Basic Microbiology

Introduction

Microbiology is the study of microorganisms, a large and diverse group of microscopic

organisms that exist as single cells or cell clusters; it also includes viruses, which are microscopic but not
cellular. Microorganisms have a tremendous impact on all life and the physical and chemical makeup of
our planet. They are responsible for cycling the chemical elements essential for life, including carbon,
nitrogen, sulfur, hydrogen, and oxygen; more photosynthesis is carried out by microorganisms than by
green plants.

Objectives

At the end of this section, the students can:

 Define the term “Microbiology”.

 Describe common microbiologic methods such as:
 Visualization of microorganism through microscopy
 Types of microscope and their uses
 Compare prokaryotic cells from eukaryotic cells.
 Perform proper handwashing and familiarized with the different sterilization and disinfectant
technique
 Describe the different bacterial structure and morphology.
 Draw a bacterial growth curve and label its four phases.
 Differentiate the difference between a drug susceptible and a multi-drug resistance bacterium.

Topic 01: Basic Microbiology Laboratory safety

Every student and instructor must focus on the need for safety in the microbiology laboratory.
While the lab is a fascinating and exciting learning environment, there are hazards that must be
acknowledged and rules that must be followed to prevent accidents and contamination with microbes.
The following guidelines will provide every member of the laboratory section the information required to
assure a safe learning environment.

Standard Laboratory Rules and Practices

The following set of rules have been formulated to avoid danger of infection arising from failure to
observe the necessary precautions in handling any material or specimen in the laboratory. These rules
shall be strictly enforced.

1. Students should store all books and materials not used in the laboratory in areas or receptacles
designated for that purpose. Only necessary materials such as a lab notebook, the laboratory
manual, and pen/pencil should be brought to the student work area.

2. Eating, drinking, chewing gum, and smoking are not allowed in the laboratory. Students must
also avoid handling contact lenses or applying makeup while in the laboratory.
3. Safety equipment:

a. labs will require that lab coats be worn in the laboratory at all times. Others may make this
optional or not required. Lab coats can protect a student from contamination by
microorganisms that he/she is working with and prevent contamination from stains and
chemicals. At the end of the laboratory session, lab coats are usually stored in the lab in a
manner prescribed by the instructor. Lab coats, gloves, and safety equipment should not be
worn outside of the laboratory unless properly decontaminated first.

b. You may be required to wear gloves while performing the lab exercises. This is especially
important if you have open wounds. They protect the hands against contamination by
microorganisms and prevent the hands from coming in direct contact with stains and other
reagents.

c. Face protection/safety glasses may be required by some instructors while you are performing
experiments. Safety glasses can prevent materials from coming in contact with the eyes. They
must be worn especially when working with ultraviolet light to prevent eye damage because
they block out UV rays. If procedures involve the potential for splash/aerosols, face
protection should be worn.

d. Know the location of eye wash and shower stations in the event of an accident that requires
the use of this equipment. Also know the location of first aid kits.

4. Sandals or open-toe shoes are not to be worn in the laboratory. Accidental dropping of objects or
cultures could result in serious injury or infection.

5. Students with long hair should tie the hair back to avoid accidents when working with Bunsen
burners/open flames. Long hair can also be a source of contamination when working with
cultures.

6. Before beginning the activities for the day, work areas should be wiped down with the
disinfectant that is provided for that purpose. Likewise, when work is finished for the day, the
work area should be treated with disinfectant to ensure that any contamination from the exercise
performed is destroyed. Avoid contamination of the work surface by not placing contaminated
pipettes, loops/ needles, or swabs on the work surface. Dispose of contaminated paper towels
used for swabbing in the biohazard container.

7. Use extreme caution when working with open flames. The flame on a Bunsen burner is often
difficult to see when not in use. Caution is imperative when working with alcohol and open
flames. Alcohol is highly flammable, and fires can easily result when using glass rods that have
been dipped in alcohol. Always make sure the gas is turned off before leaving the laboratory.

8. Any cuts or injuries on the hands must be covered with band-aids to prevent contamination. If
you injure or cut yourself during the laboratory, notify the laboratory instructor immediately.
 9. Pipetting by mouth is prohibited in the lab. All pipetting must be performed with pipette aids. Be
especially careful when inserting glass pipettes into pipette aids as the pipette can break and
cause a serious injury.
10. Know the location of exits and fire extinguishers in the laboratory.

11. Most importantly, read the exercise and understand the laboratory protocol before coming to
laboratory. In this way you will be familiar with potential hazards in the exercise.

12. When working with microfuges, be familiar with their safe operation and make sure that all
microfuge tubes are securely capped before centrifuging

13. When working with electrophoresis equipment, follow the directions carefully to avoid electric
shock.

14. If you have any allergies or medical conditions that might be complicated by participating in the
laboratory, inform the instructor. Women who are pregnant should discuss the matter of
enrolling in.

15. Unless directed to do so, do not subculture any unknown organisms isolated from the
environment as they could be potential pathogens.

16. Avoid handling personal items such as cell phones, calculators, and cosmetics while performing
the day’s exercise.

17. You may be required to sign a safety agreement stating that you have been informed about safety
issues and precautions and the hazardous nature of microorganisms that you may handle during
the laboratory course.

18. Avoid wearing dangling jewelry to lab.

Disposal of Biological Wastes

Dispose of all contaminated materials properly and in the appropriate containers:

1. Biohazard containers—biohazard containers are to be lined with clear autoclave bags; disposable petri
plates, used gloves, and any materials such as contaminated paper towels should be discarded in these
containers; no glassware, test tubes, or sharp items are to be disposed of in biohazard containers.

2. Sharps containers—sharps, slides, coverslips, broken glass, disposable pipettes, and Pasteur pipettes
should be discarded in these containers. If i instructed to do so, you can discard contaminated swabs,
wooden sticks, and microfuge tubes in the sharp’s containers.

3. Discard shelves, carts, bins, etc.—contaminated culture tubes and glassware used to store media and
other glassware should be placed in these areas for decontamination and washing.

4. Trash cans—any noncontaminated materials, p per, or trash should be discarded in these containers.
Under no circumstances should laboratory waste be disposed of in trash cans. Discard other materials as
directed by your instructor. This may involve placing materials such as slides contaminated with blood in
disinfectant baths before these materials can be discarded.

Emergencies Surface Contamination

1. Report all spills immediately to the laboratory instructor.

2. Cover the spill with paper towels and saturate the paper towels with disinfectant.

3. Allow the disinfectant to act for at least 20 minutes.

4. Remove any glass or solid material with forceps or scoop and discard the waste in an appropriate
manner.

Topic 02: Different Types of Microscope and Manipulation

Bright Field Microscope Compound Light Microscope

 Principle: utilizes transmitted light

 Magnification: as much as 1000 – 1500 times
 Limit of resolution: 0.2 um.
 Uses: visualization of bacteria and fungi

Dark Field Microscope

 Principle: utilizes a special condenser so that reflected light is made use of

 Objects being examined appear bright in a dark background.
 Uses: study of organisms or structures that are difficult to stain (e.g. spirochetes and capsules)

Phase Contrast Microscope

 Principle: optical illumination technique where brightness is changed as it passes through a

transparent specimen in the image. Some portions appear darker than the others and as a result
there is better contrast.
 Uses: useful in the study of binary fission, motility and endospores.
Fluorescent Microscope

 Principle: makes use of fluorescent dyes (e.g. isothiocyanate, rhodamine, and carbol auramine) to
make objects stand out due to their fluorescence
 Uses: very useful in diagnostic microbiology to detect antigens and antibodies.

