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MICROBIOLOGY REVIEWER 3. Combating diseases

• Etiology and epidemiology, control and
INTRODUCTION TO MICROBIOLOGY prevention
- Microorganisms cause diseases but
BACTERIUM can also be used to cure them
• The first living thing. 4. Industry and biotechnology
• First organism = blue-green algae. • Antibiotics and vaccines and other
• First parents of every living thing on pharmaceutical products.
Earth. • Genetic engineering
• Functions:
- Evolved to make oxygen and turned Comparative Sizes of Microorganisms
our world blue.
- Decompose Earth’s organic wastes
and clean up our mess.
- Protect our skin from invaders and
help us digest food.
- Eat our sewage and are an ingredient
in many foods.

MICROBIOLOGY
• Prokaryotes were the first living
organism.
• The study of all living organisms that are Microbial World
too small to be seen visible with the Bacteria
naked eye. • Cyanobacteria (Blue green algae)
- You need the aid of magnifying/lenses, - The first microorganism
microscopes, etc. - Prokaryotic
• An ancient biological science in which • Magnetotactic bacteria
identification and characterization of - Attracted to magnetic field
microorganisms and their interactions • Bacteria can be grown in liquid, solid,
with the surrounding environment are jelly-like environment
studied. Fungi
- Understand the physiology and • Uni-cellular
biochemistry of microorganisms. • Yeast and Molds
- Must know about the identification, - Unicellular fungi
characterization, form and structure, - Eukaryotic
interaction with the environment. - Another growth, another yeast cell
- Can be seen in bread, cheese, food
Why Microbiology Matters spoilage
1. Keeps the planet healthy • Mycosis – disease caused by fungi
• Play a major role in recycling essential • There are millions of species of fungi
elements Protists
2. Agriculture • Usually uni-cellular, but can also be
• Enable farmers to increase yield and multicellular in some cases.
productivity in a sustainable way. • Eukaryotic
- Even uses parasites to combat the • Protozoa
pests that might affect the crops.
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- May cause malabsorption and fatty Very simple Quite complicated,

diarrhea (appears bubbly) architecture, freely has a lot of
• Malarial Parasite loose nucleoids membrane-bound
- Young form looks like a ring organelles including
- Infects RBCs its nucleus, has a
- Can be seen in the human host nucleolus
Algae Some cells may not Should always be
• Eukaryotic be complete but can complete to function
Viruses still survive properly
• They are technically not Optional structures: Has no optional
microorganisms, because they are not Fimbriae, endospore, structures
cellular. flagella, pilus,
• Thrive on living cells for growth and plasmid (self-
survival replicating genetic
• Acellular material), capsule
• Bacterial Viruses Helmet-shaped, not
- Viruses attach and inject their genetic easily invaded by
material into the host cell (humans) immune cells since it
• Examples: COVID, SARS, Ebola, Dengue, is encapsulated
Rhodophites (Red algae), Escherichia Photosynthetic,
Coli, Salmonella (causes typhoid fever), disease-causing
Lactobacillus, Herpes, Streptococcus, Filamentous (forms
Becteriophage, Hepatitis B, Adenovirus, chain of cells),
Influenzaetc. Decomposes (feed
on the dead), Colony
Types of Microbial Cells (forms a film)

DIVISIONS AND TYPES OF MICROBES

PROKARYOTIC EUKARYOTIC
Both are cellular, has cell envelope, has a
cytoplasm, ribosomes, genetic material • Different ways of classifying microbes
Cells lack a true Cells have a • Because of the technology of molecular
membrane-delimited membrane-enclosed biology, different classification schemes
nucleus except nucleus, are more arise.
Planktomycetes complex Classification Schemes
morphologically • Three domain system based on a
comparison of ribosomal RNA genes,
divides microorganisms into:

- Bacteria (true bacteria)
- Archaea
- Eukarya (eukaryotes)
Cellular
• They live in extreme environments
• Fungi, Protists, Bacteria, Archaea
• Has BOTH DNA and RNA
Acellular
• Has no cell envelope and cytoplasm
• Only has genetic material (DNA only OR
RNA only)
• Viroids and Satellites – only has RNA
• Prions – used to be viruses but their
makeup is made up of protein only, may
cause encephalitis (makes your brain
look like a sponge)
• Viruses
Based on chemical and fossil evidences,
microbes are ancient and were the only
inhabitants of our planet for billions of years.
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Indications on the presence/impact of
microorganisms in the early history (B.C.)
• Fermentation is the oldest and most
popular technology used by humankind,
dating back to the Neolithic period. Its
exploitations was mostly used in dairy
products, baking, wine making, and
brewing.
- Used as a means of livelihood
- Only effective since there are
microorganisms involved
NOTABLE PERSONS
ANTONY VAN LEEUWENHOEK
• Universally recognized as the father of
microbiology
• Discovered both protists and bacteria
• He was the first with the power to see
using microscopes and he explored its
uses to feed his curiosity
• Simple microscope invented by him
- only has one type of lens, 3-4 inches
long, requires good lighting
- he used this to check the quality of his
textile

