense Bootcamp.com

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Antibody
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 Microbiology: Infectious Neuropathology Bootcamp.com

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 Microbiology: Opportunistic Infections Bootcamp.com

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• Antifungal therapy II
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