MICROBIOLOGY AND PARASITOLOGY

JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

1. Definition of Microbiology

Microbiology is the scientific study of microorganisms, which are organisms too small to be seen
with the naked eye. This includes bacteria, viruses, fungi, protozoa, and algae. Microbiology plays
a key role in understanding disease processes, environmental functions, and industrial applications.

2.Subdivisions of Microbiology

Bacteriology: Study of bacteria.

Virology: Study of viruses.
Mycology: Study of fungi.
Parasitology: Study of parasites, including protozoa and helminths.
Immunology: Study of the immune system and how it defends the body against microorganisms.
Microbial genetics: Study of how microbes inherit traits.
Environmental microbiology: Study of the roles microorganisms play in ecosystems.

3. Personalities Paving the Study of Microbiology

Anton van Leeuwenhoek: First to observe and describe microorganisms (referred to as

"animalcules") using a microscope.
Louis Pasteur: Disproved the theory of spontaneous generation, developed pasteurization, and
contributed to the Germ Theory of Disease.
Robert Koch: Formulated Koch’s postulates, linking specific organisms to specific diseases.
Edward Jenner: Developed the smallpox vaccine, the first successful vaccine.
Joseph Lister: Introduced antiseptic surgery, reducing surgical infections.

4. Spontaneous Generation Theory vs. Theory of Abiogenesis

Spontaneous Generation: The idea that life could arise from non-living matter. For example,
maggots appearing from decaying meat. Disproved by experiments from Louis Pasteur.
Abiogenesis: The theory that life can originate from simple organic compounds under certain
conditions. This is different from spontaneous generation as it deals with the early origin of life on
Earth, not regular generation from non-living materials.

5. Germ Theory of Disease

Proposed by Louis Pasteur and Robert Koch, it states that microorganisms are the cause of many
diseases. It replaced earlier beliefs that diseases were caused by "miasma" or bad air.

6. Koch’s Postulates

A series of criteria to establish a causative relationship between a microbe and a disease:

The microorganism must be found in all organisms suffering from the disease but not in healthy
organisms.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

The microorganism must be isolated from a diseased organism and grown in pure culture.
The cultured microorganism should cause disease when introduced into a healthy organism.
The microorganism must be reisolated from the newly infected host and identified as being
identical to the original specific causative agent.

7. Eukaryotes vs. Prokaryotes

Eukaryotes:
Have a true nucleus enclosed by a nuclear membrane.
Membrane-bound organelles (e.g., mitochondria, ER).
Larger and more complex cells (e.g., fungi, plants, animals).
Prokaryotes:
No true nucleus; DNA is in the nucleoid region.
No membrane-bound organelles.
Smaller, simpler cells (e.g., bacteria).

8. Morphologic Classification of Bacteria

Cocci: Spherical-shaped bacteria (e.g., Staphylococcus, Streptococcus).

Bacilli: Rod-shaped bacteria (e.g., Escherichia coli).
Spirilla: Spiral-shaped bacteria (e.g., Spirillum).
Vibrios: Comma-shaped bacteria (e.g., Vibrio cholerae).
Pleomorphic: Bacteria with variable shapes (e.g., Mycoplasma).

9. Anatomy of the Bacterial Cell

Cell wall: Provides structure and shape, protects against osmotic pressure (peptidoglycan in most
bacteria).
Cell membrane: Phospholipid bilayer responsible for controlling the movement of substances in
and out.
Cytoplasm: Contains ribosomes, plasmids, and the nucleoid (region containing DNA).
Flagella: Responsible for motility in some bacteria.
Pili/Fimbriae: Hair-like structures for attachment and conjugation.

10. Special Structures of the Bacterial Cell

Capsule: Protects bacteria from phagocytosis and aids in attachment to surfaces.

Endospores: Dormant, resistant structures formed by some bacteria (e.g., Bacillus and
Clostridium) to survive harsh conditions.
Plasmids: Extra-chromosomal DNA that can carry antibiotic resistance genes.

11. Phases of Bacterial Growth

Lag phase: Bacteria adapt to the environment, no growth.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

Log (exponential) phase: Rapid cell division and growth.

Stationary phase: Growth rate slows as nutrients deplete and waste accumulates.
Death phase: Bacteria die as resources are exhausted and toxic byproducts accumulate.

12. Nutritional Requirements for Bacterial Growth

Carbon source: Autotrophs (CO₂), Heterotrophs (organic compounds).

Nitrogen source: For amino acids, nucleic acids.
Vitamins and minerals: Essential for enzymatic activity.
Water: Necessary for metabolic reactions.

