MICROBIOLOGY AND PARASITOLOGY
Prelims (Chapters 1-5)
Chapter 1: THE SCIENCE OF MICROBIOLOGY
Microbiology
 Greek words: mikros (small) bios (life)
logia/logos (study of)
 Study of microorganisms
 Microorganisms- small organisms that cannot
be seen by naked eye
o Category of Microorganism (2)
1. Cellular- prokaryotes or eukaryotes
2. Acellular- viruses
 Classification of Microbiology (6)
1. Bacteriology- study of bacteria
2. Virology- study of viruses
3. Mycology- study of fungi
4. Parasitology- study of protozoa and
parasitic worms
5. Phycology- study of algae
6. Immunology- study of immune system and
response
Normal flora or indigenous flora- organisms inhabit the
human body
EVOLUTION OF MICROBIOLOGY
3180 BC- epidemic “plague” in Egypt
1122 BC- outbreak of smallpox-like
 Robert Hooke- discovered cell; mid-1600s; cell
theory
 Anton Von Leeuwenhoek- Dutch merchant;
single-lens microscope; microorganisms that he
called animalcules; Father of Microbiology
 Louis Pasteur- mid & late 1800s; initiate germ
theory of disease; pasteurization; term
Live only in the absence of oxygen
anaerobes & aerobes; fermentation process
Require oxygen to grow
 Robert Koch- Koch’s postulates-
microorganisms caused certain diseases
Golden Age of Microbiology- later 1800s & first decade
of 1990s
 Edward Jenner- vaccine for smallpox
 Joseph Lister- septic surgery
After World War II- antibiotics were introduced
 Paul Ehrlich- Salvarsan(magic bullet of
chemotherapy)- treatment for syphilis
 Alexander Fleming- penicillin from Penicillium
notatum
1930- electron microscope was developed
MICROSCOPY
Microorganisms- miniscule organisms
Microscope- instrument that can magnify organisms
 Types of Microscope (9)
1. Compound Microscope- more than one
magnifying lens
 Two magnifying lens system (2):
o Eyepiece contains ocular lens-
magnifying power of 10x
o Objective- directly above the
organism
 Component of Compound
Microscope (17):
 Ocular lens/eyepiece- the
viewer looks through
 Revolving nose piece- holds the
objective lenses
 Dioptre adjustment- to change
focus
 Body tube or head- connects
eyepiece to objective lenses
 Arm- connects body to the base
 Coarse adjustment- brings
specimen to general focus
 Fine adjustment- fit and focus
details
 Objective lenses- lenses that
are closest to specimen
 Stage- flat platform
 Stage clips- holds the slide
 Stage control- move the stage
right or left, forward or
backward
 Aperture- allows light to reach
the slide
 On/off switch- turns illuminator
on/off
 Illuminator- light source
 Iris diaphragm- adjust amount
of light
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  Condenser- gathers and focus all bacilli are gram- except
light Corynebacterium, Clostridium,
 Base- supports microscope Bacillus and Mycobacterium
2. Brightfield Microscope- series of lenses;
Reagent Function Gram+ Gram-
bacteria and fungi; specimen appears dark Crystal Primary stain Purple/blue Purple/blue
against surround the bright field violet
3. Darkfield Microscope- utilizes reflected Gram’s Mordant* Purple/blue Purple/blue
iodine
light instead of transmitted light; specimen Acetone Decolorizer Purple/blue Colorless
appears bright against dark background or 95%
4. Phase-contrast Microscope- contrast- alcohol
Safranin Counterstain/secondary Purple/blue Red/pink
enhancing optical technique
stain
5. Differential Interference Contrast
Microscope- utilizes two beams of light
instead of one; George Nomarski 1952; b. Acid-fast stain- used for bacteria w/
living specimens high lipid
6. Fluorescence Microscope- makes use of Two methods (2):
ultraviolet light; use fluorochromes- i. Ziehl-Neelsen Stain- hot
fluorescent dyes; specimen appears to method; will appear red on
shine; genetic material of cell (DNA/RNA) blue background
7. Confocal Microscope- uses optical imaging ii. Kinyoun Stain- cold
technique; specimen stained w/ method; will appear red on
fluorochrome; produced 3D green background
8. Electron Microscope- utilizes beam of
Check book page 12 for Acid-fast staining*
electrons;
a. transmission electron microscope Special Stains- used to demonstrate specific structures
(TEM)- original form of electron in a bacterial cell
mic.
 LAMB (Loeffler Alkaline Methylene Blue) stain
b. Scanning electron microscope
 Hiss stain (capsule or slime layer
(SEM)- interactions rather
 Dyer stain (cell wall)
transmission
 Fischer-conn stain (flagella)
9. Scanning Probe Microscope- used to study
 Dorner and Schaeffer-Fulton stain (spores)
molecular and atomic shapes; Dr. Gerd
 India ink/nigrosine (capsule of the fungus
Binning & Dr. Heinrich Rohrer
Cyrptococcus neoformans)
STAINING
CULTURE MEDIA
Staining- are meant to give color to organisms
Culture media- to identify a specific organism
Types of Staining (2):
Culture medium- basically an aqueous solution
1. Simple Stains- use of single and basic dyes Classified to three primary levels (3):
(safranin. Methylene blue, crystal violet);
quick and easy way 1. Physical State
2. Differential Stains- differentiate one group 2. Chemical Composition
3. Functional type
bacteria from another
Two procedures of Differential Staining (2): According to Physical State (3):
a. Gram Stain- distinguishes gram+
 Liquid media- broths, milk or infusions; water-based
(blue or purple) from gram- (red or
solution that do not solidify at temperature
pink) all cocci are gram+ except  Semi-solid media- clot-like consistency at ordinary
Neisseria, Veilonella & Branhamella; room temperature; soft consistency

