MICROBIOLOGY, PARASITOLOGY, PUBLIC HEALTH

 Microbiology
- Study of organisms that cannot be seen by the naked eye
 Parasitology
- Study of parasites
- Parasites: organisms that would acquire nutrients via intimate contact
 Public Health
- Art and science
 Preventing diseases
 Promoting life
 Promoting health and … via organized community effort

CHAPTER I: General Principles

I. Introduction
A. History
1. Robert Hooke
 Cell theory, prison cell
2. Anton Van Leuwenhoek
 First to visualize a living organism under the microscope (sperm cell)
 “animalcules”

Debate over spontaneous generation

3. Francesco Redi (opponent)
 Maggots in not covered container
4. John Needham (proponent)
 Nutrient bath  heat  cool  no cover : (+) maggots
5. Lazzaro Spallanzani (opponent)
 Cover  heat  cool  (-) maggots

Theory of Biogenesis
6. Rudolf Virchow
 Pre-existing living cells  organisms
 But no evidence
7. Louis Pasteur
 Microorganisms are present in the air but did not come from the air
 Formed the basis of “aseptic techniques”
 “Pasteurization”
» Home Pasteurization ≈ 63°C (30 min)
» High temp / Short time ≈ 72°C (15 sec)
» Ultra high temp ≈ 140°C (4 sec)
8. John Tyndall
 Tyndallization: intermittent sterilization

Golden Age of Microbiology

9. Benjamin Martin
 Book on Germ Theory of Disease: diseases are caused by germs
10. Robert Koch
 Discovered Bacillus anthracis (Anthrax) – used for bioterrorism
 Koch’s Postulates
i. Microorganisms are present in diseased individuals but absent in healthy ones.
ii. Microorganisms can be grown in pure culture
iii. … (when inoculated) obtained from the culture, when introduced to a healthy
diseased person that person can (?) have the disease
iv. Organisms from the diseased person can be grown into reisolate a pure culture in the
laboratory
  Exceptions:
» Typhoid Mary
 Salmonella typhi
 Carrier: carry the microorganism but carry the disease
 -oid: resembles typhus (typhus: Rickettsia spp.)
» Mycobacterium leprae
 Cannot be grown in pure culture
 Causative agent of leprosy
 Grow in Armadillo and mouse foot pad

B. Organisms of Medical Importance

1. Prokaryote vs Eukaryote
Prokaryote Eukaryote
“true nucleus”
membrane bound organelles
binary fission mitosis
bacteria fungi

2. Carl Woese: 3 Domains (?)

Eubacteria Archaebacteria Eukaryota
“true bacteria”
prokaryote prokaryote eukaryote
thick – thin peptidoglycan layer ???
(present in the cell wall)
 extreme thermophiles protists, fungi, plants,
(survive in extremely high animals, algae
temperature (heat loving)
 Halophiles (salt loving)
 Methanogens (generate
methane from CO2 and
H2O)

C. Microbial Growth
1. Stages of Microbial Growth
a. Lag phase
» There is no growth rate … but metabolically active
b. Log phase (exponential)
» (+) positive growth rate
» # of new > # of dying
» Cells are actively dividing
» Target of bactericidal agents (kill)
c. Stationary phase
» Ubos na ang nutrients
» No new organisms added
» # of new = # of dying
» Time when organisms can form spores
d. Decline phase
» (-) negative growth rate
» # of dying organisms > # of new organisms
 6

no. of vioable organisms

5
4
3
2
1
0
1 2 3 4 5
Time

2. Factors that will affect growth

a. Physical
i. Temperature
 Optimal temperature for organism to grow inside the body and cause disease:
37°C
 Danger Zone of Food: (6 - 40°C) temperature where organisms are more likely to
grow  spoil
psychrophile cold temperature
mesophile moderate
thermophile high temperature

ii. pH
 growth of organism (6.5 – 7.5) ≈ neutral
 exception: Fungi (5.5 – 6.5), relatively acidic
iii. Osmotic Pressure
 Osmosis: flow of water from region of high water concentration to low water
concentration
 Hypertonic – high salt concentration (outside); water will go out (shrink)

b. Chemical Factors
i. Carbon
 Carbon is the structural backbone of living matter
chemoheterotroph obtain carbon from multiple sources
- CHO (carbohydrates)
- CHON (proteins)
- lipids
chemoauto / photoautotroph source of carbon is carbon dioxide
(CO2)

ii. Oxygen
 Based on oxygen demand
 Oxygen –use metabolites (ROS): Reactive Oxygen Species
 ROS is toxic can kill organism
  Organisms have defenses against ROS – enzymes
 Enzymes against ROS
1. superoxide dismutase
2. peroxidase
3. catalase