13. Environmental Requirements for Bacterial Growth

Temperature: Psychrophiles (cold), Mesophiles (moderate), Thermophiles (hot).

pH: Most bacteria grow best at neutral pH (6.5-7.5).
Oxygen:
Obligate aerobes: Require oxygen.
Obligate anaerobes: Cannot tolerate oxygen.
Facultative anaerobes: Can grow with or without oxygen.
Microaerophiles: Require reduced oxygen levels.

14. Changes Seen Indicating Bacterial Growth

Turbidity: Cloudiness in a broth culture indicates bacterial multiplication.

Colony formation: Visible clusters of bacteria on solid media.
Color change in indicators: Some growth media contain pH indicators that change color in
response to bacterial metabolic products.

15. Methods of Studying Organisms

Microscopy: Direct observation of organisms.

Culture: Growing organisms on artificial media.
Biochemical tests: Identifying organisms by their metabolic properties.
Molecular methods: DNA, RNA, and protein analysis (e.g., PCR, sequencing).

16. Kinds of Microscope

Light microscope: Basic microscopy for observing stained bacteria.

Electron microscope: High-resolution imaging for viral structures and detailed bacterial cell
components.
Fluorescence microscope: Used to detect fluorescently labeled cells or antibodies.
Phase-contrast microscope: Enhances contrast for observing live cells.

17. Techniques for Microscopic Study of Microorganisms

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

Staining: Enhances contrast in samples.

Gram Staining: Differentiates bacteria into Gram-positive (purple) and Gram-negative (pink)
based on cell wall structure.
Acid-Fast Staining: Identifies acid-fast organisms, such as Mycobacterium tuberculosis.
Wet Mount: Observes live organisms in a liquid sample to study motility.
Hanging Drop Technique: Studies the motility of live microorganisms.
Fluorescence Microscopy: Uses fluorescent dyes to visualize organisms under UV light.

18. Steps in Acid-Fast Staining

Primary Stain (Carbolfuchsin): Stains all cells.

Heat Fixing: Helps dye penetrate the waxy cell wall of acid-fast bacteria.
Decolorization (Acid-Alcohol): Non-acid-fast bacteria are decolorized.
Counterstain (Methylene Blue): Stains non-acid-fast cells blue, while acid-fast organisms remain
red or pink.

19. Culture Techniques

Streak Plate Method: Isolates pure bacterial colonies by streaking an inoculum on solid media.
Pour Plate Method: Bacteria are mixed with molten agar and allowed to grow within and on the
surface.
Spread Plate Method: Spreads a liquid sample evenly on a solid medium for quantification.
Broth Culture: Grows bacteria in a liquid medium to increase bacterial mass.

20. Inspection of Culture

Colony Morphology: Observation of bacterial colony shape, color, and texture.

Hemolysis: On blood agar, checks for red blood cell lysis:
Alpha: Partial hemolysis (greenish discoloration).
Beta: Complete hemolysis (clear zone).
Gamma: No hemolysis.
Growth Patterns: Observed in liquid media (e.g., pellicle, sediment).

21. Culture Media

Defined Media: All chemical components are known.

Complex Media: Contains complex ingredients like yeast extract; not all components are
chemically defined.
Selective Media: Inhibits certain bacteria while allowing others to grow (e.g., MacConkey agar for
Gram-negative bacteria).
Differential Media: Differentiates organisms based on reactions (e.g., blood agar for hemolysis).
Enrichment Media: Enhances the growth of specific organisms in a mixed culture.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

22. Biochemical Tests

Catalase Test: Differentiates catalase-positive bacteria (bubbles with H₂O₂) from catalase-
negative.
Oxidase Test: Identifies bacteria producing cytochrome c oxidase (turns purple if positive).
Coagulase Test: Differentiates Staphylococcus aureus (positive) from other staphylococci.
Indole Test: Identifies bacteria that produce indole from tryptophan.
Citrate Utilization Test: Detects the ability of bacteria to use citrate as a carbon source.

23. Animal Inoculation Tests

Used to study pathogenicity and identify certain microorganisms.

Example: Inoculating mice with Mycobacterium tuberculosis to study virulence factors.

24. Most Common Biochemical Tests

Triple Sugar Iron (TSI) Agar: Differentiates bacteria based on glucose, lactose, and sucrose
fermentation, and hydrogen sulfide production.
Urease Test: Identifies urease-producing organisms (e.g., Proteus spp.) that hydrolyze urea to
ammonia.
Methyl Red Test: Detects mixed acid fermentation by bacteria.
Voges-Proskauer Test: Identifies bacteria producing acetoin during glucose metabolism.