LOUIS PASTEUR
• Reverred by his successors in the life
sciences, as well as by the general
public.
• “Pasteurized”
• Microorganisms cause both
fermentation and disease which
supported the Germ Theory
• He created the first vaccine for fowl
cholera and major livestock diseases
which is used by humans in warfare.
ROBERT KOCH
• 1843-1910
• Invented the Koch’s Postulates
• Founder of modern bacteriology
• Father of bacteriology (as well as
Pasteur)
• Discovered the bacteria that causes
anthrax, septicemia, tuberculosis, and
cholera.
• His method served as a guide for others
to discover many other pathogens
• Anthrax disease
- Disease that killed a large number of
livestock and some humans
- Rod-shaped structures were observed
in blood of infected animals, but the
causes of this disease is still uncertain
• Koch’s Postulates
- Koch discovered bacilli in blood tissues
so he invented this postulate
FLORENCE NIGHTINGALE
• Was once to believe that diseases were
caused by a foul air
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• Over the course of her work, she
started to accept the new idea of germ
theory.
• Environmental theory
• “Always wash your hands after
handling a patient in order to eliminate
the germs that you might have
touched.”
NOTABLE EVENTS
The effects of penicillin on a bacterial lawn in a
petri dish
• Used in the discovery of antibiotics
- antibiotics came from microorganisms
• Penicillin inhibited bacterial growth:
mold (yung white part)
• When the bacteria grows and
encounters the chemicals/juices coming
from the mold, the growth is inhibited.
- The juice produced serves as the
antibiotic
Important events in microbiology
• 1665-1911
• 1900-2010

HISTORY OF MICROBIOLOGY
• Events caused by microorganisms are
already recognized
Development of ideas about microbes
• Germ theory of disease (relationship
between microbes and diseases of
plants, animals, and humans)
- Leeuwenhoek, Pasteur
• Controversy of spontaneous generation
• Immunology
- Where the idea of vaccination arise
• Microbial ecology (unique physiology,
enrichment culture)
• Industrial microbiology (fermentations,
pasteurization)
- Wine and meat
Development of tools used to study them
• Microscopes
• Culture techniques
• Molecular genetics
- DNA/RNA vaccines
• Genomics
Basic and applied microbiology
• Basic aspects are considered with
achieving a deeper understanding of
the workings of the microbial cell
- Microbial physiology
- Microbial ecology
- Genetics and molecular biology
- Taxonomy and systematics of various
groups of microbes
• Applied aspects are concerned with
practical problems
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• How do you address a particular issue
with the use of
microbiology/microorganisms
- Disease
- Water and food production
- Industrial microbiology
MAJOR FIELDS IN MICROBIOLOGY
• Medical microbiology
- diseases of humans and animals
• Public health microbiology
- control and spread of communicable
diseases
• Immunology
- how the immune system protects a
host from pathogens
• Microbial ecology
- relationship of organisms with their
environment
- less than 1% of earth’s microbial
population has been cultured
• Agricultural microbiology
- concerned with the impact of
microorganisms on agriculture
- food and safety microbiology
- animal and plant pathogens
• Industrial microbiology
- fermentation
- antibiotic production
- production of cheese, bread, etc
• Microbial physiology
- studies metabolic pathways of
microorganisms
• Molecular biology, microbial genetics,
and bioinformatics
- nature of genetic information and how
it regulates the development and
function of cells and organisms
- microbes are a model system of
genomics
Notes:
• Microbes are small, diverse, and ancient
• Microbiology is a field with a long
history
• The field continues to provide insights
and a greater understanding of the

