OVERVIEW: THE SCIENCE OF MICROBIOLOGY, CELL

STRUCTURE & CLASSIFICATION OF BACTERIA

Microorganisms
● Refer to organisms that exist as single cells or cell clusters
● It also includes viruses, which are MICROSCOPIC but not
cellular
● Also known as MICROBES

Microbiology
● mikros – “small” + bios – “life” + logia – “study of”
● Refers to the scientific study of microbes

FOUNDATION OF MICROBIOLOGY

Microbes – What comes to mind? VIRUS

● Diseases ● Lack many of the attributes of the cells (i.e. ability to
● Infections replicate)
● Epidemics ● Vary in diameter from 15 to 300 nm
● Food Spoilage ● Reproduction can be acquired only after infecting another
cell
★ Only 1% of all known bacteria cause human diseases ● Host-virus interactions
★ 95% of known bacteria are non-pathogenic ● Differ from other microbes in at least two ways:
A. Simple and acellular (obligate intracellular
Benefits to humans: parasites)
● Bacteria are primary decomposers. B. Absence of both DNA and RNA in the same virion
● They recycle nutrients back into the environment (sewage
treatment plants) ● Virophages
● Microbes produce various food products (fermentation): ● Viruses that infect other viruses
cheese, pickles, sauerkraut, green olives, yogurt, soy ● Highly specific
sauce, vinegar, bread beer, wine, alcohol
● Generally small and consist of:
★ Microbes are used to produce antibiotics ● Nucleic acid molecule ─ Either DNA or RNA
● Ilosome (Erythromycin) ● Capsid
○ Protein coat that encloses the nucleic acid
★ Bacteria synthesize chemicals that our body needs but molecule
cannot synthesize. ○ Sometimes enveloped by lipids, proteins and
● Vitamin B (for neural development) carbohydrates
● Vitamin K ○ Proteins (frequently glycoproteins) determine
specificity of host-virus interaction
★ Recombinant DNA Technology ○ Protects the nucleic acid
● Gene Therapy ○ Facilitates attachment and penetration by the
● Genetic Engineering virus

★ Bacteria can be manipulated to produce enzymes and

proteins they normally would not produce
● Insulin – genetically derived
● Human Growth Hormone
● Interferon-antiviral proteins given to patients with
chronic hepatitis

★ Can carry out photosynthesis more than plants can

perform

___________________________________________

Cell Theory
1. All living organisms are composed of one or more cells.
2. The cell is the basic unit of structure and organization in
organisms.
3. Cells arise from pre-existing cells.

★ Viruses are not living organisms because they do

not follow the cell theory (they are not cellular).
REMEMBER: cells are the basic structural unit of
all organisms; all cells come from pre-existing
cells
CLASSIFICATION OF MICROBES
Hierarchical Levels of Taxonomy
● Genus - consists of species that differ from each other in
certain ways but are related by descent
● Species - group of closely related organisms that breed
among themselves
★ Note: of these ranks, the family, genus, and
species are most useful.
● Binomial nomenclature - uses the genus and species
names to identify each creature.
Three Domain of Life PROKARYOTE VS EUKARYOTE
● Bacteria
● Archaea
● Eukarya PROKARYOTE EUKARYOTE

Nuclear Absent Present

DOMAIN EXAMPLES Membrane (nucleoid) (nucleus)

Domain Eukarya ● Animals Nucleoli Absent Present

(Eukaryotic) ● Fungi
● Protozoans Site of ribosome Cytosol Nucleoli
● Helminths production

Domain Bacteria ● Bacteria Presence of Absent Present

(Prokaryotic) membrane-bound
organelles
Domain Archaea ● Contains organisms that can
live in extreme environments; Number of 1 >1
Not medically important chromosomes

Site of ATP Cellular Mitochondria /

production membrane Chloroplast

Presence of Present Absent

peptidoglycan
layer

OVERVIEW OF THE CELLULAR MICROBES

DOMAIN DOMAIN DOMAIN

EUKARYA BACTERIA ARCHAEA

Fungi Bacteria “Living on the

Multicellular, Unicellular, edge” organisms
eukaryotes prokaryotes residence in
extreme
Helminths environments
TERM DEFINITION Multicellular,
eukaryotes Not medically
Prokaryotes ● pro – “before” + karyote – “nucleus” important
● Domain Bacteria, Archaea Protozoans
Unicellular,
Eukaryotes ● eu – “true” + karyote – “nucleus” eukaryotes
● Domain Eukarya
 CLASSIFICATION REMARKS