25. Serologic Tests

Agglutination Tests: Detects antibodies or antigens (e.g., Widal test for typhoid fever).
ELISA: Detects specific antibodies or antigens.
Western Blot: Identifies specific proteins, commonly used for HIV diagnosis.
Rapid Diagnostic Tests: Used for diseases like malaria and COVID-19.

26. Sterilization Methods

Moist Heat Sterilization: Uses steam under pressure (autoclaving) to kill all microorganisms,
including spores.
Dry Heat Sterilization: Uses hot air to sterilize items that cannot withstand moisture.
Filtration: Used for heat-sensitive liquids; filters with pore sizes small enough to remove bacteria.
Radiation: Sterilizes equipment using ionizing (gamma rays) or non-ionizing (UV light) radiation.

27. Physical Agents of Sterilization

Autoclaving: Moist heat at 121°C under pressure for 15-20 minutes.

Dry Heat: Oven sterilization at 160-170°C for 1-2 hours.
UV Light: Disinfects surfaces by damaging microbial DNA.
Filtration: Used for heat-sensitive materials.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

28. Chemical Agents of Sterilization

Alcohols: Denature proteins and dissolve lipids; effective against bacteria and fungi.
Aldehydes: High-level disinfectants (e.g., glutaraldehyde) effective against spores.
Chlorine Compounds: Oxidize microbial components (e.g., bleach).
Ethylene Oxide: Gaseous sterilant for heat-sensitive materials.

29. Chemotherapeutic Agents and Antibiotics

Chemotherapeutic Agents: Chemical compounds used to treat diseases by inhibiting or killing

microorganisms.
Antibiotics: Natural or synthetic substances that kill or inhibit bacteria (e.g., penicillin,
tetracyclines).

30. Mode of Action of Antibiotics

Inhibition of Cell Wall Synthesis: (e.g., Penicillins, Cephalosporins).

Inhibition of Protein Synthesis: (e.g., Tetracyclines, Macrolides).
Inhibition of Nucleic Acid Synthesis: (e.g., Fluoroquinolones).
Disruption of Plasma Membrane: (e.g., Polymyxins).
Inhibition of Metabolic Pathways: (e.g., Sulfonamides).

31. Specimen Collection

Aseptic Technique: Prevent contamination.

Timing: Before antibiotics are administered.
Transport Media: Preserve viability of organisms during transport.

32. Common Clinical Specimens in the Laboratory and Related Diseases

Blood: For detecting septicemia (e.g., Staphylococcus aureus).

Urine: For diagnosing UTIs (e.g., Escherichia coli).
Sputum: For respiratory infections (e.g., Mycobacterium tuberculosis).
Cerebrospinal Fluid: For diagnosing meningitis (e.g., Neisseria meningitidis).

33. Blood

Blood samples are used in microbiological studies to detect systemic infections like bacteremia or
septicemia.
Common pathogens detected in blood cultures include Staphylococcus aureus, Escherichia coli,
and Streptococcus pneumoniae.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

34. Clinical Indicators of Blood Culture

Fever: Persistent or intermittent high temperature.

Chills: Accompanied by fever, suggesting a systemic infection.
Septicemia Symptoms: Rapid heart rate, low blood pressure, altered mental state.
Leukocytosis/Leukopenia: Abnormal white blood cell count indicating infection.

35. Types of Urine Specimens Used in Microbiological Studies

Midstream Clean-Catch: Preferred for routine urine cultures to avoid contamination.

Catheterized Urine: Collected from patients who cannot produce a clean-catch specimen.
Suprapubic Aspiration: Used in cases where contamination is a concern, typically in pediatric
patients.
Timed Urine Collection: Useful for quantifying specific substances or organisms over a period of
time.

36. Sputum

Collected to diagnose respiratory infections such as tuberculosis, pneumonia, and bronchitis.

Pathogens commonly detected include Mycobacterium tuberculosis, Streptococcus pneumoniae,
and Haemophilus influenzae.

37. Cerebrospinal Fluid

Collected through a lumbar puncture for diagnosing meningitis, encephalitis, or other CNS
infections.
Pathogens detected include Neisseria meningitidis, Streptococcus pneumoniae, and viruses like
Enterovirus.

38. The Disease Process

Refers to the sequence of events that occur from the initial infection to the resolution of the disease.
Includes stages such as incubation, prodromal, illness, decline, and convalescence.

39. Definition of Related Terms

Infection: Invasion of the host by pathogens.