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  Solid media- contain solidifying agent; used for
bacteria and fungi
o Come in two forms:
a. Liquefiable
b. Non-liquefiable
According to Chemical Composition (2):
 Synthetic media- chemically-defined substances
 Non-synthetic media- contain at least one ingredient
that is not chemically defined
According to Functional Type (2):
 General Purpose media- for primary isolation;
support growth of pathogenic and non-pathogenic
 Enrichment media- complex organic substances
o Two commonly used Enrichment media (2):
1. Blood agar- blood added to a blood
agar base
a. Beta hemolysis- complete lysis
of rbc
b. Alpha hemolysis- incomplete
c. Gamma hemolysis- no
hemolysis
2. Chocolate agar- used for culture of
fastidious organisms; heat is applied
and will turn brown
3. Selective media- growth of only a
specific microorganism
a. Thayer-Martin agar-
antibiotics
b. Mannitol Salt agar- nacl
c. MacConkey’s agar- growth for
gram-
d. Lowenstein-Jensen medium-
recover mycobacterium
tuberculosis
e. Saboraud’s dextrose agar-
isolation of fungi
4. Differential media- growth of several
types of microorganisms; show visible
differences
5. Transport media- used for clinical
measurements; prevent the drying of
specimen
6. Anaerobic media- for organisms that
can’t survive presence of oxygen
Chapter 2: PROKARYOTIC AND EUKARYOTIC
CELLS
Living cells- prokaryotes and eukaryotes
Prokaryotes- no true nucleus and membrane-bound
organelle
Eukaryotes- possess true nucleus and membrane-bound
organelle
Check page 20 for table comparing prokaryotes and
eukaryotes*
MEDICALLY IMPORTANT MICROORGANISMS
 Viruses- acellular organism; possess either DNA
or RNA but never both; not a cell
Capsid- outer surface of viruses, which composed of
sub-units called capsomeres.
Viruses are classified by:
1. Type of Nucleic acid they possess
2. Shape of the capsid
3. Number of capsomeres
4. Size of the capsid
5. Presence or absence of an envelope
6. Type of host they infect
7. Type of disease they produce
8. Target cell or tropism
9. Immunologic or antigen properties
 Bacteriophages- special type of viruses that
primarily infect bacteria
 Bacteria- prokaryotic cells; possess nucleoid;
possess both DNA and RNA; uses CO2 as energy
source
 Fungi- outer surface composed mainly of chitin
 Protozoa- unicellular parasites
 Algae- plant-like organisms; capable of
photosynthesis
Diatoms- unicellular algae; both fresh and saltwater
Dinoflagellates- phytoplankton group; unicellular algae;
responsible for “red tide”; produce powerful neurotoxin
and responsible for potential fatal disease called
paralytic shellfish poisoning
Chapter 3: BACTERIAL MORPHOLOGY
Bacteria- prokaryotic; simpler structures than eukaryotic
Morphology of Bacteria (classification according to shapes)
1. Coccus/cocci(pl)- spherical/round-shaped organisms
(staphylococcus, streptococcus)
Can be arranged:
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 a. Singly  Periplasmic space- fluid-filled
b. Pairs (diplococci) space between outer membrane
c. Chains (streptococci) and inner plasma membrane
d. Clusters (staphylococci)
e. Tetrad- groups of 4
f. Octad- groups of 8 Acid-fast cell wall
2. Bacillus/bacilli(pl)- rod-shaped organisms
(Escheriachiacoli, Salmonella)  composed of mycolic acids- large amount of waxes
a. May be very short  Hydrophobic
b. Coccobacilli- resembling elongated cocci
3. Spiral-shaped or curved PROJECTING STRUCTURES
1. Flagella- thread-like structures; made up of
Vibrio cholera- causing cholera; comma-shaped; syphilis- protein and flagellin
causative agent Classification (4)
a. Monotrichous- single polar flagellum
Treponema pallidum- spiral
b. Laphotrichous- a tuft of flagella at the
end of bacterium
ENVELOPE STRUCTURE- protect bacteria from harsh c. Amphitrichous- flagella at both ends of
environment bacterium
d. Peritrichous- flagella all around the
1. Glycocalyx
bacterium
 Outermost layer covering
 Located to cell wall Atrichous- bacteria without flagella
 Gelatinous substance
2. Pili or Fimbriae- many gram-negative bacteria;
 Capsule- strongly attached to cell
fine and short; pilins- structural protein sub-
 Slime layer- loosely attached
units; for motility, attachment and to adhere to
 Protect from hydration
cell surface
2. Cell wall
 Murein sacculus- bacterial cell wall Conjugation- form of bacterial gene exchange (sex pili)
 Peptidoglycan
 Provides rigid support 3. Axial Filaments- also called endoflagella;
 Gives shape composed of bundles of fibrils
 Protects bacteria
 Role in cell division
 Multiple-layered in gram-positive, single-layered Cytoplasmic membrane- also called cell membrane/plasma
gram-negative membrane- located beneath cell wall, sometimes called call
sac; encloses cytoplasm; selectively permeable membrane
that allows transport of selected solutes
Components of gram-positive cell walls
INTERNAL STRUCTURES
 Teichoic acids- elicit antibody
1. Nucleoid- bacteria has no true nucleus, nucleoid ang
response; attachment
tawag sa material package na meron sila
 Polysaccharides- includes neutral
2. Mesosomes- functions for cell division; secretion of
sugars and acidic sugars
substances
Components of gram-negative cell walls 3. Ribosomes- function for protein synthesis; bacterial
ribosome is smaller (70S)
 Outer membrane- bilayered 4. Granules or Inclusion Bodies- found in certain
structure; composed of bacteria; serve for food storage and energy
lipopolysaccharide: allow passage 5. Endospores- produced when bacteria are placed in
of hydrophilic substances; lipid a- hostile environment
for endotoxin activity Dipicolinic acid- confers resistance to heat,
 Lipoprotein- anchors outer drying, chemical agents and radiation
membrane to peptidoglycan;
stabilizes outer membrane