Polarizing Microscope

 Principle: modified compound microscope that uses a special polarizer that allows only certain
light waves to pass through it
 Uses: mostly used in the field of geology to study rocks and minerals

Confocal Laser Scanning Microscope

  Principle: utilizes the process of optical sectioning to acquire images from selected depths giving
the objects a tridimensional quality
 Uses: examination of the vertical cross section of specimens; localization and identification of the
presence of fungal elements in corneal lesions
Electron Microscope

 Principle: utilizes a beam of electrons to illuminate a specimen and produce a magnified image
 Magnification: from 30,000 times or more.
 Limit of resolution: 0.5 nm
 Uses: visualization of viruse s and sub-cellular structures
Manipulation of Microscope Step by Step procedures

If the microscope has three objectives, we have three magnification options:

1. Low power or 100x total magnification

2. High-dry magnification or 400x total with a 40x objective
3. 1000X total magnification with a 100x oil immersion objective.

Low Power Examination

1. Position the slide on the stage with the material to be studied on the upper surface of the slide. Figure
1.6 illustrates how the slide must be held in place by the mechanical stage retainer lever.

2. Turn on the light source, using a minimum amount of voltage. If necessary, reposition the slide so
that the stained material on the slide is in the exact center of the light source

3. Check the condenser to see that it has been raised to its highest point.

4. If the low-power objective is not directly over the center of the stage, rotate it into position. Be sure
that as you rotate the objective into position it clicks into its locked position.

5. Turn the coarse adjustment knob to lower the objective until it stops. A built-in stop will prevent the
objective from touching the slide.

6. While looking down through the ocular (or oculars), bring the object into focus by turning the fine
adjustment focusing knob. Don’t readjust the coarse adjustment knob. If you are using a binocular
microscope, it will also be necessary to adjust the interocular distance and diopter adjustment to
match your eyes.

7. For optimal viewing, it is necessary to focus the condenser and adjust it for maximum illumination.
This procedure should be performed each time the objective lens is changed. Raise the iris diaphragm
to its highest position. Close the iris diaphragm until the edges of the diaphragm image appear fuzzy.
Lower the condenser using its adjustment knob until the edges of the diaphragm are brought into
 sharp focus. You should now clearly see the sides of the diaphragm expand beyond the field of view.
Refocus the specimen using the fine adjustment.

8. Once an image is visible, move the slide about to search out what you are looking for. The slide is
moved by turning the knobs that move the mechanical stage.

9. Check the cleanliness of the ocular, using the procedure outlined earlier.

10. Once you have identified the structures to be studied and wish to increase the magnification, you
may proceed to either high-dry or oil immersion magnification. However, before changing objectives,
be sure to center the object you wish to observe.

Topic 03: Types of Staining and Culture media

Visualization through Stains

Because many bacteria lack contrast, they are very difficult to see even with the use of a light
microscope. To increase their contrast and to enable us to appreciate these cells and their structure we
have to stain them.

1. Simple or Direct Stain

 Makes use of aniline dyes (e.g. malachite green, Bismarck brown, crystal violet,
methylene blue, safranin, carbol fuchsin)
 Stained with the dye for 1 minute and organism retains color of the dye
 Not very informative and only demonstrates the shape and basic structures of the
organism

2. Differential Stain – most important to the clinician

A. GRAM STAIN
 Differentiates Gram positive from Gram negative bacteria. Gram positive bacteria are
stained violet while Gram negative bacteria are stained red or pink.
 General rules for Gram straining:
 All Bacilli are Gram negative (e.g. Haemophilus, Enterobacter, E. coli) EXCEPT
Mycobacterium, Corynebacterium, aerobic spore-formers (Bacillus), and anaerobic spore-
formers (Clostridium)
 All cocci are Gram positive (e.g. Staphylococcus, Streptococcus) EXCEPT Neisseria,
Veillonella, Branhamella
 Spiral organisms (spirochetes) usually are not stained by Gram staining but if stainable
are usually Gram negative

B. ACID FAST STAIN

 Differentiates acid fast from non-acid fast bacteria
 Types: Ziehl Neelsen stain (hot method), Kinyoun stain (cold method)
 Bacteria stains red against blue or green background depending on the type of stain used
  Useful in the diagnosis of Mycobacterium (M. tuberculosis and M. leprae)
 General rule: All bacteria are non acid fast with the exception of Mycobacterium and
Nocardia (partially acid fast)
3. Special (Selective) Stain

 Emphasizes certain structures or features of the bacteria

 Includes the following:
 Dyar cell wall stain
 Flagellar stain – Leifson or Fischer and Conn
 Spore stain – Dorner OR Schaeffer & Fulton or Wirtz-Conklin
 Loeffler alkaline methylene blue (LAMB) stain – metachromatic granules
 Hiss capsular stain

4. Indirect (Relief) Stain

 Used for bacteria or structures difficult to stain

 Organism or structure will be unstained while background will appear dark
 Includes the following:
 Burri’s method: utilizes Dorner or nigrosine
 India ink method or Nigrosin to demonstrate capsule of C. neoformans

Topic 04: Prokaryotic and Eukaryotic Cells

All living things can be divided into three basic domains: Bacteria, Archaea and Eukarya. The
primarily single-celled organism found in the Bacteria and Archaea domains are known as prokaryotes.
The organism is made of prokaryotic cells – the smallest, simplest and most ancient cells.

Organism in the eukarya domain is made of the more complex eukaryotic cells. It can be
unicellular or multicellular and include animals, plants, fungi and protists.

Characteristic Prokaryotic Eukaryotic

 DNA within a nuclear No Yes
membrane
Mitotic division No Yes
DNA associated with No Yes
histones
Chromosome number One More than one
Chromosomal DNA Circular; complexed with Linear, complexed with histones
RNA
Membrane-bound No Yes
organelles (e.g.
mitochondria)
Size of ribosome 70S 80S
Sterols in cytoplasmic Absent, except for Mycoplasma Present
membrane spp.
Cell wall, if present Peptidoglycan in most bacteria Cellulose, phenolic polymers, lignin
(plants), chitin (fungi), or other
glycans (algae)
Pili and fimbriae Present Absent

Characteristics of Prokaryotic and Eukaryotic cells

Topic 05: Sterilization and Disinfection

One way of preventing the spread of infectious microorganism is to destroy or inactivate the
organism either by physical means or by use of chemical substances.

Factors that influence the degree of killing

 Type of organisms
 Size of inoculum
 Concentration of disinfecting agent
 Nature of surface to be disinfected
 Contact time
 Temperature – generally at room temperature (20-22 degree Celsius)
 pH
 Biofilm formation
 Compatibility of disinfectants and sterilant.

Physical method of Sterilization

I. Heat
- Most reliable and universally applicable method of sterilization
- A gradual process; kinetics of death are exponential
- The relationship between sterilization and the temperature of exposure is expressed in terms of
 thermal death time.