world we can’t see with our eyes – even
today
• Microbiology, with all its aspects and
assets, will continue to lead to new and
useful scientific discoveries well into the
future
CHAPTER 14
INFECTION, INFECTIOUS DISEASES, AND
EPIDEMIOLOGY
EFFECT OF COLONIIZATION
• There must be an interaction between a
host and a microorganism and the
resulting relationship is called a
symbiotic relationship.
Colonization
• Persistent survival or presence of
microorganism on a surface of the host
Symbiosis
Mutualism • Persistent survival or
presence of
microorganism on a
surface of the host.
• Both symbionts benefit
from the interaction.
• Ex: Bacteria in your
colon receive a warm,
moist, nutrient-rich
environment in which to
thrive, while you absorb
vitamin precursors and
other nutrients released
by the bacteria.
Commensalism • Host provides shelter
and food.
• One symbiont benefits
while the other is not
affected significantly.
Amensalism • One symbiont is harmed
by a second symbiont,
while the second
symbiont is neither
harmed nor helped by
the first.
• Not a part of the
infectious diseases
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paradigm because the
host involved is usually
humans sa paradigm.
• Ex: The fungus
penicillium produces
penicillin, which inhibits
nearby bacteria, but the
bacteria have no effect
on the fungus.
- Yung microorganism na
nasa petridish, there
was a mold then merong
bacteria, parang walang
naggrown na bacteria
near the mold because it
means that it grows a
bacteria inhibitor which
protects itself. The
symbiont is the mold.
They host is not helped.
Walang benefit sa
penicillium yung
pagkakainhibit ng
growth ng bacteria.
Parasitism • Unilateral benefit
causing damage.
• One partner benefits at
the expense of the
other.
• The core of infectious
disease process.
• Host is damaged,
microorganism benefits.
• Members of a symbiotic relationship are
called symbionts.
• Symbiosis = “to live together”
• We have symbiotic relationships with
countless microorganisms.
• Refers to an intimate relationship
between two organisms.
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of the urethra and microorganisms,

- Degree of harm to the host is high in vagina elimination by the
parasitism and low in commensalism and body’s defense
mutualism. cells, and by the
- Benefit to the two species is high in chemical or
commensalism and mutualism than in physical changes in
parasitism. the body.
Pathogen
• An organism that can cause an infection The Normal Flora
with normal host defenses. • Fetus in the womb is free of
Commensals microorganisms
• An organism that is found normally on • Acquired during and shortly after birth
those parts of the body. and changes continuously throughout
Opportunists life.
• An organism that can cause infection in • Beneficial to the host
individuals. - Colonization resistance
- Encountered when our system is down. - Release of bacteriocin and colicin to
- We encounter this everyday but we prevent pathogen growth
don’t get sick from them because we have o -E. coli is one of the
very good immune system. predominating normal flora
especially in the gut.
SYMBIOTIC RELATIONSHIPS BETWEEN - Vitamin K production in the gut
MICROBES AND THEIR HOSTS o Benefits the host
Normal microbiota in hosts - Continued antigenic stimulation from
• Organisms that colonize the body’s commensals
surfaces without normally causing disease o Has its protection
• Also termed “normal flora” and • Changes in the normal flora
“indigenous microbiota” - Variation in the hormonal cycle
• Even though many parts are anexic - Effects of antibiotics
environments, other parts of your body - May be acquired
shelter trillions of mutualistic and - Ex: neonate from maternal genital
commensal symbionts (normal flora and tract during birth
microbiota). - The main factor determining the main
- anexic environment: site free of composition of the normal for the body
microbes region is the nature of the local
TWO TYPES OF MICROBIOTA environment which is determined by
RESIDENT TRANSIENT the age, temperature, redox potential,
• Remain a part of • Remain in the body oxygen, water, nutrient levels,
the microbiome for in a short period of variations in the hormonal cycle,
most of a person’s time peristalsis, enzyme secretion
life. • Found in the same (lysozymes), effects of antibiotics,
• Found on the skin regions as resident secretion of immunoglobulins play roles
and on the mucus microbiota in flora control.
membranes of the • Cannot persist on • Disadvantages
digestive tract, the body because - Escape of normal flora to abnormal
upper respiratory of competition sites
tract, distal portion from other
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o Normal flora becomes a

pathogen
o Ex. In surgery, the colon was cut
accidentally, essentially there
will be escape of normal flora
usually going to sterile sites
which become pathogens.
- Alteration in the gut flora by misuse of
antibiotics
• The normal flora in humans usually
develop in an orderly sequence or
succession after birth, leading to a • All found externally:
stable population of bacteria that - Normal flora are found mostly:
makeup the normal adult flora. o On the skin
• Bacterial colonization of the baby o In the eyes
usually occurs by acquisition of o In the nose
maternal genital flora. o In the mouth
• Colonization of the neonate’s skin, eyes, o In the upper throat
mucous membranes, and umbilical cord o In the lower urethra
occurs during vaginal birth, whereas o In the lower intestine
babies born by cesarean section are o Especially in the large intestine
relatively sterile in the first hours after - This list basically includes all of the
birth. body surfaces exposed to the external
• The importance of the presence of the environment.
normal flora is colonization resistance
because of space competition. Reservoirs of Infectious Diseases of Humans
- You don’t have anymore space for the • Most pathogens cannot survive for long
potential pathogen to occupy. outside their host that’s why you have
reservoir of infections.
How Normal Microbiota Become Opportunistic • Reservoirs of infection
Pathogens - Site where pathogens are maintained
• Opportunistic Pathogens as a source of infection
- Normal microbiota that cause disease THREE TYPES OF RESERVOIRS
under certain circumstances HUMAN CARRIERS • Asymptomatic
• Conditions that provide opportunities infected
for pathogens individuals can be
- Introduction of normal microbiota into infective to others
unusual site in the body • Some individuals
- Immune suppression eventually
- Changes in the normal microbiota develop illness
o May be due to hormonal whereas others
changes never get sick.
o Changes in relative abundance • Healthy carriers
may allow opportunity for a may have
member to thrive and cause defensive systems
disease that protect them.
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NONLIVING • Soil, water, and OUTCOME OF THE HOST-MICROBE