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 Sporulation- process of spore production;
occurs when environment is harmful to
bacteria
Germination- process to return to
vegetative state
Chapter 4: BACTERIAL GROWTH
REQUIREMENTS
Growth- increase in sum of components of the organism
Microbial growth- increase in the number of cells and not the
size of the organism
NUTRITIONAL REQUIREMENTS
1. Carbon- structural backbone or skeleton of all
organic molecule
a. Autotrophs (lithotrophs)- utilize inorganic
compounds and inorganic salts
b. Heterotrophs (organotrophs)- make use of
organic substances
- Both derived energy from light
or oxidation of inorganic
substances
- Chemoorganotrophs- most
medically important bacteria
2. Nitrogen, Sulfur, Phosphorous- for synthesis of
cellular materials; nitrogen and sulphur- for
synthesis of proteins; nitrogen and phosphorous-
synthesis of nucleic acids and ATP
3. Inorganic Ions- magnesium, potassium, calcium, iron
and trace elements; serves as co-factor in the
activity of many enzyme
- Potassium- required for normal
functioning and integrity of
ribosomes
- Calcium- contributes to the
resistance of bacterial
endospores
- Iron- component of cytochrome-
component of the electron
transport chain
4. Growth Factors- includes vitamin B complex and
amino acids
PHYSICAL REQUIREMENTS
1. Moisture/Water- medium to acquire nutrients
2. Oxygen- used by aerobic bacterial for cellular
respiration
- Aerobes- w/ oxygen
- Anaerobes- w/o oxygen
- Obligate anaerobes- cannot
survive in the presence of
oxygen
- Facultative organisms- survive
under both aerobic and
anaerobic conditions; most
medically important
- Microaerophils- able to grow at
low oxygen pero nabawasan
buhay
- Capnophiles- kelangan mas
maraming oxygen to enhance
growth
5. Temperature- classifcations:
a. Thermophiles- grow higher than 40 degrees
C
b. Mesophile- optimal temperature 20-40;
most medically important bacteria
c. Psychrophiles- 10-20
6. Ph- extent of acidity or alkalinity
a. Alkalophiles- grow best at ph 8.4-9.0
b. Neutrophils- ph 6.5-7.5- most medically
important
c. Acidophiles- less than 6.0
7. Osmotic Conditions- salt concentration;
a. Halophiles- require high salt concentrations
for growth
b. Osmophiles- require high osmotic pressure
for optimal growth
BACTERIAL GROWTH- illustrate the phases in the growth of
the population of bacteria
1. Lag phase- period of adjustment in the new
environment; slow; increase in metabolic activity
2. Log/Logarithmic/Exponential Phase- rapid cell
division; increase in number of bacteria
3. Stationary Phase- period of equilibrium; maintain
4. Death or Decline Phase- death of cell
Chapter 5: NORMAL FLORA OF THE HUMAN
BODY
Microbial Ecology- study of relationship between
microoragnisms and their environment
Normal Flora- group of organisms that inhabit the body
TWO TYPES OF FLORA
• 1. RESIDENT FLORA- are microorganisms that are
always present on or in a person and usually do not
cause any disease. ... For instance, on the skin,
normal flora is made up of bacteria such as
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 staphylococci. In the mouth, bacteria called
streptococci can be found.