A. Moist Heat
- Preferred over dry heat because of its more rapid killing action.
- Destroy vegetative forms of microorganisms at a temperature of 80 0C for 5 to 10 minutes but spores are
more resistant and would require 4 minutes exposure at 1200C or 5.5 hours at 100oC

B. Dry Heat
- Requires higher temperature and longer exposure to heat
- Its effectiveness depends on the penetration of heat through the material to be sterilized
- Most widely used type is the hot air oven
- Sterilization takes place at 180’C for 2 hours
- Used in the sterilization of powders, oils, jellies and glassware
- Other useful forms: incineration and open flame
II. Desiccation
- Mechanism of action: removal of moisture -> bacteria cannot grow in an environment without
moisture -> bacterial multiplication is inhibited
- Bacterial spores are resistant to drying or desiccation.
- Used only in the preservation of foods

III. Freezing
- Many microorganisms can survive low temperature for very long periods of time -> freezing
cannot be used as a means of sterilization
- Used to preserve microorganisms and bacterial culture
- LYOPHILLIZATION – a technique of preserving microorganisms where in the organism is frozen
rapidly and dehydrated in high vacuum and then stored under vacuum in sealed ampules in cold
storage.

IV. Radiation

A. Ultraviolet light (UVL)

- The most effective bactericidal wavelength of UVL is 240-280 nm with an optimum of 260 nm that
corresponds to the maximum absorption of the bacterial DNA
- Mechanism of Action: disrupt H bonds in microbial cell resulting to the formation of thymine
dimers -> produce lethal frame shift mutations
- Has limited application because of its poor penetrating ability and its absorption by glass and
water
- Primarily used in the reduction of airborne infections in enclosed areas like operating rooms and
hospital wards.
B. Ionizing radiation
- Has greater penetrating ability than UVL but are potentially hazardous to human cells
- Mechanism of action: cause the formation of free radicals that chemically interact with proteins
and nucleic acids causing cell death

V. Filtration
- A form of mechanical sieving or physical separation of microorganisms from the fluid

VI. Makes use of high-efficiency particulate air filters tor cellulose ester membranes but the filter pore
size of 0.22 um allows very small organisms to pass through (e.g. viruses, Mycoplasma)

VII. Osmotic Pressure

- When the concentration of the solution surrounding the bacterial cell is altered it may cause the
bacterial cell to collapse or become turgid
- Used in food preservation

VIII. Ultrasonic and Sonic Vibrations

 - Principle: sound vibrations at high frequency in the upper audible and ultrasonic range are very
useful in disrupting the cell
- Sound wave generators employed operate at a range of 9-100 kc
- Mechanism: passage of sound through the liquid -> produce alternating pressures -> cause
cavities to form in the liquid -> cavities continue to grow in size -> burst violently -> cause the
cells to disintegrate
- Cavitation also produces chemical and physical changes in the suspending medium which may
be deleterious to certain enzymes

Chemical Methods of Sterilization

Factors Affecting Disinfectant Potency

1. Concentration of the Chemical Agent

2. Time
3. Temperature
4. pH
5. Nature of the Medium
6. Nature of the Organism

Mechanism of Action of Chemical Agents:

A. Damage the Cell Membrane

- Chemical agents interfere with the normal membrane function -> release of small metabolites and
interference with active transport and energy metabolism

1. Surface active disinfectants

- Agents that alter the energy relationships at interfaces producing a reduction of surface tension

a. Cationic agents – quaternary ammonium compounds

o Mechanisms:
1. Distortion of cell membrane and loss of membrane permeability -> leakage of nitrogen
and phosphorous containing compounds
2. Denature of proteins
o Bacteriostatic at low concentration and bactericidal at high concentration but not effective
against viruses & bacterial spores
o Most effective at alkaline pH
o Example: zephiran, benzalkonium chloride, cetylpyridinium chloride
b. Anionic Agents
o Mechanism: disruption of the lipoprotein framework of the cell membrane
o Most effective at acid pH
o Example: soaps and detergents

2. Phenolic Compounds
- Mechanism: cause disruption of lipid-containing membranes causing leakage of cell contents and
irreversible inactivation of membrane bound oxidases and dehydrogenases
- Includes phenols and cresols
o Phenols are now used only as reference to testing new chemical agents because they are
 toxic to human cells
o Cresols are alkyl phenols that are less toxic and more active than phenol
 Example of cresols are Lysol and creolin
o Bis-phenols – linked phenol compounds whose activity is enhanced by halogenation
 e.g. hexachlorophene which effective against gram (+) bacteria

3. Alcohols
- Mechanisms:
a. Disorganize lipid structure by penetrating into the hydrocarbon region
b. Denatures cellular proteins
- Capable of destroying almost all microbes except spores
- Inactivated by organic matters
- Activity is greater in the presence of water
- Includes:
a. Ethyl alcohol
o Most effective at concentration of 50-70%
o Widely used as skin disinfectant because it is bactericidal and remove lipids from the skin
surfaces
o Cannot destroy spores at normal temperature
b. Isopropyl alcohol
o Bactericidal activity is slightly greater than ethanol and less volatile
o Has greater toxic effect than ethanol like narcosis due to the absorption of vapors

B. Agents That Denature Proteins

- The backbone of cellular structures is made up primarily of proteins and enzymes that catalyze
metabolic reactions are also made up of proteins. Any changes in these proteins would greatly
affect the structure of the cell
- Includes:
1. Acids and alkalis – extent their action through their free H and OH ions -> alter the pH of the
organism’s environment
2. Alcohol and acetone
3. phenol

C. Agents That Modify Functional Groups of Proteins & Nucleic Acids

1. Heavy Metals
- Mechanism: poison the enzyme activity forming mercaptides with the SH groups of cysteine
residues
- Includes: mercurial and silver compounds

2. Oxidizing Agents
- Mechanism: poison the enzymes by converting functional SH groups to oxidized S-S form
- Stronger agents also attack amino groups, indole groups and phenolic hydroxyl group of tyrosine
- Includes:
a. Halogens – bactericidal and effective against sporulating organisms
o Iodine – considered the best antiseptic
 Active against spores, viruses, fungi and amoeba
 Mixtures of iodine with surface active agents are known as iodophores and widely used
for the sterilization of dairy equipment
b. Chlorine – disinfectant action is due to the liberation of free chlorine
o Used as water disinfectant
o Hypochlorite (OC12) – widely used in the food and dairy industries for sanitizing dairy and
 food processing equipment
o Also used in households and hospitals
c. Hydrogen peroxide – weak antiseptic and primarily used in cleansing wounds and in the
disinfection of surgical devices and soft plastic contact lenses
o H202 vapors – used in the sterilization of instruments
o Plasma gas sterilization – replaced ethylene oxide in many applications because it produces
nontoxic by products
d. Peracetic acid – a reliable sterilant who’s by products (acetic acid & oxygen) are nontoxic

3. Dyes
- Its use is limited to the treatment of dermatologic lesions
- Also used in staining bacteria
- Include:
a. Triphenymethane dyes
o Brilliant green, malachite green, crystal violet
o Highly selective for gram positive bacteria
b. Acridines
o Used as wound antisepsis
o Unlike aniline dyes, they retain their antimicrobial activity in the presence of serum or pus

4. Alkalating Agents
a. Formaldehyde
o Commercially available as formalin
o Uses:
 Preservation of specimens
 Preparations of vaccines
 Kill M. tuberculosis in sputum and fungus in athlete’s foot
o Destroy organism including spores
o Formaldehyde gas – its use is limited to sterilization of filters and treatment of textiles
because it is carcinogenic
b. Glutaraldehyde
o Ten times more effective than formaldehyde and less toxic
o Used as cold sterilant for surgical instruments especially respiratory therapy instruments
c. Ethylene oxide
o Used extensively in gaseous sterilization; slow acting
o Effective against all types of bacteria including spores and tubercle bacilli
o Used for materials that would be damaged by heat like polyethylene tubes, electronic and
medical equipment, biologicals and drugs
o Especially useful in sterilization of heart lung machines
o Potentially mutagenic and carcinogenic to humans
Chain Of Infection