RESERVOIRS food can be INTERACTION IN THE CONTEXT OF THE
reservoirs of DAMAGE/INFECTIOUS DISEASE FRAMEWORK
infection
• Presence of
microorganisms is
often due to
contamination by
feces or urine
ANIMAL RESERVOIRS • These
microorganisms
stay in animal
reservoirs to
cause zoonotic
infections.
• Zoonoses –
diseases that THE INFECTIOUS DISEASE PARADIGM
naturally spread • Double-headed arrows: Indicate
from animal host conditions where there may be variable
to humans amounts of damage.
• Acquire zoonoses • Single-headed arrows indicate the ff:
through various - A:
routes: o Acquisition of a microbe can be
-Direct contact followed by elimination through
with animal or its physical defenses or immune
waste mechanisms.
- Consumption of - B:
animals o Acquisition of certain microbes
- Bloodsucking results in damage and disease
arthropods in certain hosts.
• Humans are - C:
usually dead-end o Certain commensal microbes
host to zoonotic can cause disease if the state of
pathogens commensalism is disturbed by
• Difficult to immune impairment or
eradicate alterations of the host microbial
flora
o Ex: C. albicans can cause
pharyngeal candidiasis and
vaginal candidiasis in the
settings of immune suppression
and antibiotic use respectively
- D:
o The state of colonization may
be terminated by an immune
response

o Ex: Transient nasopharyngeal
carriage of N. meningiditis or S.
pneumoniae.
o The trigger for the immune
response is not well understood
but may occur after the damage
threshold is reached.
- E:
o The state of colonization may
lead to disease if sufficient
damage ensues from the
interaction.
o The damage may be host-
mediated, pathogen-mediated,
or both.
- F:
o The state of colonization may
lead to a state of persistence
(chronicity and latency),
whereby the immune response
is unable to eradicate the
infection despite continued
damage
o Ex: Latent M. tuberculosis or
Histoplasma capsulatum
infection in tissue granuloma
- G:
o An immune response or
therapy may eradicate the
infection but this does not
always terminate disease,
because the damage may be
irreversible (Ex: poliomyelitis)
o Or continue through
immunological mechanisms (Ex:
reactive arthropathies)
- H:
o If sufficient damage is incurred
as a result of the host-microbe
interaction, death ensues.
- I:
o Persistent infections may
reactivate and cause overt
disease
o Ex: Reactivation tuberculosis
Trivia:
• It was believed that if you step on a
rusty nail, you might get lockjaw.
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• When nails are manufactured, it comes
with a thin film of oil which prevents
them from rusting. If the nail lays on the
ground for an extended period of time,
the oil is washed away and the nail
rusts. The rusty nail was contaminated
with spores from various animal wastes.
That’s why the horse died after 9
months after stepping on a rusty nail.
• Clostridium tetani: Bacteria that causes
tetanus
• You need to have tetanus shots inorder
to prevent infection.
THE INVASION AND ESTABLISHMENT OF
MICROBES IN HOSTS: INFECTION
PORTALS OF ENTRY
Sites through which pathogens enter the body
THREE MAJOR PATHWAYS (ENTERAL)
SKIN • Outer layer of dead skin cells
act as a barrier to pathogens.
- Our external defense
• Some pathogens can enter
through openings or cuts.
- Paper cut can cause your part
to be inflamed but they won’t
lead to serious infections.
• Others enter by burrowing into
or digesting outer layers of
skin.
- Going deep into the layers of
the skin usually your nematode
(??) parasites.
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• Through the skin by needle (subcutaneous,

intramuscular, or intravenous route (ex.
most vaccines); by patch (transdermal; ex.
skin tests), or implantation