Bacteria ● Unicellular
● Has cell wall formed by
peptidoglycan layers –
except Mycoplasma
● Has both DNA & RNA

Fungi ● Multicellular
● Has cell wall formed by chitin
● Has both DNA & RNA

Protozoan ● Unicellular
● Absence of cell wall
● Has both DNA & RNA

Helminth ● Multicellular B. Selective Media

● Absence of cell wall ● used to eliminate large numbers of irrelevant
● Has both DNA & RNA bacteria in specimens
● From Kingdom Animalia ● Incorporation of an inhibitory agent that
specifically selects against the growth of
Arthropod ● Multicellular irrelevant bacteria
● Has both DNA & RNA
● From Kingdom Animalia Examples:
➔ MacConkey agar - contains bile that
secretes for the Enterobacteriaceae
CELLULAR MICROBES
● With true nucleus
● Contain membrane-bound organelles, microtubules, and ➔ CNA blood agar - selects Staphylococci and
microfilaments Streptococci; contains Colistin and Nalidixic
● Taxonomic groupings based on shared morphologic Acid, gram-positive bacteria
properties

❖ Algae
● all organisms that produce oxygen as a product of
photosynthesis
● Many are unicellular while some may form large
multicellular structures

❖ Protozoans
- unicellular, non-photosynthetic, with three forms:
● Flagellates (flagella) – resemble algae and
May not have chloroplasts
● Amoeboids (pseudopodia)
● Ciliated (cilia)
● Sporozoa (non-motile)

❖ Fungi
● non-photosynthetic, grow as a mass of branching,
interlacing filaments (“hyphae”)
○ mycelium
C. Differential media
● Evolutionary offshoot of protozoa
● some bacteria produce characteristic
● The mycelial forms are called molds, while the
pigments upon culture while bacteria can be
non-mycelial / unicellular forms are called yeasts.
differentiated on the basis of their complement
of extracellular enzymes
● Enzyme activity detected as zones of clearing
CLASSIFICATION OF BACTERIA
surrounding colonies grown in the presence of
insoluble substrates
Criterion for Classification of Bacteria
● Formulated to display a color change when
1. Culture Media
the growing of bacteria metabolizes an
A. Nonselective Media
ingredient
● support the growth of many different bacteria to
● Ex. Agar in a medium with RBC
cultivate as many species as possible
● Give rise to numerous bacteria colonies
● Ex. Blood agar and chocolate agar
 CLASSIFICATION OF BACTERIA

2. Bacterial Microscopy
● divides bacteria on the basis of fundamental
differences in the structure of their cell walls

❖ Gram Staining
● gram's method, also called Gram's method, is a
method of staining used to distinguish and classify
bacterial species into two large groups: gram-positive
bacteria and gram-negative bacteria.

HIGHLIGHTS IN THE HISTORY OF MICROBIOLOGY

HISTORICAL CONTRIBUTION
FIGURE

Elie Metchnikoff ● Discovered the process of

STEP PROCEDURES REAGENT phagocytosis
● Nobel Prize in Physiology or
1 Primary Stain Crystal Violet Medicine 1908

2 Mordant Iodine Robert Koch ● Established experimental steps

for directly linking a specific
3 Decolorizing agent Alcohol/acetone microbe to a specific disease

4 Counterstain Safranin Louis Pasteur ● Disproved the theory of

spontaneous generation or
abiogenesis – the hypothetical
process by which living
organisms develop from
nonliving matter
● Developed the first vaccine
against rabies
● Developed pasteurization

Joseph Lister ● Performed surgery using aseptic

conditions using phenol

Anton Van ● Discovered animalcules under

Leeuwenhoek the light microscope
● Credited as the first person to
see microbes

Koch’s Postulates
1. The microbe must be found in diseased but not
GRAM (+) VS GRAM (-) healthy individuals
2. The microbe must be cultured from the diseased
individual
COMPONENT GRAM (+) GRAM (-) 3. The cultured microbe should cause disease when
CELLS CELLS introduced into a healthy organism
4. The microbe must be reisolated from the inoculated,
Peptidoglycan Thicker; Thinner diseased experimental host and identified as being
multilayer identical to the original specific causative agent