Stages Of Infection
Topic o6: Bacterial Structure and Morphology

Fundamental Shape of Bacteria

1. Coccus
 Round or spherical
 Morphologic variations: Coffee bean shaped, lancet shaped
 Average diameter: 1um
 E.g. Staphylococcus, Gonococcus, Meningococcus

2. Bacillus
 Rod shaped
 Morphologic variations: club shaped, comma shaped, filamentous
 Average diameter: 2 x 0.5um
 E.g. Clostridium, Corynebacterium, mycobacterium

3. Spirillum
 Spiral or coiled organisms
 3 forms: Treponema – with fine regular coils
Borrelia – coarse, irregular coils
Leptospira – very fine coils
 Average size: may be as long as 40um

Structure of an Idealized Bacterium

I. Envelope Structure

A. Glycocalyx – located outside the cell that contains polysaccharide.

- also called Capsule or slime layer and its main function if for adherence to cell surfaces.

B. Cell wall – composed of peptidoglycan

- Functions:
 Give form and rigidity to bacteria
 Provides protection to the bacterial cell
 Target of beta lactam antibiotics
 Lipoteichoic acid component- for attachment and adherence
 Mycolic acid- responsible for acid fastness

C. Outer Membrane – part of the cell wall in gram negative bacteria

- Functions:
 Maintains the structure of the bacteria
 Barriers to noxious environmental compound
D. Periplasmic Space – fluid filled space located between outer membrane and the plasma
membrane
- Contains hydrolytic enzymes and components of various transport systems.

E. Plasma Membrane (Cytoplasmic Membrane)

- Made up of 2 layers of lipids, the inside layer is consisting of actin-like filaments which is
responsible for the spiral appearance of treponemes.
- Functions:
 Physical and metabolic barrier between interior and exterior of bacterial cell
  Exhibits selective permeability
 Location of bacterial electron transport system
 Excretion of hydrolytic exoenzymes
 Contains enzyme and receptors important in various system of cells.

II. Internal or Cytoplasmic Structure

A. Bacterial Nucleus (Nucleoid)

- Not a true nucleus since it is not enclosed by a nuclear membrane and without nucleolus
- Mitosis not demonstrable -> considered as prokaryotic cells
- Appears as concentrated DNA in cytoplasm
- Consist of one double stranded, circular, covalently closed, supercoiled DNA molecule that is not
associated with histones
- Demonstrable by Feulgen staining or by electron microscopy
- Bearer of hereditary characteristic
B. Mesosome
- Formed by invagination of plasma membrane
- Lamellated or whorled-like structure
- Associated with division septa during binary fission

C. Ribosomes
- Complex globular structures demonstrable by electron microscopy
- Composed of RNA molecules and many associated proteins involved in protein synthesis
- Size: 70S
- Composed of 2 subunits -> 50S and 30S
- Target of many antimicrobial agents like aminoglycosides

D. Storage Granules (Inclusion bodies)

- Temporarily holds excess metabolites
- May be used for storage of food and energy, carbon, phosphates, etc.
- Metachromatic granules of C. diphtheria made up of volutin or polyphosphates.
- Much granules of M. tuberculosis – Gram positive granules

III. Surface Appendages

A. Flagella
- Organ of locomotion; seen usually in bacilli
- Originates from cytoplasmic membrane
- Slender whip like structures -> exhibit lashing,
forward and rotatory movements
- Made up of protein called flagellin
- Parts: basal body, hook, filament
- Classification:
o Monotrichous – single polar flagellum
o Lophotrichous – a tuft of flagella at one end or at both ends
o Amphitrichous – single flagella at both ends
o Peritrichous – flagella all around the bacillus
 o Atrichous – without flagella
- Demonstrable by electron microscopy or silver impregnation techniques (Fisher and Conn
flagellar or Leiffson stain)
- Highly antigenic (H antigen)
o Not vital to survival of bacteria
o Mutation or use of Waning blender can mean loss of flagella

B. Pili (Fimbriae)
- Pili and fimbriae regarded synonymous (common pili)
- Thread-like or hair-like structures found in Gram negative bacteria
- Composed of structural proteins (pilins) & adhesins
- Fimbriae can be distinguished from flagella by its smaller diameter and it is not coiled
- Twitching motility
- Demonstrable by electron microscopy
- Types
1. Common pili – thousands of pili around bacteria
2. Sex (F) pili – one or 2 in a bacterium
- Functions:
1. Adhesion – adherence to glycoproteins of GUT; common pili
2. Used in transfer of genetic material by the process of conjugation
3. Virulence
4. Antigenic – can induce antibody production
5. Antiphagocytic

C. Spores (Endospores)
- Resistant structures which enable bacteria to withstand adverse environmental conditions;
convert to vegetative forms under favorable conditions
o Spores of C. tetani – can remain alive in soil for as long as 20 years and as long as 5 years in
chopped meat medium
- Found only in few gram-positive bacteria: Clostridium, Bacillus and a species of Rickettsia (Coxiella)
- Round, oval or elliptical structures; located terminally, sub-terminally or centrally in bacilli
- Demonstrated by Dorner spore stain, Schaeffer & Fulton stain, heat and acetic acid method
- Components:
Topic 7: Major Viral, Fungal, and Bacterial Disease of Humans

Expanded Program On Immunization

This module presents a series of interactive discussion about the pathogenesis of medically
important microorganism includes the initiation of the infectious process and the mechanism that lead to
the development of signs and symptoms, the mode of transmission that help student to grasp and be
familiarize with different disease and how to control them.

• Topic 01: Infectious Disease of the Skin and Eyes

• Topic 02: Infectious Disease of the Nervous System

• Topic 03: Infectious Disease of the Cardiovascular and Lymphatic Vessels

• Topic 04: Infectious Disease of the Respiratory System

• Topic 05: Infectious Disease of the Gastrointestinal Tract

• Topic 06: Infectious Disease of the Genitourinary tract

Introduction

Human diseases fall into many different categories, including:

• Degenerative diseases

• Immune disorders

• Infectious diseases
 • Metabolic disorders

• Neoplasms (cancers and other types of tumors)

• Nutritional disorders

• Psychiatric disorders of these disease categories,

Only infectious diseases are caused by microbes. Infectious diseases (or infections, follow
colonization of some body site by a pathogen. This module provides an overview of the major infectious
diseases of humans of various anatomical sites, including skin, ears, eyes, respiratory system, the oral
region, gastrointestinal (GI) tract, GU system, circulatory system, and central nervous system (CNS).
Student should keep in mind that some infectious diseases involve several body systems simultaneously,
and that the pathogens causing a particular infection may move from one body site to another during the
course of that disease.
TOPIC 01: INFECTIOUS DISEASES OF THE SKIN and EYES

Intact skin is a type of nonspecific host defense mechanism, serving as a physical barrier. It is
part of the body’s first line of defense. Very few pathogens can penetrate intact skin. The indigenous
microbiota of the skin, a low pH, and the presence of chemical substances such as lysozyme and sebum
also serve to prevent colonization of the skin by pathogens. Nonetheless, skin infections do occur.