• 2. TRANSIENT FLORA- temporary skin flora refers to

the microorganisms that transiently colonise the
skin. This includes bacteria, fungi and viruses, which
reach the hands, for example, by direct skin-to-skin
contact or indirectly via objects

NORMAL FLORA ON DIFFERENT SITES OF THE BODY

1. Skin – mainly bacteria and fungi

STAPHYLOCOCCUS EPIDERMIS- Major skin inhabitant

approx. 90% of resident aerobic flora.

STAPHYLOCOCCUS AUREUS – Most commonly found in nose

and perineum.

MICROCOCCI – Accounts for 20-80% of micrococci in the skin.

DIPTHEROIDS (CORYNEFORMS)- classified in lipophilic

(common in axilla) or non-lipophilic ( hairless skin such as
palms of hands).

GRAM (-) BACILLI ( ENTEROBACTER, KLEBSIELLA, E. COLI,

AND PROTEUS SPP.) – Seen in moist intertriginous areas such
as toe webs and axilla.

NAIL FLORA – Similar to that of the skin

Fungi may also be present ( Aspergillus, Penicillium,

Cladosporium, Mucor).

2. Mouth and Respiratory Tract- streptococcus group:

S. mutans, S. milleri, S. salivaris,S. sanguis
3. Conjunctiva- flow of tears that contain lysosome
4. Digestive Tract
5. Genitourinary Tract

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