Teichoic acids Yes No

Lipopolysaccharides No Yes

Periplasmic space No or small Yes

 METHODS OF MICROBIAL CONTROL PHYSICAL AGENTS USED IN DISINFECTION

METHOD DEFINITION EXAMPLE Flash pasteurization ● Heating milk at 72 Celsius

for 15 seconds → rapid
Sterilization Destroys or Autoclaving cooling
eliminating ALL ● Sufficient to kill the
forms of microbial Exposure to vegetative cells of
life, including ethylene milk-borne pathogens (e.g.
bacterial spores oxide gas (for Mycobacterium Bovis,
surgical Salmonella, Streptococcus,
instruments) Listeria, Brucella), but not to
sterilize milk
Filtration (for most
IV solutions) UV light ● Greatest antimicrobial
activity is achieved at 250 to
Disinfection Eliminates many or Application of 260 nm
all pathogenic rubbing ● For disinfection of air in the
microorganisms, alcohol – to OR
except bacterial inanimate objects
spores, X Rays ● More powerful than UV light
on inanimate ● Cannot sterilize due to the
objects lower amount of water in
spores
Antisepsis Refers to the Preoperative skin
application of prep
CHEMICAL AGENTS USED IN DISINFECTION
chemicals on the
surface of the skin Hand rubbing
and mucous Chlorhexidine ● To disinfect the surgeon’s
membranes hand prior to surgery.

Sanitization Reducing microbial Heating cutlery Iodophor ● To disinfect surgical site

contamination to an (e.g. at KFC!) prior to surgery
acceptable “safe”
level (terminology 70% ethanol ● To disinfect skin prior to
used in food safety) venipuncture or
immunization
Degerming Physical removal of Handwashing with ● To disinfect stethoscope
or Cleaning microorganisms by soap and running
using such things water Thimerosal ● Used as a preservative in
as soaps or vaccines
detergents
Hydrogen peroxide ● To cleanse wounds
STERILIZATION TECHNIQUES
Hypochlorite (bleach) ● To cleanup blood spill
from a patient with
Autoclaving ● Exposure to steam (moist heat) hepatitis B, hepatitis C or
at 121 Celsius under a HIV
pressure of 15 lb/in2 for 15-20
minutes Benzalkonium chloride ● To disinfect floor of OR

Ethylene oxide ● Gas used in hospitals for the

gas sterilization of heat-sensitive
materials (e.g. surgical
instruments and plastics)
Glutaraldehyde ● Chemical used to sterilize
respiratory therapy equipment,
endoscopes, and hemodialysis
equipment
Filtration ● Use of filter composed of
nitrocellulose with pore size of
0.22 mm
● Preferred method of sterilizing
solutions (with heat-sensitive
components)
BACTERIAL STRUCTURE
Bacterial Shape and Size
Three shapes:
1. cocci (spheres)
Arrangement of Cocci:
● pairs (diplococci)
● chains (streptococci)
● clusters (staphylococci)
● sarcina (eight-membered cocci formation)

Sterilization by ● Uses dry heat at 180 Celsius for

dry heat 2 hours
● Primarily used for glassware

2. bacilli (rods)
 3. spirochetes (spirals)
● Leptospira Mycoplasma No cell wall NONE
● Treponema Very small (SEROLOGIES)
● Borreliella (the new name of Borrelia since 2019)
Arrangement of Spirochetes: Chlamydiae Intracellular GIEMSA STAIN
❖ Vibrio → INCLUSION
❖ Spirillum Lacks classic BODIES
❖ Spirochete peptidoglycan
because of ↓
SHAPES OF BACTERIA muramic acid

Bacterial Cell Wall Legionella Poor uptake of red SILVER STAIN

● All bacteria have a cell wall composed of peptidoglycan counterstain
except Mycoplasma
● Peptidoglycan = sugar backbone (glycan) + peptide side Intracellular
chains (peptido) cross-linked by transpeptidase

COMPONENTS OF BACTERIA

Essential
● Refers to structures the bacterium cannot live without.
● It is inherited from the parents via the chromosome itself
by binary fission.
● Vertical transfer