Obligate PMNL Pseudomonas require oxygen (have

aerobes Mycobacteria superoxide dismutase,
Nocardia peroxidase, catalase)
Leptospira
Facultative Ec Eschirichia coli no oxygen 
anaerobes oxygen 
greater growth in the presence
of oxygen
Obligate ABC Actinomyces do not need oxygen they will
anaerobes Bacteriodes die in the presence of oxygen
Clostridium (no enzymes)
Aerotolorent LP Lactobacillus no oxygen 
Propionibacterium oxygen 
tolerate oxygen, deadma lang
Microaerophile S Treponema pallidum only require small amounts of
Borella spp. oxygen
(spirochetes)

except: Leptospira
enterogans (obligate
aerobe)

D. Control of Microbial Growth

1. History
 Semelweiss and Lister
» Homebirths vs hospital birth
» Hospital birth higher infection rate maybe because doctors perform autopsy before
assisting in delivery
» Credited for hand washing, introduced to decrease infection
 Lister
» Phenol or carbolic acid
» Method of antisepsis prior to surgery
2. Definition of Terms
 Sterilization
» Complete removal of microbes (ALL FORMS)
» Including the spores
 Microbial Cell Death
» Irreversible loos of the ability to reproduce
 Antiseptic
» “living thing”
» Animate object
 Disinfectant
» Inanimate object
» Decrease organisms to a level that will not cause disease
 Degerming
» Mechanical removal of organisms
» Ex. alcohol swab
 Sanitization
» Decrease number of organisms to a safe public health level
3. Physical Control
MOA
Heat denature proteins
Moist Heat ? autoclave
Dry Heat ? oven
Low Temperature bacteriostatic (static: retard)
Filtration for heat sensitive
HEPA Filter high efficiency particulate air
filter
remove > 0.3 μm organisms
Membrane Filter exception:
- Spirochetes
(Leptospira,
Treponema, Borella)
- Mycoplasma –
smallest free living
organism
High Pressure for preparation of liquid
(i.e. fruit juices)
Lyophilization / Freeze remove water / moisture but
Drying some organisms can still be
alive

Limitations
1. spore: can only be killed by
sterilization
2. molds: can survive low
moisture / low water
environment
Hypertonic Environment water goes  shrink
Radiation damage to the DNA
form “thymidine dimers”
Ionizing
Non – ionizing

4. Chemical Methods
a. Methods of Evaluation
i. Use dilution
 Microorganism in a chamber dip cylinder then dip cylinder in chemical
ii. Disk Diffusion
 Antibiotic disk, petri disk, zone of inhibition
b. Chemicals

Phenol / Carbolic acid  Previously considered as the most widely used

method of chemical control
 Became method of … “phenol coefficient”: compare a
certain chemical vs phenol

 Throat lozenges (phenol derivatives); local anesthetic

and antibacterial effects
 O – diphenyl phenol (active ingredient in Lysol©)
 Triclosan (soaps, kitchen ware handles)
Biguanides  Chlorhexidine: pre – operative procedures
Halogens  Chloride disinfectant: add H2O to produce
hypochlorous acid (disinfectant properties)
  Iodine antiseptic:
- Iodine tincture: solution of aqueous alcohol
- Iodophore: add organic compound; Povidone -
Iodine©
Alcohol  Replaced phenol, now the most widely used method
 Limitation:
- No activity vs spore; vs Clostridium spp.; vs
naked virus

 Ethanol ~ 70% (MOA: denaturation; require water for

the action to work)
 Isopropyl (more superior because it is less volatile
and less expensive)
Heavy Metals  “oligodynamic property”: ability to tract vs organisms
even in small quantities

 1% AgNO3 – prophylaxis ophthalmia nenonatorum

gonorrhea; replaced by erythromycin
 Silver coins
Soaps and Detergents  Surfactants: decrease surface tension between liquid
molecules

 Quaternary Ammonium Salts (Quats) vs g(+)

 Benzalkonium chloride
 Cetylpridinium chloride
Aldehyde  Formaldehyde: formalin (~37% formaldehyde),
preserve specimen
 Glutaraldehyde (Cidex©): for surgical instruments
Chemical Preservatives  Sorbic acid, Benzoic acid, Parabens
 Sodium Nitrate  nitrite: vs Clostridium botulinum;
impart red coloration
Ethylene oxide  Gas sterilization

Summary for all chemical

Membrane Disruption  Halogens
 Phenol
 Surfactants
Protein Denaturation  Alcohols
 Aldehydes
 Ethylene oxide (alkylation)
 Reducing … ??
 Oxidizing agent
 Quaternary Ammonium Compounds
(AEHOQ)

5. Trends of Resistance
 Prions
» Considered to be the most resistant
» Non cellular proteins that are infections
Kuru ingestion of brain tissue
(+) cerebellar symptoms
Scrapre “funny sheep”
Borna horses
Bovine Spongiform Encephalopathy mad cow
 Creutzfeldt – Jakob Disease neurodegenerative disorder similar to
Parkinsons

Compare:
 G(-) is more resistant, hospital acquired; G(+) more community acquired
 Naked is more resistant vs Enveloped

II. Methods of studying organisms

A. Microscope
1. Light
 Visible light
a. Lens
i. Simple (one lens)
ii. Compound (multiple lens)
b. Field
i. Bright field (background is lighter than specimen)
ii. Dark field (background is darker than specimen); for spirochetes
2. Electron
 Beam of electron
a. Scanning (SEM): 3D image
b. Transmission (TEM): 2D image
B. Stain
 Most stains are salts: (+) cation and (-) anion
 One of them is a chromophore (responsible for the color)
 If chromophore is:
 Anion  acidic stain
 Cation  basic stain
 Considering that bacteria is (-) charged  mostly basic stains are used (+)

Types
1. Simple
 Aqueous solution of a single dye
2. Compound
3. Differential
 Classify organisms based on their appearance

Examples
a. Gram stain: G(+), G(-)
b. Acid fast stain: CHAMBA
i. Carbol fuschin
ii. Heat
iii. Alcohol
iv. Methylene
v. Blue
vi. Acid – fast
 CHAMBA is the Ziehl – Neelsen Technique (!not a stain it is a technique that uses HEAT,
Z – zzissling)
 Kinyoun Technique (K – kold; no heat)

Special Stains
India ink / nigrosin capsule
Schaeffer – fulton spores
Malachite green spores
Carbolfuchsin flagella
 C. Culture
 GOLD STANDARD: for diagnosis  CULTURE of all infectious diseases
 Culture Medium: allows growth of the organism in the laboratory setting
 Patient  blood  culture medium  microorganisms Identify  Check if susceptible.
 If susceptible: (-) no growth; if resistant: (+) growth
 Agar
 Solidify the medium
 Inoculum
 Sample of organism

Types of Culture Medium

1. Chemically defined
 Known chemical composition
2. Complex with nutrients
 Solid nutrient agar, liquid nutrient broth
3. Reducing
 Anaerobes
 “candle jar method”
4. Selective
 Suppress the unwanted organisms and favor the desired
 i.e. SDA: Saboraud Dextrose Agar (for fungi only)
5. Differential
 Can classify organisms into groups
a. Lactose fermenter vs non lactose fermenter
i. McConkey Agar: (+) pink colonies
ii. Eosin Methylene Blue: (+) purple to black, (-) colorless
iii. Colistin – Nalidixic Acid: favor G(+) organism
b. Hemolytic Pattern
i. Blood Agar Plate
α green partial hemolysis
β clear complete
γ non hemolytic

6. Enriched
 Fortified with added nutrients
a. Lowenstein – Jensen (Mycobacterium tuberculosis)

III. Ecology and PH

A. Basic of Ecology
 Study of relationships between organisms
 Factors: agent, host, environment
 Ecologic Models: lever, wheel, web of causation

Definitions of Terms
1. Infections
 The presence of the organism in the body
 With or without clinical manifestation
2. Disease
 The presence of the organism in the body
 With clinical manifestation
3. Opportunistic infection
 Infection that will occur in immunocompromised (host) patients
 Ex. AIDS, cancer (chemo), patients with steroids (drug-induced), burn patients
 Fungal infections more common in immunocompromised host
4. Symbiosis
  Mutualism: both will benefit (E.c. and human intestine)
 Commensalism: one benefits but the other has no effect (Staphylococcus epidermidis)
 E. coli is part of the normal flora
 Normal Flora
» Bacterial residents of a particular part of a body which would not cause a disease
unless inoculated elsewhere
» Promote formation of Vitamin K
 Vitamin K – dependent clotting factor: 10, 9, 7, 2 (X, IX, VII, II)
B. Classification of Infectious Diseases
1. Based on Communicability
a. Communicable: may be transmitted from one person to another
 Contagious: rapidly transmitted from one person to another (ebola: direct contact, SARS:
respiratory)
b. Non communicable: cannot be transmitted from one person to another
2. Based on Occurrence
 Prevalence: new cases + old cases (cross sectional: survey --> prevalence)
 Incidence: new cases

a. Endemic: disease will occur in a particular place or particular group of people (Palawan:
malaria, Samar & Leyte: schistosomiasis, Mindoro & Bicol: filariasis)
b. Epidemic: the number of cases is greater than the expected frequency (based on a five
year data)
b.1. Common source: point (one source in a particular point in time), intermittent (not
always present), continuous
b.2. Propagated source: person to person
i.e. small pox: because one case greater than expected (eradicated)
c. Sporadic: erratic / irregular interval
d. Pandemic: worldwide
C. Natural History of Disease
1. Stages
 Susceptibility: risk factor
 Pre-clinical/Pre-symptomatic/Subclinical: pathologic changes
 Clinical / Symptomatic: organ changes (sign: objective/doctor, symptom: from
patient/subjective)
 Recovery / Disability / Death
2. Levels of Prevention
Primordial Decrease the General population Clean air act
occurrence of trends
associated with the
diesease
Primary Prevent the disease in a Susceptible Population a. Seminar on how to
well person sanitize water
a. Health promotion b. PPE
b. Specific measure
Vaccine for babies in
Asia (susceptible
population)
Secondary Early diagnosis and Asymptomatic SRI screening
treatment population
Disease screening
Tertiary Limitation of disease Asymptomatic Rehab
and disability population
Patient has been
operated and given
tamoxifen for breast
 cancer

3. Stages of Infectious Disease

Incubation Period Time from infection to symptoms

*important for observation

- Ebola (21 days)
- SARS (2 weeks)
Prodrome Symptomatic (mild)
Acme Symptomatic (full blown)
Peak
Decline Improvement
Outcome (Recovery/ Disability / Death) /
Convalescent

D. Spread of Infection
 Reservoir: continual source of the organism (zoonotic / animals, fomites / nonliving)
 Most common living reservoir: humans
 Transmission
CONTACT VEHICLE VECTOR
Direct Foodborne (S.a. food poisoning) Will transmit organism from one
host to another
Indirect Fomites i.e. malaria
Waterborne (cholera, Agent: Plasmodium spp.
leptospirosis) Vector: mosquito Anopheles
(female)

????

DROPLET AIRBORNE
can be ??? Measles, tuberculosis, varicella
(MTV)
Bigger than airborne Smaller than droplet
Will stay less than 1 min Will stay longer than 1 min
Ordinary face mask N95 mask

E. Nosocomial Infections (hospital acquired)

 "Health care associated infection" the term covers hospitals, nursing homes, dialysis center
 ESKAPE Pathogens: most common cause of nosocomial infections
1. Enterococcus faecium
2. Staphylococcus aureus
3. Klebsiella pneumoniae
4. Acinetobacter baumani
5. Pseudomonas aeruginosa
6. Enterobacter spp.
IV. Immunology and PH
A. Types of Immunity
Natural Present even before the infection
Innate

1st line of defense: skin / mucus

membrane
2nd line of defense: natural killer
cells (macrophage, dendritic
cells)
Acquired Activated in the presence of
Infection

3rd line: WBC/ leukocytes

Humoral Plasma cells --> antibodies (Ab)
Cell mediated T cells

Immunoglobulins
IgA Secretion CD4 + T cells : Class II 4×2=8
luhA, semilyA, gatas ng MHC
inA
IgE Ellergy CD8 + T cells : Class I 8x1=8
MHC

CD8 is directly cytotoxic

IgG PreGGy
IgM Malaki - biggest
Mauuna

 Acute infection / first line --> Maunang tumaas ang IgM

 Chronic --> IgG
B. History of Immunization
 Edward Jenner: smallpox and cowpox
 Vaccination : vaca, Variolation : variola virus

Naturally Acquired Artificially acquired

Active Passive Active Passive
Prior infection Pregnant Toxoid Ig administration
Vaccine (acTiVe)
Slow onset, long Fast onset, short
duration duration
Ex. Px bitten by dog: administer both toxoid and Ig

Types of vaccine
1. Live attenuated
 Weakened
 Mimic symptoms of an actual infection
 Fever when given
 Affected by circulating antibodies, NOT GIVEN IF PX IS < 6 months
 Exceptions
 Measles vaccine: can be give as early as 6 months in cases of outbreak
 Orally administered vaccines: i.e. OPV
 BCG: at birth; Bacillus-Calmette-Guerin; vs disseminated TB because it is endemic in the
Philippines
 *???* usually given in one dose: SQ, ID, oral, intranasal
2. Inactivated
 Less affected by circulating antibodies
 Can be given before 6 months ***why***
 Usually multiple doses (booster)
 IM
DPT Diphtheria, Pertussis, Tetanus Children because of higher risk
Tdap Tetanus, Diphtheria, Acellular Adult lower risk of diphtheria
pertussis
(All caps larger doses)
Hepa B vaccine
"Polysaccharide", "conjugated"
Pneumococcal conjugated
vaccine

EPI - Expanded Program on Immunization

B B H
ir C e
t G p
h
B
6 O P Pe
w P C nt
e V V av
e 1 ale
k 1 nt
s 1
1 O P Pe
0 P C nt
w V V av
e 2 ale
e 2 nt
k 2
s
1 O Pe
4 P nt
w V av
e 3 ale
e nt
k 3
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9 m
m e
o a
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12 months MMR
* Pentavalent:
1. Hep B
2. DPT
3. HiB (Haemophilus influenzae)
4. Rotavirus 1
5. Rotavirus 2

Rotavirus: cannot be given if baby > 30 weeks because they are at risk for introsusception /
telescoping (a part of the intestine goes into another part of the intestine)

V. PH Services
MACRO MICRO
planning implement action
asses needs provider to patient services
plan, develop strategies to assess needs program to population
1. Disease screening
2. Immunization
3. Counseling program for at risk patients
4. Tobacco cessation
(DICT)

CHAPTER II: Bacterial Infections and their Implications in Public Health

I. Introduction
A. Gram staining

G (+) G (-) Use

crystal violet violet violet Primary stain
Iodine violet violet Mordant
Alcohol violet colorless Decolorizing agent
Safranin violet red Counter stain /
secondary stain
VIAS

G (+) G (-)
Surface proteins, polysaccharide
Teichoic acid (antigenic Outer membrane
determinant) (contribute to antibiotic
i.e. M antigen (present in resistance)
Streptococcus pyogenes) 1. Somatic O-antigen
Forsman antigen (S. 2. Core polysaccharide
pneumoniae) 3. Lipid A (endotoxin
contribute to septic
shock)
Thick peptidoglycan layer Periplasmic space (contain Cell wall
lysozymes)
Trans peptidase (enzyme Thin peptidoglycan layer
that will promote cross
linking, target of cell wall
synthesis inhibitors)
CELL MEMBRANE

B. Bacterial Morphology
C. Virulence Factors
 D. Bacterial Genetics
E. Endotoxin and Exotoxin
II. G (+) cocci
A. Staphylococcus spp.
B. Streptococcus spp.
III. G (+) bacilli
A. Spore forming
B. Non spore forming
IV. G (-) cocci
A. N. meningitides
B. N. gonorrhea
V. G (-) bacilli
A. Enterics
B. Predominantly Respiratory Tract Infections
C. Zoonotic
D. Others
VI. Gram stain limitations
A. Spirochetes
B. Mycobacteria
C. Mycoplasma pneumonia
D. Rickettsia spp.
E. Chlamydia spp.

CHAPTER III: Antibiotics

I. Cell Wall Synthesis Inhibitors
A. Beta – lactams
II.

CHAPTER V: Mycology
I. Introduction
II. Skin / Cutaneous
A. Tinea corporis
B. Tinea cruris
C. Tinea pedis
D. Tinea capitis
E. Tinea unguium
F. Tinea imbritica
III. Superficial
A. Pityriasis versicolor