Skin Diseases caused by Microorganisms

Skin and soft tissue infections are the second most common infections encountered in primary
care settings. They are also the leading infectious cause of visits in the emergency department.

MRSA Skin and Soft Tissue Infections

Methicillin-resistant staphylococcus aureus (MRSA) is a common cause of skin lesion in

nonhospital people. It can be highly virulent, but it also appears as “normal” Biota on the skin of one
third of the population. Strains that are methicillin-resistant are also found on healthy people.

Signs and Symptoms:

MRSA infections of the skin tend to be raised, red, tender, localized lesions, often featuring pus
and feeling hot to the touch. Fever is a common feature.

Mode of Transmission: Direct Contact

Diagnosis:

1. Polymerase Chain Reaction (PCR)

2. Primary Isolation

3. Selective media such as Mannitol salt agar

4. Catalase Test

Prevention and treatment: Prevention is only possible with good hygiene. Treatment of these
infections often start with incision of the lesion and drainage of the pus. Antimicrobial treatment should
include more than one antibiotic.

Impetigo

Impetigo is a superficial bacterial infection that cause skin to flake or peel off. It is not a serious
disease but is highly contagious and children are the primary victims. Impetigo can be caused by either
staphylococcus aureus or Streptococcus pyogenes, and a mixture of two probably causes most cases.

The lesion of impetigo looks variously like peeling skin, crusty, and flaky scans, or honey-colored
crusts. Lesion are most often found around the mouth, face, and exterimities, though they can occur
anywhere on the skin. It is very superficial and it iches.

The most important virulence factors relevant to S. aurues impetigo are exotocins called Exfoliative toxins
A and B. The breakdownt of the skin architecture also facilitates the spread of the bacterium.

Cellulitis

Cellulitis is a condition caused by a fast-spreading infection in the dermis and in the

subcutaneous tissue below. It causes pain, tenderness, swelling and warmth. Fever and swelling of the
lymph node draining the are may also occur. Frequently, red lines leading away from the are visible, this
symptom is the result of microbes and inflammatory products being carried by the lymphatic system.
Although septicemia can develop, most cases of the disease are uncomplicated and patients have a good
prognosis.

Cellulitis generally follows the introduction of bacteria or fungi into the dermis, either trauma or
by subtle means with no obvious break in the skin. People who are immunocompromised is at greater
risk.

Staphylococcal Scalded Skin Syndrome

SSS can be thought of as a systemic form of impetigo. Like impetigo, it is an exotoxin-mediated

disease. The phage-encoded exfoliative toxins A and B are responsible for the damage. Unlike impetigo,
the toxins enter the bloodstream from the site of initial infection and then travel throughout the body,
interacting with the skin at many different sites. The A and B toxins cause bullous lesions, which often
appear first around the umbilical cord or in the diaper and axilla. Eventually the top layers of epidermis
peel off completely. The split occurs in the epidermal tissue layers just above the basal layer.
Widespread desquamation of the skin follows, leading to a burned appearance.

It is important, however, to differentiate this disease from a similar skin condition called toxic epidermal
necrolysis (TEN) which is caused by reaction to antibiotics, barbiturates or other drugs.

Gas Gangrene
 Clostridium perfringens is a gram positive, endospore-forming bacterium which causes gas
gangrene or clostridial myonecrosis. The endospores of this species can be found in soil, human skin,
intestine and vagina. This bacterium is anaerobic and requires anaerobic conditions to manufacture and
release the exotoxins that cause the damage in this disease.
Vesicular or Pustular Rash diseases

In describing skin lesions, it is important to share a common vocabulary. There are three diseases
that present as rashes on the body in which individual lesion contains fluid. Chickenpox is very common
and mostly benign, but even a single case of smallpox constitute a public health emergency.

1. Maculopapular Rash Diseases

2. Wartlike Eruptions

Wart is also known as papilloma’s and it can develop in nearly all individuals. Warts are caused
by HPV which can be benign but can also be malignant. The warts contain variable amount of virus.
Transmission occurs through direct contact, and often warts are transmitted from one part of the body to
another by autoinoculation.

While molloscum contagiosum virus is a poxvirus, containing double-stranded DNA and

possessing an envelope. It is spread Via direct contact and through fomites. A clinician can perform a
simpler “Squash Procedure”, in which fluid from the lesion is extracted onto a microscope slide, stained
and examined for the presence of the characteristic inclusion bodies in the epithelial lesion.

Large Pustular Skin Lesions

Two infections that result in large lesions. First is Leishmaniasis, a zoonosis transmitted among
various mammalian hosts by female sand flies. Leishmania is transmitted to mammalian host by sand fly
when it ingests the host’s blood. In cutaneous leishmaniasis, a small, red papule occurs at the site of the
bite and spreads laterally into a large ulcer. While, Mucocutaneous leishmaniasis usually begins with a
skin lesions on the head or face and then progress to single or multiple lesions, usually in the mouth and
nose. Lesion can be quite extensive.

Cutaneous anthrax is the most common and least dangerous version of infection with Bacillus
Antracis. It is caused by endospores entering the skin through small cuts or abrasions. Germination and
growth of the pathogen in the skin are marked that becomes necrotic and later ruptures are formed a
painless, black eschar.

Cutaneous Mycoses

A group of fungi collectively termed dermatophytes causes a constellation of integument

condition. All these conditions have different names that begin with the word tinea which derives from
the erroneous belief that they were caused by worms. That misconception is also the reason theses disease
are often called ringworm. Transmission of the fungi that cause theses disease is direct and indirect
contact with other humans or with infected animals. The only way to avoid contact with infection is to
avoid contact.

Superficial Mycoses

Superficial mycosis often involves the outer epidermal surface and is ordinarily an innocuous
infection with cosmetic rather than inflammatory effects. It is often called tinea versicolor. Tinea
versicolor is cause by the yeast genus Malassezia. The yeast feeds on high oil content of the skin glans.
The disease if most pronounced in young people who are frequently exposed to the sun because the
affected area does not tan well.

Eye Diseases caused by microorganisms

The eye is a complex organ with many different tissue type, but the most commonly part that is
affected by the microorganism is the outer surface such as conjunctiva and cornea.

The eye best defense is the film of tears, which consist of aqueous fluid, oil, and mucus. And because the
eye’s primary function is vision, anything that hinders vision would be counterproductive. For that
reason inflammation does not occur in the eye readily as it does elsewhere in the body.

The normal biota of the eye so far is generally sparse. Populated with Corynebacterium, Staphylococcus
epirdemidis, Micrococcus and Streptococcus species.

Conjunctivitis

Infection of the conjunctiva is relatively common. It can be caused by specific microorganism that
have a predilection for eye tissue, by contaminants introduced by the presence of a contact lens or an eye
injury, or by accidental inoculation of the eye by a traumatic event.

Most bacterial infection produce a milky discharge, whereas viral infections tend to produce a clear
exudate. It is typical for a patient to wake up in the morning with an eye “glued “shut by secretions that
have accumulated and solidifies through the night.

Trachoma

Ocular trachoma is a chronic Chlamydia trachomatis infection of the epithelial cells of the eye.
The first sign of infection are a mild conjunctival discharge and slight inflammation of the conjunctiva.
These symptoms are followed by marked infiltration of lymphocytes and macrophages into the infected
area. In time, a vascular pseudo membrane of exudates and inflammatory leukocytes form overs the
cornea, a condition called pannus, which last a few weeks.