Non-essential
● Acquired from genetic mobile elements via special genetic
transfers (e.g. conjugation, transduction,
transformation)
● Horizontal transfer
BACTERIAL STAINING ● Makes the bacteria more virulent

NAME REMARKS
ESSENTIAL COMPONENTS OF BACTERIA
Giemsa stain ● Rickettsia, Chlamydia,
Trypanosomes, Plasmodium, COMPONENTS DESCRIPTION FUNCTION
Borrelia, Helicobacter pylori
Cell Wall As described previously
Periodic ● Stains glycogen,
acid-Schiff mucopolysaccharides Cytoplasmic Lipoprotein bilayer Site of oxidative and
(PAS) stain ● Used to diagnose Whipple disease membrane ETC enzymes
(Tropheryma whipplei)
● PAS the sugar (glycogen) Ribosome RNA and protein Protein synthesis

India Ink stain ● Uses negative staining Nucleoid DNA Genetic material
technique
● Cryptococcus neoformans Mesosome Invagination of Participates in cell
plasma division and
Mucicarmine ● It directly stains the thick membrane secretion
stain polysaccharide capsule of
Cryptococcus neoformans with a Periplasm Space between Contains many
red the plasma hydrolytic
membrane and enzymes, including
Silver stain ● Coccidioides, Pneumocystis outer beta-lactamase
jirovecii, Legionella, membrane
Helicobacter pylori

Fluorescent ● Used to identify bacteria, viruses,

antibody stain P. jirovecii, Giardia lamblia,
Cryptosporidium
● FTA-ABS for syphilis

Bacteria NOT seen in Gram Stain

NAME REASON ALTERNATIVE

APPROACH

Mycobacteriae Too much mycolic ACID-FAST

acid (lipid) in cell STAIN
wall so dye cannot
penetrate Positive - red
Negative - blue

Spirochetes Too thin to see DARK FIELD

MICROSCOPY
 NON-ESSENTIAL COMPONENTS OF BACTERIA

COMPONENT FUNCTION

Capsule Protects against phagocytosis

Pilus or fimbria Attachment (ordinary pili)

Conjugation (sex pili)

Glycocalyx Mediates adherence to surfaces

→ biofilms

Flagellum Motility

Spore Resistance to heat, and chemicals

Plasmid Genes for antibiotic resistance and

toxins

Capsules
● All bacterial capsules are composed of polysaccharide
EXCEPT Bacillus anthracis BACTERIAL GROWTH
● Bacterial growth is a coordinated process of increase in
❖ Spore individual cell mass and size and duplication of the
● formed by gram-positive rods, especially chromosome, followed by cell division
Bacillus and Clostridium spp ● Bacterial reproduction occurs via binary fission

Plasmids BACTERIAL GROWTH CYCLE

● Extrachromosomal, double-stranded, circular DNA is
capable of replicating independently of the bacterial
chromosome. PHASE REMARKS
● Can sometimes be integrated into the bacterial
chromosome → called episomes PHASE I: ● Phase during which vigorous
LAG PHASE metabolic activity occurs, but
Significance of Plasmids cells do not divide
● Antibiotic resistance ● Can last for minutes up to hours
● Resistance to heavy metals ● Zero growth rate
● Resistance to UV light
● Exotoxins and several enterotoxins. PHASE II: ● When rapid cell division occurs
● Bacteriocins – toxic proteins produced by certain LOG OR ● b-lactam antibiotics are most
bacteria that are lethal for other bacteria. EXPONENTIAL efficacious during this phase
PHASE

PHASE III: ● Occurs when nutrition depletion

STATIONARY or toxic products cause growth to
PHASE slow until the number of new cells
produced balances the number of
cells that die
● When bacterial spores are
formed
● Zero growth rate

PHASE IV: ● Marked by a decline in the

DEATH PHASE number of viable bacteria
● Negative growth rate
 BACTERIAL OXYGEN METABOLISM

Aerobic and Anaerobic Growth

● oxygen metabolism generates toxic products such as
superoxide and hydrogen peroxide
● superoxide dismutase, peroxidase, and catalase are
needed to survive in aerobic environments