Pathogenicity: The ability of an organism to cause disease.
Virulence: The degree of pathogenicity, including factors that enhance infection.
Contamination: The presence of unwanted microorganisms in a specimen.

40. Immunology

The study of the immune system, its components, and how it protects the body from pathogens.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

Includes understanding of innate immunity (first-line defenses) and adaptive immunity (specific
responses involving B and T cells).

41. Immunization

The process by which the immune system is fortified against pathogens.

Involves active immunity (via vaccination) and passive immunity (via antibody transfer).
Vaccines stimulate the immune system to produce antibodies without causing disease.

42. Clinical Bacteriology

Focuses on the identification, characterization, and treatment of bacterial infections.

Includes diagnostic techniques like culture, biochemical tests, and antibiotic susceptibility testing.
Examples of bacterial pathogens include Escherichia coli, Staphylococcus aureus, and
Mycobacterium tuberculosis.

43. Virology

The study of viruses and viral infections.

Focuses on virus structure, replication, pathogenesis, and interactions with the host immune
system.
Examples of viral infections include influenza, HIV, and hepatitis.

44. COVID-19: SARS-CoV-2: Structure, Pathogenesis, Transmission, and Diagnosis

Structure: Enveloped virus with a positive-sense single-stranded RNA genome. Spike (S) protein
is critical for binding to ACE2 receptors on human cells.
Pathogenesis: Infects respiratory epithelial cells, leading to symptoms ranging from mild
respiratory illness to severe pneumonia and ARDS (Acute Respiratory Distress Syndrome).
Transmission: Spread through respiratory droplets, aerosols, and contaminated surfaces.
Diagnosis: Done using RT-PCR (gold standard) to detect viral RNA or antigen-based rapid tests.

45. SARS-CoV-2: Structure and Genome

The SARS-CoV-2 genome is approximately 30,000 nucleotides long.

Major structural proteins include:
Spike (S): Facilitates viral entry.
Nucleocapsid (N): Encapsulates the viral RNA.
Envelope (E) and Membrane (M): Maintain the viral structure.

46. COVID-19 Vaccines

mRNA Vaccines: Pfizer-BioNTech and Moderna vaccines use mRNA encoding the spike protein
to induce an immune response.

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

Viral Vector Vaccines: AstraZeneca and Johnson & Johnson vaccines use an adenovirus vector to
deliver the spike protein gene.
Protein Subunit Vaccines: Contain harmless pieces of the virus to stimulate the immune system
(e.g., Novavax).

47. Mycology

The study of fungi, including yeasts, molds, and mushrooms.

In medical mycology, it focuses on pathogenic fungi that cause diseases like candidiasis and
aspergillosis.

48. Fungi

Yeasts: Unicellular fungi (e.g., Candida albicans).

Molds: Multicellular fungi with filamentous structures (e.g., Aspergillus).
Fungi are eukaryotic organisms that reproduce through spores and thrive in moist environments.

49. Molds

Molds grow as multicellular filaments called hyphae.

Common molds in human infections include Aspergillus and Rhizopus.
Molds reproduce by releasing spores into the environment.

50. Clinical Classification of Pathogenic Fungi

Superficial Mycoses: Affect the skin, hair, and nails (e.g., tinea, ringworm).
Subcutaneous Mycoses: Infections under the skin (e.g., sporotrichosis).
Systemic Mycoses: Infections that spread to internal organs (e.g., histoplasmosis).
Opportunistic Mycoses: Affect immunocompromised individuals (e.g., candidiasis, aspergillosis).

51. Clinically Significant Fungi

Candida albicans: Causes candidiasis, commonly affecting the mouth, throat, and genitals.
Aspergillus: Causes aspergillosis, particularly in immunocompromised individuals.
Cryptococcus neoformans: Causes cryptococcal meningitis, primarily in HIV/AIDS patients.

52. Diagnostic Parasitology

Focuses on the detection and identification of parasitic organisms in clinical specimens.

Techniques include microscopic examination of stool, blood, and tissue samples, as well as
serologic and molecular tests.

53. Types of Parasites and Diagnostic Techniques

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JOSEPH T. GUDELOS, LPT, RN, MATS, EDD-SCIED (CAND)

Protozoa: Single-celled organisms (e.g., Plasmodium in malaria). Diagnosed via blood smears and
rapid tests.
Helminths: Worms, including nematodes (roundworms), trematodes (flukes), and cestodes
(tapeworms). Diagnosed through stool sample analysis.
Ectoparasites: External parasites like lice and mites, diagnosed by direct observation.

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