Keratitis

It is a more serious eye infection involving deeper eye tissues and can lead to complete corneal
destruction The usual cause of herpetic keratitis is a misdirected reactivation of herpes simplex virus type
1 (HSV 1). The virus upon reactivation travels into the ophthalmic rather than mandibular branch of
trigeminal nerve. Preliminary symptoms are a gritty feeling in the eye, conjunctivitis, sharp pain and
sensitivity to light

River Blindness

River blindness is a chronic parasitic (helminthic) infection. The organisms if a filarial (threadlike)
helminthic worm transmitted by small biting vector called black flies. These flies often attack in a large
number and it is uncommon in endemic areas to be bitten several hundred times a day.
 The Onchocerca Larvae are deposited into a bite wound and develop into adultes intermediate
subcutaneous tissues where disfiguring nodules form within 1 to 2 years after initial contact.

River blindness has been a serious problem in many areas of Africa. In some villages, nearly half
of the residents are affected by the disease. The approach is to treat people with ivermectin, a potential
ant filarial drug and to use insecticides to control the black flies.

Topic 02: Infectious Disease of the Nervous System

The Nervous system can be thought of as having two components the CNS consisting of brain
and spinal cord and the PNS which contain the nerves that emanate form the brain and spinal cord.

It is still believed that the CNS and PNS both lack normal biota of any kind and that finding
microorganisms of any type in this tissue represents a deviation from the healthy state. Viruses such as
herpes simplex live in a dormant state in the nervous system between episodes of acute disease.

Meningitis

Meningitis, an inflammation of the meninges, is an excellent example of an anatomical syndrome.

Many cause of meningitis some are noninfectious but the more serious forms of acute meningitis are
caused by bacteria, but it is thought that their entrance to the CNS is often facilitated by coinfection or
previous infection with respiratory viruses.

No matter the cause, meningitis has these typical symptoms: Photophobia, headache, painful or stiff neck,
fever and usually increased number of white blood cells in the CSF.

Meningoencephalitis

Two microorganisms cause a distinct disease called Meningoencephalitis and they are both
amoebas. Naegleria fowleri and Acanthamoeba are protozoans considered to be accidental parasites that
invade the body only under unusual circumstances.

Rabies

Rabies is a slow, progressive zoonotic disease characterized by fatal encephalitis.

The average incubation period of rabies is 1 to 2 months or more, depending on the wound site,
its severity and the inoculation done. The incubation period is shorter in facial, scalp, or neck wounds
because of closer proximity to the brain.

The Rabies virus is in the family Rhabdoviridae genus lyssavirus. The virus has distinctive,
bulletlike appearance, round on one end and flat on the other.

Poliomyelitis

Poliomyelitis is an acute enteroviral infection of the spinal cord that cause neuromuscular
paralysis. Because its often affects small children, in the past it was called infantile paralysis. Most
infections are contained as short term, mild viremia. Some persons develop mild, nonspecific symptoms
of fever, headache, nausea, sore throat and myalgia.

The poliovirus is in the family Picornaviridae, genus Enterovirus. It is nonenveloped and

nonsegmental. the naked capsid of the virus confers the chemical stability and resistance to acid, and
detergents. By this means, the virus survives the gastric environment and other harsh condition. After
being ingested polioviruses absorb tor receptors of mucosal cells in the oropharynx and intestine. Thus
they multiply in the mucosal epithelia and lymphoid tissue.

Polio can usually be isolated by inoculating cell culture with stool or throat washings. Treatment
of polio rest largely on alleviating pain and suffering. The mainstay of polio prevention is vaccination as
early as possible.

Tetanus

Tetanus is a neuromuscular disease whose alternate name, lockjaw. The etiologic agent,
Clostridium tetani, is a common resident of soil and the gastrointestinal tracts of animals. It is a gram-
positive, endospores-forming rod. The endospores is produce often swell the vegetative cell but are only
produced under anaerobic conditions.

Botulism

Botulism is an intoxication associated with eating poorly preserved foods, although it can occur
as a true infection. It its due to Clostridium botulinum which also an endospore-forming anaerobic that
does its damage through the release of an exotoxin. Its is commonly inhabitants to soil and water and
occasionally the intestinal tract of animals.

African Sleeping Sickness

This condition is cause by Trypanosoma Brucei, a member of the protozoan group known as
hemoflagellates because of their propensity to live in the blood and tissue of the human host.
Trypanosomiasis affects the lymphatics and areas surrounding blood vessels. Usually, a long
asymptomatic period precedes onset of symptoms including intermittent fever, enlarged spleen, swollen
lymph nodes, and joint pain. In both forms, the central nervous system is affected, the initial signs being
personality and behavioral changes that progress to extreme fatigue and sleep disturbances.

Trypanosoma Brucei is a flagellated protozoan, an obligate parasite that is spread by a blood

sucking insect called the tsetse fly which serves as its intermediate host.
Topic 03: Infectious Disease of the Cardiovascular and Lymphatic Vessels

The cardiovascular system is the pipeline of the body. It is composed of the blood vessel to and
from all regions of the body; the heart, which pumps the blood. This system moves the blood in a closed
circuit, and it therefore known as circulatory system. A closely related but largely separate system, the
lymphatic system is a major source of immune cells and fluids, and it serves as a one-way passage,
returning fluid from the tissues to the cardiovascular system.

The Cardiovascular system is highly protected from microbial infection. Microbes that
successfully invade the system however, gain access to every part of the body, and every system may be
affected. For this reason, bloodstream infections are called systemic infection.

Endocarditis
Endocarditis is an inflammation of the endocardium, or inner lining of the heart. Most of the
time, endocarditis refers to an infection of the valves of the heart, often the mitral or aortic valve. The
signs and symptoms are similar for both types of endocarditis, except that in the subacute condition they
develop more slowly and are less pronounce than with the acute disease. Symptoms include fever,
anemia, abnormal heartbeat, sometimes symptoms similar to myocardial infarction.

Sepsis
Many different bacteria can cause this condition. Because organisms are actively multiplying in
the bloodstream, sepsis is also called septicemia. Patients suffering from theses infections are sometimes
described as “septic”. Fever is a prominent feature of sepsis. The patient appears very ill and may have
an altered mental state, shaking chills, and gastrointestinal symptoms. Often an increased breathing rate
is exhibited, accompanied by respiratory alkalosis. Low blood pressure is a hallmark if this condition and
is caused by inflammatory response to infectious agents in the bloodstream, which lead to a loss of fluid
form the vasculature. This condition is the most dangerous feature of the disease, often culminating in
death.

Plague
The last great pandemic occurred in the late 1800s and was transmitted around the world,
primarily by rat infested ships. The disease was brought to the united states through the port of San
Francisco around 1906, Infected rats eventually mingled with native population and gradually spread the
disease throughout the west and southwest, where it is endemic today.

The cause if this dreadful disease is a tiny, harmless-looking, gram-negative rid, yersinia Pestis, a
member of the family Enterobacteriaceae which display usually bipolar staining that makes it look like a
safety pin.

Plague is one of a handful of internationally quarantinable disease. Streptomycin or gentamicin

can be used in the treatment of disease in most cases, though the looming threat of drug resistance in Y.
Petis could make these drugs infective in the future.