CULTIVATION OF MICROORGANISMS

Aerobic Metabolism Bacterial Nutrition

● Obligate Aerobes ● Water constitutes 80% of the total weight of bacterial cells.
○ completely dependent on oxygen for ATP-generation ● Proteins, polysaccharides, lipids, nucleic acids,
muropeptides, and low molecular weight compounds
● Microaerophiles make up the remaining 20%
○ use fermentation but can tolerate low amounts of ● For growth and multiplication, the minimum nutritional
oxygen because they have Superoxide dismutase requirements are:
(SOD) ○ water
○ source of carbon
Anaerobic Metabolism ○ a source of nitrogen
● Facultative Aerobes ○ some inorganic salts
○ utilize oxygen if it is present, but can use ● Desiccation is important to eliminate bacteria
fermentation in its absence
TERMS:
● Aerotolerant Anaerobes
○ exclusively anaerobic but insensitive to the presence ❖ Culture Medium – nutrient material prepared for the
of oxygen growth of microorganisms in a laboratory

● Obligate Anaerobes ❖ Inoculum – microbes that are introduced into a culture

○ cannot grow in the presence of oxygen because they medium to initiate growth
lack SOD, peroxidase, and catalase.
❖ Culture – the microbes that grow and multiply in or on a
culture medium

❖ Batch culture – if many of them are inoculated at the

same time

★ The medium must be sterile – must initially contain no

living microorganism

❖ Nutrient agar – default medium of choice

❖ Peptone and Beef extract – primary sources of protein
❖ NaCl – provide ions
❖ Agar – complex upon which all is suspended, upon
solidification, then add water
Types of Plating
● For urine – single streaking all the
time
● For blood and other body fluids –
quadrant streaking
● Aims to isolate bacterial cells that
can be characterized.

Culture in tubes – agar slant or agar broth

● Strictly aerobes – streak on surface
● Anaerobes – stab

Plating Method
➔ Pour Plate Method
➔ Spread Plate Method

❖ Pour Plate Method

● Start inoculum, place agar, swirl, and allow the agar
to harden
● Inoculum dies if the agar is too hot. If too cold, NORMAL FLORA
impossible to pour ● Refer to microbes that are permanent residents of the
body
● Advantages: gives more even lawn ● Normal flora are low-virulence organisms in their usual
● Disadvantages: requires universal bottles of agar at anatomic site
just the right temperature
❖ Resident microbiota
❖ Spread Plate Method ➢ Microbes regularly found in a given area of the body
● Use L-rod after inoculum introduction, spread evenly at a given time
and place agar
❖ Transient microbiota
● Advantage: easier to do ➢ are nonpathogenic or potentially pathogenic
● Disadvantage: may give an uneven lawn microbes that inhabit the skin or mucous membranes
for hours, days, or weeks

BACTERIAL GENETICS ❖ Colonization resistance

➔ DNA transfer between bacterial cells: ➢ occurs when normal flora occupy receptor sites
preventing pathogens from binding

Skin Staphylococcus epidermidis

Nose Staphylococcus aureus

Mouth Viridans Streptococci

A bacteriophage is a type of virus that infects bacteria. In
Dental plaque Streptococcus mutans
fact, the word "bacteriophage" literally means "bacteria
eater," because bacteriophages destroy their host cells.
Colon Bacteroides, Escherichia coli
Bifidobacteria – dominant intestinal
microbiota in among breastfed children

Vagina Lactobacillus vaginalis

Escherichia coli
Streptococcus agalactiae

★ NSVD infants harbor bacterial communities (in all body

habitats) that are most similar in composition to the
vaginal community of their mothers.

VIRAL REPLICATION ★ CS-delivered infants lack bacteria from the vaginal

2 cycles:
❖ Lytic Cycle
➢ The lytic cycle involves the reproduction of viruses
using a host cell to manufacture more viruses; the
viruses then burst out of the cell.
❖ Lysogenic Cycle
➢ The lysogenic cycle involves the incorporation of the
viral genome into the host cell genome, infecting it
from within.
community (eg. Lactobacillus, Prevotella, Atopobium,
Sneathia spp) instead, harbor bacterial communities most
similar to the skin communities of the mother.
★ Viridans streptococci become established as the most
prominent resident flora within 4-12 h after birth and
remain so for life.
How are Dental Caries produced?
- Involves genetic, hormonal, and nutritional Influences
1. Plaque formation – an essential first step in caries
production
2. