MICROBIOLOGY AND
procedures, start aseptic surgery.
PARASITOLOGY – PRELIMS
THE SCIENCE OF MICROBIOLOGY
WEEK 1
MICROBIOLOGY
- Is the study of organisms that are so small that
cannot be seen by the naked eye.
- Microbiology is derived from the Greek words
mikros (small), bios (life), and logia or logos
(study of).
MICROORGANISMS:
Cellular – prokaryotes: bacteria
- Eukaryotes: fungi, protozoa, algae
Acellular – viruses
DIVISION OF MICROBIOLOGY
Bacteriology – the study of bacteria
Virology – the study of viruses
Mycology – the study of fungi
Parasitology - the study of protozoa and parasitic
worms
Phycology – the study of algae
Immunology – the study of the immune system and the
immune response.
EARLIEST MICROBIOLOGISTS
Robert Hooke – discovered the cell.
Anton van Leeuwenhoek – father of microbiology,
bacteriology, and protozoology.
- Created the single lens microscope.
Louis Pasteur – developed the process of pasteurization
and he also introduced the term aerobes and anaerobes
and developed the fermentation process.
Robert Koch – developed the germ theory.
- It is the Scientific steps to identify the causative
agent of a certain disease.
Edward Jenner – discovered the vaccine for smallpox.
Joseph Lister – applied the germ theory to medical
Paul Ehrlich – Discovered salvarsan for the treatment of
syphilis.
- Magic bullet – treatment for disease by using
chemical substances.
Alexander Fleming – discovered penicillin from a mold
called penicillin notatum.
Hans Christian Gram – develop gram staining procedure.
TYPES OF MICROSCOPES
MICROSCOPE – an optical instrument that can
magnify organisms a hundredfold or even thousandfold.
Compound microscope – contains more than one
magnifying lens. It can magnify objects approximately a
thousand times their original size.
Brightfield microscope – made up of series of lenses
and utilizing visible light as its source of illumination, it
can magnify an object 1,000 to 1500 times.
Darkfield microscope – utilizes reflected light instead
of transmitted light, with a special condenser that has an
opaque disc that blocks the light, such that only the
specimen is illuminated. Spirochetes.
Phase-contrast microscope – was first introduced by
Dutch physicist Frits Zernike in 1934. It has a contrast-
enhancing optical technique to produce high-contrast
image.
Differential Interference Contrast microscope – it
utilizes two beans of light instead of one and therefore
has higher resolution. Developed by George Nomar ski.
Bright against a dark background.
Fluorescence microscope – makes use of ultraviolent
light and fluorescent dyes called fluorochromes. Shinny
against a dark background.
Confocal microscope – also known as confocal laser
scanning microscope (clsm) or laser confocal scanning
microscope. It is used to increase optical resolution and
contrast of micrography.
Electron microscope – used to visualize viruses and
subcellular structure of the cell. TEM – original form of
the electron microscope. SEM – relies on interactions at
the surface rather than transmission.
Scanning probe microscope – developed by gerb STAINING
binnig and Heinrich rohrer. Used to study the molecular - It gives color to the organism to see them
and atomic shapes of organisms on a nanoscale. under microscope.

SIMPLE STAINS
- Use of single dye either WATER or ALCOHOL
based.
- To identify shape and basic structure.
- Crystal violet, Carbon fuchsin, Methylene blue,
Saffranine.
DIFFERENTIAL STAINS
1. GRAM STAIN
- GRAM (+) BACTERIA - Stain PURPLE or
BLUE
- GRAM (-) BACTERIA -Stain RED or PINK
General rule:
- All cocci are gm (+) except for Neisseria,
Branhamella, Veillonella.
- All bacilli are gm (-) except for Mycobacterium,
Bacillus, Corynebacterium, Clostridium.
2. ACID FAST STAIN - Used for high lipid
content bacteria.
- ZIEHL-NEELSEN STAIN - also known as “Hot
Method Steam bathing with AQUEOUS DYE
and BLUE background.
- KINYOUN STAIN - also known as “Cold
Method” – Using GREEN background.
SPECIAL STAINS
“LAMB” Loeffler alkaline methylene blue
HISS STAIN – capsule or slime layer.
DYER STAIN – cell wall
FISHER_CONN STAIN – flagella
DORNER, SCHAEFFER, FULTON STAIN – spores
INDIA INK–capsule fungus “Cryptococcus
Neoformans”