MUCOUS • Lines the body cavities that are

MEMBRANES open to the environment
• Provides a moist, warm Why do certain bacteria cause disease?
environment hospitable to
pathogens.
• Respiratory tract is the most
common site of entry
- Entry is through nose, mouth,
or eyes
• Gastrointestinal tract may be a
route of entry
- Microbe/pathogen must
survive the acidic pH of the
stomach (a natural defense)
PLACENTA • Typically forms effective barrier
to pathogens
• Pathogens may cross the • Infection enters and establishes itself
placenta and infect the fetus in an area and colonizes.
- Can cause spontaneous • Infections may not necessarily mean
abortion, birth defects, that it develops to a disease.
premature birth • They cause disease because they
compete with the normal flora and
inhibit the toxic enzymes produced by
the E. coli in the normal flora.
• They colonize habitats which makes
them pathogenic. They have
structures that makes them adhere to
an area thereby natural defenses are
not effective.
PARENTERAL ROUTE • They have virulence factors which
• Entry via the parenteral route circumvents causes the diseases.
the usual portals.
• Not a true portal of entry The Role of Adhesion in Infection
• Means by which portals of entry can be • Attachment proteins help in adhesion
circumvented - They have structures that would
• Pathogens are deposited into tissues make them attach to an area.
beneath the skin or mucous membranes

• Interaction can determine host cell
specificity
- If you have a genital disease, they
attach to the host of the genital area.
You cannot find this genital disease in
respiratory areas because of the
specificity,
- Found on viruses and many bacteria
- Viral or bacterial ligands (anchors)
binds to host cell receptors
• Changing/blocking a ligand or its
receptor can prevent infection
• Inability to make attachment proteins
or adhesins renders microorganisms
avirulent
- Removing a virulence factor
• Some bacterial pathogens attach to
each other to form a biofilm
- Biofilm: A layer of bacteria which has
a capsule
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- Ligand anchors in a specific center. Sakto yung
ligand sa sugar molecule ng host cell. There is
specificity.
- E. coli attaches to the mucous membrane of
the intestine.
ADHESION
• Process by which microorganisms
attach themselves to cells
• Required to successfully establish
colonies within the host
• Uses adhesion factors
- Specialized structure > capsule, pili.
Fimbriae, attachment proteins
Virulence Factors that Promote Colonization
and Invasion
• Adhesins
- Surface proteins in the bacterial cell
wall
- Bind to receptor molecules on the
surface of a susceptible host cell
enabling the bacterium to make
intimate contact with the host cell,
adhere, colonize, and resist flushing.
• Urinating
- In a way, a form of natural defense
mechanism
- Washes out bacteria
- But for those bacteria with fimbriae, it
may be difficult to be washed out
because of adherence to the lining,
therefore UTI results.
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- The flushing effect of the urine is a • Asymptomatic, or subclinical, infections

natural defense. It washes out possible may lack symptoms but may still have
bacteria but not all. signs of infection.
Terminology of Diseases
THE NATURE OF INFECTIOUS DISEASES
• First, there should be an interaction
before infection.
• Infection is the invasion of the host by a
pathogen.
• Disease results if the invading pathogen
alters normal body functions.
• Disease is also referred to as morbidity
(incidence/prevalence).
• Mortality
- death rate or number of deaths in a
certain period of time.
- may be reported for people who have
certain disease, live in one area of the - Ex: When you say that a compound is
country, or who are of a certain gender, teratogenic, it means that it can cause
age, or ethnic group. birth defects.
- Ex: carcinogenic = can give rise to
Typical Manifestations of Disease cancer
Causation of Disease: Etiology
• Study of the cause of the disease
• Etiology = the causative agent
• Diseases have various causes

- When it develops to a disease,

nagkakaroon ng layover yung pathogen,
when it starts to populate (start of
symptoms, signs, syndromes) - Koch’s postulates are used to know
• Symptoms the etiologic relationships usually
- Subjective characteristics of disease investigated in the lab.
felt only by the patient. - Koch’s postulate is not the same
• Signs practice until today because hindi lang
- Objective manifestations of disease animals yung involved, humans are
observed or measured by others. involved narin.
• Syndrome
- Symptoms and signs that characterize
a disease or abnormal condition.
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Categories of Diseases o Extracellular enzymes

o Toxins
o Antiphagocytic factors
Extracellular Enzymes
• Secreted by pathogens
• Dissolve structural chemicals in the
body
• Help pathogen maintains infection,
invade, and avoid body defenses
• Important to virulence of the pathogen
- Mutant species that do not secrete the
enzymes are often avirulent.

Koch’s Postulates - May intact na cellular matrix but

because of the hyaluronidase, it
dissolves so that the pathogens can
easily infect the cells.
Toxins
• Toxemia refers to the presence of
toxins in the bloodstream.