Tularemia

Tularemia is a zoonotic disease that is endemic throughout the northern hemisphere. After an
incubation period ranging from a few days to 3 weeks, acute symptoms of headache, backache, fever,
chills, malaise, and weakness appear. Further clinical; manifestation is tied to the portal of entry. They
include Ulcerative skin lesions, swollen lymph glands, conjunctival inflammation, sore throat, intestinal
disruption, and pulmonary involvement.

The Causative agent of tularemia is a facultative intracellular gram negative bacterium called
Fancisella Tularensis.

Lyme Disease
Lyme disease was shown to be caused by Borrelia Burgdorferi. It is shown to be a slow-acting,
but if often evolve into a progressive syndrome that mimics neuromuscular and rheumatoid conditions.
An early symptoms in 70% of cases is a rash at the site of tick bite. The lesion called erythema migrants
can look like a bull’s- eye with raised, erythematous (reddish) ring that gradually spreads outward and a
pale central region.

Burgdorferi is transmitted primarily by hard tick of the genus Ixodes. And the bacterium is master of
immune system evasion. It changes its surface antigens while it is in the tick ang again after it has been
transmitted to mammalian host. It proves a strong humoral and cellular immune response, but this
response is mainly ineffective, perhaps because of the bacterium ability to switch antigens.

Infectious Mononucleosis

This lymphatic system disease, which is often simply called “mono”or “kissing disease” can be
caused by a number of bacteria or viruses but the vast majority of cases are caused by the Epstein Barr
Virus (EBV) a member of the family Hherpesviridae.

The symptoms include sore throat, high fever and cervical lymphadenopathy which develop after a long
incubation period of 30 to 50 days. Many patient also jave a gray-white exudate in the throat, a skin rash
and enlarged spleen and liver.

Hemorrhagic Fever Diseases

A number of agents that infect the blood and lymphatics cause extreme fevers; some are
accompanied by internal hemorrhaging. Most of these viruses are zoonotic and their geographic pattern
of distribution is determined by the presence of their natural host.

Nonhemorrhagic Fever Diseases

In this module were going to summarized disease that result in a syndrome by high fever but
without the capillary fragility that leads to hemorrhagic symptoms. All of these diseases are caused by
bacteria.

Malaria
The origin of the name is from the Italian words mal, “Bad” and aria “Air”. And after a 10 to 16 days
incubation period the first symptoms are malaise, fatigue, vague aches, and nausea with or without
diarrhea, followed by bouts of chills, fever, and sweating. These symptoms occur at 48 to 72 hours
interval, as a result of the synchronous rupturing of red blood cells.
Topic 04: Infectious Disease of the Respiratory System

The respiratory tract is the most common place for infectious agents to gain access to the body.
Obviously, we breath 24 hours a day, and anything in the air we breathe passes at least temporarily into
this organ system. Because of its constant contact with the external environment, the respiratory system
harbors a large number of commensal microorganisms.

Whooping Cough
Whooping cough is also known as Pertussis. The disease has two distinct symptoms phases
called catarrhal and paroxysmal stages, which are followed by a long recovery phase during which a
patient is particularly susceptible to other respiratory infection.

Pertussis commonly due to Bordetella Pertussis is a very small, gram negative rod. Sometimes it
looks like a coccobacillus. It is strictly aerobic and fastidious, having specific requirements for successful
culture.

Respiratory Syncytial Virus Disease

It is a member of paramyxovirus family and contains a single stranded, negative sense RNA. It is
an enveloped virus. The first symptoms are fever that lasts for approximately 3 days, rhinitis, pharyngitis
and otitis. More serious infections progress to the bronchial tree and lung parenchyma, giving rise to
symptoms of croup, which include acute bouts of coughing, wheezing, difficulty in breathing and
abnormal breathing sounds. This condition is often called “croup” and bronchiolitis.

Influenza
The “flu” is a very important disease since influenza virus almost circulate every year. Influenza
begins in the upper respiratory tract but in serious cases my also affect the lower respiratory tract. There
is 1-to-4-day incubation period, after which symptoms begin very quickly. These include headache,
chill’s, dry cough, body aches, fever, stuffy nose and sore throat. Even the sum of all these symptoms, can
not described how a person actually feel.

Tuberculosis
The cause of tuberculosis is primarily the bacterial species Mycobacterium tuberculosis,
informally called the tubercle bacillus. The majority of tuberculosis are contained in the lungs, even
though disseminated TB bacteria can give rise to tuberculosis in any organ of the body.

Mycobacterium TB is the cause of tuberculosis in most patient. It is long and thin acid-fast rod. It
is a strict aerobe and is it not referred to as gram positive or gram negative because its acid-fast nature is
much more relevant in a clinical setting. It grows very slowly, with a generation time of 15 to 20 hours. A
period of up to 6 weeks is required for colonies to appear in culture.

Pneumonia
Pneumonia is a classic example of an anatomical diagnosis. It is defined as an inflammatory
condition of the lung in which fluid fills the alveoli. The set of symptoms that we call pneumonia can be
cause by a variety of microorganisms.

Pneumonia of all types usually begin with upper respiratory tract symptoms including
congestion. Headache is common. Fever if often present and the onset of lung symptoms follows. These
symptoms are chest pain, fever cough and production of discolored sputum. Because of the pain and
difficulty of breathing, the patient appears pale and presents an overall sickly appearance. The severity
and speed of onset of the symptoms vary according to the etiologic agent.

Topic 05: Infectious Disease of the Gastrointestinal Tract

The gastrointestinal (GI) tract can be thought of as a long tube, extending from mouth to anus. It
is a very sophisticated delivery system for nutrients composed of eight main sections and augmented
four accessory organs.

The GI tract has a very heavy load of microorganism, and It encounters millions of new ones
every day. Because of this, defenses against infection are extremely important. All intestinal surfaces are
coated with layer of mucus, which confers mechanical protection. Secretory IgA can also be found on
most intestinal surfaces. The muscular walls of the GI tract keep food moving through the system
through the action of peristalsis. Various fluids in the GI tract have antimicrobial properties.

Moreover, the GI tract is home to a very large variety of normal biota. Every portion of it has a
distinct microbial property.

Mumps
The word mumps is Old English for “lump” or “Bump”. Mums is caused by an enveloped,
single-stranded RNA virus form the genus Paramyxovirus which is part of the family Paramyxoviridae.
After an average incubation period of 2 to 3 weeks, symptoms of fever, nasal discharge, muscle pain, and
malaise develop. These followed by inflammation of the salivary glands (especially the parotid),
producing the classic gopherlike swelling of the cheeks on one or both sides. Swelling of the gland is
called parotitis, and it can cause considerable discomfort.

Acute Diarrhea (with or without Vomiting)

Diarrhea usually defined as three or more loose stools in a 24 hour period and in the united state
up to third of all acute diarrhea is transmitted by contaminated food.

The incidence of diarrhea is even higher among children attending day care centers. In tropical
countries, children may experience more than 10 episodes of diarrhea a year. In fact more than 3 million
children a year mostly in developing countries die from diarrheal disease.

Chronic Diarrhea

Chronic Diarrhea is defined as lasting longer than 14 days. It can have infectious causes or can
reflet non-infectious conditions. As we discuss the few microbes that can be responsible for chronic
diarrhea in otherwise healthy people. Keep in mind that Practically any disease of the intestinal tract has
a sexual mode of transmission in addition to the ones that are commonly stated.

Hepatitis
When certain viruses infect the liver, the can cause hepatitis, an inflammatory disease marked by
necrosis of hepatocytes and a response by mononuclear white blood cells that swells and disrupts the
liver architecture. This pathologic change interferer’s with the livers excretion of bile pigment such as
bilirubin into the intestine, When bilirubin, a greenish-yellow pigment accumulates in the blood and
 tissue causing jaundice. A yellow tinged in the skin and eyes. Stated below are the different hepatitis
virus that may cause inflammation.

Gastrointestinal Disease caused by Helminths.

Helminths that parasitize humans are amazingly diverse ranging from barely visible to hug
worms. Helminth’s infection usually provokes an increase in granular leukocytes called eosinophils
which have a specialized capacity to destroy multicellular parasites. Below is the summary of different
helminths that my cause infection to human.

Topic 06: Infectious Disease of the Genitourinary tract

The genitourinary tract includes the kidneys, ureters, bladder and urethra. The kidneys remove
metabolic wastes from the blood. Acting as sophisticated filtration system.

The most obvious defensive mechanism is the flushing action of the urine flowing out of the
system. The flow of urine also encourages the desquamation of the epithelial cells. Any microorganisms
that constitute the normal biota in the gastrointestinal tract, because the two organs are in close
proximity. Probably the most common microbial threat to the urinary tract is the group of
microorganisms that constitute the normal biota in the GIT.

In both genders, the outer region of the urethra harbors some normal biota. The kidney, ureters,
bladder and upper urethra were previously thought to be sterile. However, recent data suggests that
some of these areas may actually contain microbiota that are simply unculturable using currently
available methods.

1. Urinary Tract infections

Even though the flushing action of urine helps to keep infections to a minimum in the urinary
tract, urine itself is a good growth medium for many microorganisms. When urine flow is reduced, or
bacteria are accidentally introduced into the bladder, an infection of that organ can occur.

Symptoms include pain, frequent urges to urinate even when the bladder is empty, and burning
pain accompanying urination. The urine can be cloudy due to presence of bacteria and white blood
cells. Low grade fever and nausea are frequently present.

2. Leptospirosis

This infection is a zoonosis associated with wild animals and domestic animals. It can affect the
kidneys, liver, brain and eyes. Leptospirosis has two phases. During the early-leptospiremia-phase,
the pathogen appears in the blood and CSF. Symptoms are sudden high fever, chills, headache,
muscle aches, conjunctivitis, and vomiting. During the second-immune-phase, the blood infection is
cleared by natural defenses. This period is marked by milder fever, headache due to leptospiral
meningitis and Weil’s syndrome, a cluster of symptoms characterized by kidney invasion, hepatic
disease, jaundice, anemia, and neurological disturbance.
Case study for Laboratory

Topic 01: Infectious Disease of the Skin and Eyes

Case: A 2-year-old girl presents with left eye swelling and fever that began 2 days ago. The patient was
seen at private clinic and was given ibuprofen and Benadryl for a suspected allergic process. Yesterday
the patient was brought to the emergency department for worsening left eyelid swelling with decreased
appetite.

Vital signs:

Temp: 38.4

BP: 110/90

HR: 137

RR: 22

Physical examination:

Left upper and lower eyelids appear significantly erythematous and tender to palpation. EOM
appeared intact but exam is limited due to pain. No apparent Chemosis, proptosis or purulent discharged
present.

Question:
What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.

Topic 02: Infectious Disease of the Nervous System

Case: A 4-year-old boy from Zambales came in with one week history of general malaise, indolence, mild
fever and progressive anorexia. Three days prior to presentation at the hospital he had started to refuse
all foods and fluids, accompanied by a progressive dysphagia, sore throat and sialorrhea. An
otorhinolaryngologist had been consulted two days before presentation who had considered a
peritonsillar abscess. However, his examination at that time did not provide any clues for oropharyngeal
infection. Subsequently, the boy demonstrated increased difficulties with opening his mouth and
experience a progressive dehydration.

The history revealed that the boy had recently injured his left hallux. This had resulted in a small
local hematoma and loose toenail. There were no recorded insect or animal bites. Based on religious
grounds, the boy had not received immunization.

On physical examination in the regional hospital we saw an afebrile, irritable and anxious boy
gently playing at the table, with trismus and mild dehydration. After being asked to walk, he showed
muscle spasms of the back and thighs evidently worsening during examination. There was no cervical
lymphadenopathy and the ear and nose examination were unremarkable. Inspection of the oropharynx
was not possible due to trismus. Tendon reflexes were normal, there was no meningeal irritation. The
loose toenail did not show clear signs of inflammation. The heart rate was slightly increased, the blood
pressure was normal and further clinical examination was unremarkable

Question:
What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.

Topic 03: Infectious Disease of the Cardiovascular and Lymphatic Vessels

Case: Francis Jun, a 30 years old member of the armed forces group was admitted at the AFP medical
center because of chills, irregular fever with profuse sweating for the past 2 weeks. He claimed to have
been with a group of comrades and some local health workers in the hinterlands of Palawan doing
regular medical mission for the past 4 weeks. On admission, Francis June was febrile and the admitting
physician has concluded that he has a palpable liver as well.

Question:
What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.

Topic 04: Infectious Disease of the Respiratory System

Case: A 15-year-old female with a history of hay fever develops fever, headache and malaise for 4 days
followed by a nonproductive cough and scratchy throat. Despite chicken soup and orange juice, the
cough and fever persist, and her mother drags her to your office. On examination, her temperature is
101o, pulse 90 beats/min, BP 110/70, respiratory rate 20 beats/min Physical examination is unremarkable
except for scattered rales over the left lower lung, and small bullae in her left tympanic membrane. Chest
x-ray reveals a patchy left lower lobe infiltrate. At your request, she makes a heroic effort but is unable to
produce sputum.

Question:
 What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.

Topic 05: Infectious Disease of the Gastrointestinal Tract

Case: A 27-year-old-male presented to the emergency room with five-day history of malaise, fatigue, low
grade fever and nausea. Yesterday, she noted that his urine was very dark and his stools were very light
in color. He also complained of join pain. He is still single and no sexual partner since birth. The only
thing that he enjoys to do is go to the different food park and make a vlog about different street foods
available in the barangay. Upon physical examination noted to have enlargement of the liver and
yellowish sclerae.

Question:
What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.

Topic 06: Infectious Disease of the Genitourinary tract

Case: A 28-year-old man from Tortugas, Balanga presented to the emergency department three days
prior to admission with a two-day history of fever, chills, headache, neck stiffness, productive cough,
nauseas and diffuse myalgias. And two days after his first visit, the patient developed symptoms of
photophobia, non-bloody, watery stools, non-bilious emesis up to sever time per day, bloody sputum and
dark tea colored urine. On night prior to second visit, the patient noticed yellowing of his eyes and face
and onset of abdominal pain. The patient reported swimming in freshwater 2 weeks prior to consult but
denied skin abrasions and water ingestion.  He further denied history of recent travel, sick contacts,
eating uncooked foods.

Question:
What are the salient features of this case?
What are the laboratory investigations, should be request that can aid in diagnosis?
What is the differential diagnosis? Rule in and Rule out.
What is the diagnosis of this case, management, and treatment (Non pharmacologic and
pharmacologic)
Case Discussion include the epidemiology, etiology and prognosis.