BACTERIAL STRUCTURE, MORPHOLOGY

GROWTH REQUIREMENT
GROWTH CURVE
 WEEK 2 monotrichus Single polar flagellum
lophotrichous a tuft of flagella at one
end of bacterium
FUNDAMENTAL SHAPES OF BACTERIA: amphitrichous flagella at both ends of
Coccus (cocci) – spherical oval or round-shaped bacteria the bacterium
peritrichous flagella all around the
In pairs diplococci bacillus
In chains streptococci atrichous without flagellum
In cluster staphylococci
In groups of four Tetrad
INTERNAL STRUCTURE
In groups of eight Octad

Bacillus (bacilli) – rod-shaped Nucleoid - does not contain a nucleoplasm/nuclear

Spirilla – treponema pallidum – spiral in shape
ENVELOPE STRUCTURES
Glycocalyx - outermost covering of some bacteria
gelatinous substance referred to as CAPSULE
(indicative of the virulence) or degree of pathogenicity.
Outer membrane - gram negative bacteria’s outer
membrane is composed of LPS (lipopolysaccharide)
there is a lipid portion in LPS (Lipid A) responsible for
endotoxin production.
membrane, contains genetic material (DNA).
Mesosome - for cell division involves secretion of
substance by the bacterium.
Ribosome - sites for protein synthesis target or site for
the action of antibiotics.
Endospores - has DIPICOLINIC ACID resistant to heat,
drying, chemicals agents & radiation, and difficult to
destroy.
BACTERIAL GROWTH REQUIREMENTS
NUTRITIONAL REQUIREMENTS

Cell wall - it provides rigid support and gives shape to
the bacteria.
“Murein Sacculus” -principal component of bacterial
cell wall is PEPTIDOGLYCAN.
Periplasmic space – fluid filled space.
- has enzymes for breakdown of large molecules
& transport protein for regulation of osmolality
of cells.
Cytoplasmic membrane – plasma membrane or cell
membrane located beneath the cell wall sometimes
called CELL SACK because it encloses the cytoplasm of
the cell. Function: carries enzymes, involve in selective
permeability, active transport of molecules in and out of
the bacterial cell.
PROJECTING STRUCTURES
Pilus or fimbria - thread like structure that projects
from the capsule, for adherence to cell surface
attachment during conjugation (sex pilus) Pili are
commonly seen in gram-negative organisms.
Axial filaments and flagella – whip like structures and
organs for motility.
Carbon - makes up the structure backbone(skeleton)
a. autotrophs (lithotrophs) –inorganic salts and
water as their sole source of carbon.
- photolithotrophs –their source of energy derived
from light.
- chemolithotrophs – oxidation of inorganic
substance
b. Heterotrophs (organotrophs) – utilize organic
substances like sugars or glucose.
- photo organotrophs- source of energy could be
light.
- chemoorganotrophs – oxidation
Nitrogen, sulfur, and phosphorus - necessary for
synthesis of cellular materials (protein, nucleic acids)
Inorganic ions:
a. magnesium - stabilizes ribosomes, cell
membrane and nucleic acids.
b. Potassium- required for normal functioning and
integrity of ribosomes.
c. Calcium- an important constituent of cell wall
contributes to the resistance of bacterial cell
wall.
d. Iron- part of cytochrome and functioning as a
co-factor in enzymatic activities.
PHYSICAL REQUIREMENTS
1. Moisture/water the bacterial cell is mainly
composed of water.
2. Oxygen:
a. Aerobes – utilize molecular oxygen for
energy.
Strict aerobes – strictly require oxygen for
growth.
b. Obligate/strict anaerobes – cannot survive in
the presence of oxygen.
Aerotolerant anaerobes – can resist exposure
to oxygen and not killed by its presence.
c. Microaerophilic anaerobes – able to grow at
low oxygen tension.
3. Temperature
Thermophiles – heat loving (50-60oC)
Mesophiles –optimum temp. of 20-40 C
Psychrophiles -10-20 C
Most medically important bacteria are
MESOPHILES.
4. pH
Alkalophiles – Ph 8.4-9.0
Neutrophiles pH 7.5-8.0 (mostly considered)
Acidophiles pH 6.5-7.0
5. Osmotic condition
Halophile – high salt concentrations for growth.
Osmophiles – high osmotic pressure.
BACTERIAL GROWTH CURVE
Lag phase - adjustment for the bacteria in a new
environment undergo synthesis of DNA & enzymes
increase in size of bacteria but not in number.
Logarithmic/Exponential/Log phase – rapid cell
division. Resulting in an increase in number. cells are
metabolically active. Generation time of bacteria can be
determined.
Stationary phase – period of equilibrium. The rate of
growth slows down. Nutrients are depleted. Toxic waste
accumulates.
Death/decline phase – rapid cell death.
HOT RESPONSE TO INFECTION
IMMUNOLOGY - the study of the immune system &
the immune response.
IMMUNOGEN - is any substance capable of inducing
immune response, whether humoral, cellular or both.
ANTIGEN - substance that is recognized by a particular
antibody or T cells & serves the target of the immune
response.
LINES OF DEFENSE
1st line of defense - INTACT SKIN & MUCOUS
MEMBRANE Enzymes in tears in body secretions
Normal flora.
2nd line of defense - INNATE arm of immune system:
- Inflammation, Natural killer cells (kills virus-
infected cells),
- Neutrophils & macrophages (phagocytes)
- Interferons- substance released by activated cells
inhibit viral replication.
3rd line of defense - ADAPTIVE arm of immune system.
B and T cells
THE IMMUNE SYSTEM
Function: To defend the host against infection caused
by viruses, bacteria, fungi, parasites.
Cells involve in the immune system:
- B lymphocytes or B cells
- T lymphocytes or T cells
Lymphocytes - are produced in Primary (central)
Lymphoid organs.
B cells - remain in bone marrow to reach maturity.
T cells - need to migrate in the thymus where they
mature.
Secondary or peripheral lymphoid organs
- Lymph nodes
- Spleen
- Tonsils
- Appendix
- Peyer’s patches of small intestine
B LYMPHOCYTES (B CELLS)
- Differentiate into antibody producing plasma
cells.
- Produces antibodies.
- Antigen presenting cell.
- Possesses immunologic memory, with
immunoglobulins on its surface (IgM & IgD)
T LYMPHOCYTES (T CELLS)
(CD4+ T cells)- Helper T cells promote inflammation &
antibody production.
(CD8T cells)- Cytotoxic T cells recognize & kill virus
infected cells, tumor cells & foreign cells also possess
immunologic memory.
INNATE IMMUNITY – NATURAL IMMUNITY
- EXIST FROM THE TIME WE ARE BORN
- Prior to exposure to antigen.
- Non- specific
- Includes host barriers (1st line of defense).
Phagocytosis & inflammation (2nd line of
defense)
ACQUIRED (ADAPTIVE IMMUNITY)
- occurs AFTER exposure to antigen.
- improves upon repeated exposure.
- SPECIFIC
- responsible for conferring lifetime protective
immunity to re- infection w/ same pathogen.
- mediated by B (antibody formation) and T cells.
- may be ACTIVE OR PASSIVE
ACTIVE IMMUNITY - is resistance induced after
contact w/ foreign antigens. Long term resistance. Slow
onset.
PASSIVE IMMUNITY - is resistance based on
antibodies preformed in another host.
IgG passed from mother to fetus during pregnancy IgA
passed from mother to newborn during breast feeding.
ANTIBODIES - are globulin proteins
(immunoglobulins)
- that react w/ specific antigen that stimulated
their production.
5 MAIN CLASSES OF ANTIBODIES
IgD
- predominant antibody in secondary response
major defense against bacteria & viruses.
- only antibody to CROSS THE PLACENTA
- MOST ABUNDANT ANTIBODY IN THE
NEWBORNS.
- MAIN immunoglobulin in CHRONIC
infections.
IgM
- LARGEST immunoglobulin
- Main immunoglobulin produced early in
primary response.
- Predominant immunoglobulin in ACUTE
infections.
IgD
- immunoglobulin with no known antibody
function.
IgE
- immunoglobulin that mediates immediate
(anaphylactic) or severe allergy reaction
IgA
- main immunoglobulin in secretions (colostrums,
saliva, tears, resp, intestinal, secretions)
BACTERIA AND DISEASE
Disease - the result of an undesirable relationship within
the host & the pathogen marked by interruption of
normal functioning of a body part or parts.
Infection - invasion of the body by pathogenic
microorganisms.
Symbiosis - the relationship between the indigenous
flora and the host.
Commensalism - form of symbiosis in which 1
organism benefits from another w/o causing harm to it.
Mutualism - form of symbiosis in w/c both organisms
benefit from the relationship.
Parasitism - form of relationship in w/c 1 organism
benefits from another at same time causes harm to the
other.
Pathogen - an organism that invades & causes damage
or injury to the host.
Pathogenicity - the ability of the organism to cause a
disease.
Contamination - the presence of organisms outside the
body, as well as on water, food & other biological
substances.
Pollution - the presence of undesirable substances in
water, air, or soil.
KOCH’S POSTULATES
 - The same organism must be found in all cases of
a given disease & must not be present in healthy
individuals.
- The organism must be isolated & grown in pure
culture from the infected person.
- The organisms from the pure culture must
reproduce the disease when inoculated into
susceptible animal.
- The organism must be isolated in pure culture
from the experimentally infected animal.
FACTORS THAT INFLUENCE OCCURRENCE
OF INFECTION
Portal of Entry- Mucous membrane (inhaled), skin
(wounds, abrasion) parenteral route (Injections).
Virulence of organism: Capsule enables organism to
evade phagocytosis, Enzymes, Toxins.
Number of microbes- likelihood of disease increases as
number of pathogens increases.
Defensive powers of host- immune system
HOW ORGANISMS PRODUCE DISEASE
Mechanical – organisms directly damage tissues or
surface.
Chemical – bacteria produce chemicals and toxins.
Immunologic - response of the immune system
CLASSIFICATION OF INFECTIOUS DISEASES
According to ability for person-to-person spread.
Communicable Disease- a disease that spreads from
one host to other, either directly or indirectly
Non communicable disease- not spread from one
person to another.
Contagious disease- easily spread from one person to
another.
According to source of infection
Exogenous - source of microorganism from outside of
body.
Endogenous - source of microorganisms from inside of
body.
Fulminating infection - infection that results in the
death of the patient over a short period of time.
Nosocomial infection - hospital acquired infection.
Incidence - refers to the number of people in a
population who developed a disease during a particular
period.
Prevalence - number of people in population who
developed disease at specified time.
According to occurrence of infection
Sporadic – occurs occasionally.
Endemic – constantly present in a population
Epidemic - many people develop disease in each
locality in a short period of time.
Pandemic - disease is worldwide occurrence (influenza,
AIDS)
Zoonosis - disease primarily affecting lower animals.
Epizoonosis - disease that occur epidemic in lower
animals.
Enzoonosis - endemic in lower animals.
Bacteremia- presence of bacteria in the blood.
Septicemia- presence of actively multiplying bacteria in
blood.
Toxemia- presence of toxins in the blood.
Viremia- presence of viruses in the blood.
Pyemia- presence of pus producing bacteria in the
blood.
According to severity or duration of infectious disease
Acute disease- develops rapidly but lasts for short
period of time (ex. common colds)
Chronic disease- develops more slowly & occur for
long period (ex. tuberculosis)
Latent disease - causative organism remains inactive for
a time but can become active & produce symptoms of
disease (Ex: Shingles- disease that is caused by same
virus that causes chicken pox)
According to extent of host involvement
Local infection- invading microorganisms are limited to
a relatively small area of the body (ex. boils)
Focal infection- a local infection enters a blood or
lymphatic vessel & spread to specific parts of the body
where they become confined to the specific area of body
(ex. can arise from teeth, sinuses)
Systemic or generalized infection- invading
microorganisms or their products are spread throughout
the body by blood or lymph.
STAGES OF AN INFECTIOUS DISEASE
Incubation period- refers to the time interval between
entry of microorganism & the first appearance of signs
and symptoms.
Prodromal period- mild symptoms of a disease w/c are
nonspecific (fever, cough, colds, malaise)
- refers to the spread of pathogens by droplet
nuclei in dust that travels >1 meter from the
reservoir to the host.
VECTORS
- carry organisms from one host to another Insects
(arthropods)- the most important group of
vectors.
Mechanical transmission - refers to passive transport of
organism on insect’s feet or other parts. Ex: cockroaches
& flies.

Period of decline – Period of defervescence- signs and Biological transmission- active transport of organisms.
symptoms start to subside. Patients may become Organism enters the insect vector after the insect Vector
vulnerable to secondary infections. bites an infected person.

Period of convalescence- patient regains strength, body

returns to its pre-diseased normal condition.
ROUTES OF TRANSMISSION

CONTACT transmission- refers to the spread of

microorganisms through direct contact, indirect contact,
or droplet transmission.
Direct Contact - aka person to person transmission
involves direct transmission by physical contact between
the source of infection & the susceptible host. (kissing,
touching). Ex. Common colds, Respiratory tract
infections, chicken pox, syphilis, gonorrhea.
Indirect contact - refers to transmission of causative
agent from its reservoir to a susceptible host through a
nonliving object(fomites).
VEHICLE transmission- refers to transmission of
organisms through media such as food, water, air.
Food-borne - pathogens are transmitted through
ingestion of food that is improperly cooked, poorly
refrigerated, and unsanitary conditions. ex. food
poisoning, gastroenteritis.
Water borne pathogen is spread through contaminated
water (ex, typhoid fever, cholera).
DROPLET
- is a form of contact transmission in w/c the
organism is spread in droplet nuclei that travel
only short distances usually. These droplets are
spread into the air by coughing, laughing,
talking, sneezing. Ex: pneumonia, influenza.
AIRBORNE