• These are chemicals that harm tissues

or trigger host immune responses that
cause damage.
• Toxins are carried beyond the site of
infection.
Virulence Factors of Infectious Agents
• Pathogenicity TWO TYPES OF TOXINS
- Ability of a microorganism to cause EXOTOXINS ENDOTOXINS
disease Usually heat labile Heat stable
• Virulence proteins secreted lipopolysaccharide-
- Degree of pathogenicity by certain species protein complexes
- Virulence Factors contribute to of bacteria which which form
virulence: diffuse into the structural
o Adhesion factors components of cell
o Biofilms
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surrounding wall of Gram - Leukocidins directly destroy

medium. Negative Bacteria phagocytic WBCs
- Released when and liberated only
bacterial cells are on cell lysis or The Stages of Infectious Diseases
destroyed. death of bacteria. • The disease process occurs following
infection
• Many infectious diseases have five
stages following infection
- Incubation period
o No signs or symptoms
- Prodromal period
o Vague, general symptoms
- Illness
o Most severe signs and symptoms
Antiphagocytic Factors o When the bacteria populates
• Factors that prevent phagocytosis by - Decline
the host’s phagocytic cells. o Declining signs and symptoms
• Allow pathogens to remain in a host for o When you have already taken
a longer time. antibiotics/treatments to
• Phagocytosis is a process wherein a cell address the symptoms.
binds to the item it wants to engulf on Nagsslow down yung
the cell surface and draws the item pagpopulate ng bacteria.
inward while engulfing around it. - Covalescence
- Allows pathogens to remain in a host o No signs or symptoms
for longer time. o There may still be pathogen
residues.
o When the pathogen becomes
reactivates, you will feel
symptoms again.

- The bacteria will be digested by the

lysozyme. Then it will eventually die.
But because of antiphagocytic factors, it
can cause capsule blocking
phagocytosis. Di niya makakain yung
bacteria kung encapsulated. Incubation Periods of Selected Infectious
• Bacterial capsule Diseases
- Composed of chemicals not
recognized as foreign
- Slippery and difficult for phagocytes to
engulf
• Antiphagocytic chemicals
- Prevent fusion of lysosome and
phagocytic vesicles
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The Movement of Pathogens Out of Hosts: INDIRECT CONTACT

PORTALS OF EXIT • Drinking glasses, Common cold,
• Pathogens leave host through portals of toothbrushes, toys, enterovirus
exit punctures infections,
• Many portals of exit are the same as • Pathogens are spread from influenza,
portals of entry host to host by fomites measles, Q
• Pathogens often leave hosts in fever,
materials the body secretes or excretes pneumonia,
tetanus

MODES OF TRANSMISSION

CONTACT TRANSMISSION
DIRECT CONTACT
• Handshaking, kissing, Cutaneous
sexual intercourse, bites anthrax,
• Usually involves body genital warts,
contact between hosts gonorrhea,
• Transmission w/in a herpes,
single individual can also rabies,
occur staphylococcal
infections, DROPLET TRANSMISSION
syphilis • Droplets from sneezing Whooping
Ex: Direct Fecal-Oral Transmission w/in 1 meter cough,
• Spread of pathogens in streptococcal
droplets of mucus by pharyngitis
exhaling, coughing, and (strepthroat)
sneezing.
• Humans produce droplets
in various ways (sneeze,
cough, sing) and they vary
in size.
- Large droplets
o > 5 µm
o Comprise
most of the
volume of
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expelled • Healthy people can inhale

respirator the infectious droplet
droplets and nuclei into their lungs.
they tend to
fall rapidly to
the ground
o Ex: COVID-
19 (an
enveloped
virus)
- Small droplets
o < 5 µm
o Referred to as droplet
nuclei VEHICLE TRANSMISSIONS
o May remain AIRBORNE
suspended in the air • Dust particles or droplets Chicken pox,
for significant carried more than 1 coccidiodomy-
periods of time and meter via aerosols cosis,
move with air • Aerosols can occur from histoplasmosis,
currents. various activities. influenza,
• Occurs when bacteria or • Ex: sneezing, coughing, measles,
viruses travel on relatively aircon, sweeping pulmonary
large respiratory droplets anthrax, TB
that people sneeze, cough,
or exhale.
• Travel only on short
distances (usually less
than 2 meters) before
settling.
• Droplets may be loaded
with infectious particles
and can infect another
person if the
bacteria/viruses contact
their eyes, nose, or
mouth.
• May also fall on surfaces
and be transferred onto
someone’s hands when WATERBORNE
they rub their eyes, nose, • Streams, swimming Camylobacter
or mouth. pools infections,
• Occurs when a bacteria or • Important in the spread cholera, Giardia
viruses travel in droplet of many diarrhea,
nuclei that become gastrointestinal leptospirosis,
aerosolized. diseases, as well as shigellosis
fecal oral infection
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• Bodily fluid transmission:

- Bodily fluids such as blood, urine,
saliva can carry pathogens
- Prevent contact with conjunctiva or
breaks in the skin or mucous
membranes

VECTOR TRANSMISSION
MECHANICAL
Bodies of flies, roaches E. coli diarrhea,
salmonellosis,
trachoma
FOODBORNE
• Poultry, seafood, meat Food poisoning
• Spread of pathogens in (botulism,
and on foods staphylococcal),
• Inadequately processed, heap A,
cooked, or refrigerated listeriosis,
foods tapeworms,
• Foods may become toxoplasmosis, BIOLOGICAL
contaminated with feces typhoid fever, Lice, mites, mosquitoes, Chagas’ disease,
• Ingestion of paralytic ticks Lyme disease,
contaminated food. shellfish malaria, plague,
poisoning, Rocky mountain
aflatoxins spotted fever,
typhus fever,
yellow fever

Portals of Entry
• Many organisms that cause one disease
if they enter one body sites are
harmless if they enter another
• Ex: various enteric urinary-tract
pathogens.
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Classification of Infectious Diseases
• Taxonomic categories
• The body system they affect
• Their longevity and severity
- Acute (short term), chronic (long term)
• How they are spread to their host
- Contagious, local (one area only),
systemic (whole body)
• The effects that have on populations
•
•
EPIDEMIOLOGY OF INFECTIOUS DISEASE
Frequency of Disease
• Epidemiologists track occurrence of
diseases using two measures

• Incidence
- Number of new cases of a disease in a
given area during a given period of
time.
- Includes backlogs
• Prevalence
- Number of total cases of a disease in a
given area during a given period of
time.
• Occurrence also evaluated in terms of
frequency and geographic distribution.
Epidemiology
• The study of how often diseases occur
in different groups of people and why.
• Epidemiological information is used to
plan and evaluate strategies to prevent
illnesses and as a guide to the
management of patients in whom
disease has already developed.
• Key feature: Measurement of disease
outcomes in relation to a population at
risk.
• Population at risk: Group of people,
healthy or sick, who would be counted
as cases if they had the disease being
studied.
Sporadic
Endemic
Hyperendemic Refers to persistent, high
Epidemic
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• Baseline/Endemic Level of Disease
- Amount of particular disease that is
usually present in a community
- This level is not necessarily the desired
level, which may in fact be zero, but
rather is the observed level.
- In the absence of intervention, and
assuming that the level is not high
enough to deplete the pool of
susceptible persons, the disease may
continue to occur at this level
indefinitely.
- The expected level of the disease.
• While some diseases are so rare in a
given population that a single case
warrants an epidemiologic investigation
(ex. rabies, plague, polio), other
diseases occur more commonly so that
deviations from the norm warrant
investigation.
MEASURES
Refers to a disease that
occurs infrequently and
irregularly.
Refers to the constant
presence and/or usual
prevalence of disease or
infectious agent in a
population within a
geographic area.
levels of disease
occurrence.
Refers to an increase, often
sudden, in the number of
cases of a disease above
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what is normally expected

in that population in that
area.
Outbreak Carries the same definition
of epidemic but is often
used for a more limited
geographic area.
Cluster refers to an
aggregation of cases
grouped in place and time
that are suspected to be
greater than the number - Cases (like those who can be prevented by
expected, even though the vaccines) are needed to be reported since it
expected number may not concerns worldwide.
be known.
Pandemic An epidemic that has spread Epidemiological Studies
over several countries or Descriptive Epidemiology
continents, usually affecting • Carefully tabulate data concerning a
a large number of people. disease
- Record location and time of the case
• Epidemics occur when an agent and of disease
susceptible hosts are present in - Collect patient information
adequate numbers, and the agent can • Try to identify the index case of the
be effectively conveyed from a source disease
to the susceptible hosts. • All about addressing the health issue of
concern, who are involved, which place,
time patterns
• 5 Ws
- What: health issue of concern
- Who: person
- Where: place
- When: time
- Why/how: causes, risk factors, modes
of transmission
• Covers time, place, and person
• More specifically, an epidemic may • Compiling and analyzing data by time,
result from: place, and person is desirable for
- A recent increase in amount or several reasons.
virulence of the agent
- The recent introduction of the agent
into a setting where it has not been
before
- An enhanced mode of transmission so
that more susceptible persons are
exposed
- A change in the susceptibility of the
host response to the agent
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• Steps: • Mainly categorized as experimental and

1. By looking at the data carefully, the observational studies.
epidemiologist becomes very familiar • Conducted to obtain a relationship
with the data. He or she can see what between different exposures to the
the data can or cannot reveal based on disease condition and to obtain its
the variables available, its limitations outcome in a measurable manner.
(for example, the number of records • Incorporates a comparison group in its
with missing information for each study designs.
important variable), and its
eccentricities (for example, all cases
range in age from 2 months to 6 years,
plus one 17-year-old.).
2. The epidemiologist learns the extent
and pattern of the public health
problem being investigated — which
months, which neighborhoods, and
which groups of people have the most
and least cases.
3. The epidemiologist creates a detailed
description of the health of a
population that can be easily
communicated with tables, graphs, and TWO TYPES
maps. Experimental Observational
4. The epidemiologist can identify areas • Include clinical and • Divided into 4 more
or groups within the population that community trials. types:
have high rates of disease. This • May be used to 1. Cohort
information in turn provides important study the effects of - More useful when
clues to the causes of the disease, and new drugs or the study
these clues can be turned into testable vaccines, though population is well
hypotheses. observational defined, exposure is
analytic studies of uncommon, or if
Analytical Epidemiology drugs are also there are several
• You employ an intervention. performed, after possible outcome
• Seeks to determine the probable cause, drugs or vaccines from the exposure.
mode of transmission, and methods of are licensed. 2. Case-Control
prevention - May be more
• Useful in situations when Koch's useful when the
postulates can't be applied study population is
• Categorized as experimental and not well defined, if
observational the disease is
• Often retrospective relatively rare, or if
- Investigation occurs after an outbreak there are many
has occurred. possible exposures
• Mainly concerned with finding the for a disease.
causes of the infection or the disease to - Are always
identify the interventions of the retrospective.
disease. 3. Cross-sectional
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- Aka prevalence
- Look at individual
exposures and
conditions at the
same time.
4. Ecologic
- Look at individual
exposures and
conditions at the
same time, but at
the community
level.
*3 and 4 look for
the same kind of
relationship that
might be shown by
an analytic study,
but often cost less.
Endogenous Pathogen arises from
Experimental Epidemiology normal microbiota as a
• Test a hypothesis concerning the cause result of factors within the
of a disease. healthcare setting.
• Apply Koch’s postulates. From normal flora, naging
• Outbreak analytics: A developing data pathogenic
science for informing the response to
emerging pathogens.

Iatrogenic Results from modern

medical procedures.
- Dun pa nagkasakit lalo.
Hospital Epidemiology Superinfections Use of antimicrobial drugs
• Healthcare associated (nosocomial) reduces competition from
infections some resident microbiota,
Types of Healthcare Associated Infections allowing other microbes to
(HAIs) thrive.
Exogenous Pathogen acquired from
the healthcare • Control of healthcare associated
environment. infections.
- Requires aggressive control measures.
- Handwashing is the most effective way
to reduce HAIs.

Antibiotic Resistance
- A mix of these gives you hospital-acquired
infections.
Epidemiology and Public Health
Sharing of data among public health
organizations
• Agencies at the local, state, national,
and global level share information
concerning disease.
- The US Public Health Service
o National Public Health Agency
o CDC
- World Health Organization (WHO)
o Coordinates public health
efforts worldwide
- Department of Health (DOH)
• Public health agencies work to limit
disease transmission
- Enforce standards of water and food
safety
- Work to reduce disease vectors and
reservoirs
- Establish and enforce immunization
schedules
- Locate and treat individuals exposed
to contagious pathogens
- Establish isolation and quarantine
measures
- Their role is to interrupt disease
transmission
• Public health education
- Public health agencies campaign to
educate the public on healthful choices
to limit disease.
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• Must be monitored to prevent
superinfections.
• Mutations that confer antibiotic resistance
to bacteria are evolutionarily ancient and
widespread in nature, having arisen in
response to selection pressures that
predate human activity.
• These resistance mechanisms have found a
permissive niche in the modern hospital
environment, where a high density of
susceptible patients, intense selection
pressure for antibiotic resistance, and
manifold opportunities for transmission
intersect.
• Antimicrobial resistance rates are highest in
ICUs because of antibiotic overuse,
imperfect isolation practices, and prolonged
stays of patients who are highly susceptible
to nosocomial infections because of
comorbidities and the use of indwelling
devices, such as endotracheal and
nasogastric tubes, urinary catheters, and
central venous catheters.
• The clonal spread of resistant organisms
among geographically distant regions has
added further momentum to the explosive
rise in antibiotic resistance in recent years.
• This global spread of antimicrobial
resistance is fueled by poor hygiene and
common use of over-the-counter antibiotics
in developing countries, veterinary practices
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that overuse antibiotics, and the frequency

of international travel.

Preventing Nosocomial Infections

• Hand disinfection is the most important

infection control measure.
- Alcohol/wash hands

• Examples of info campaign for public

health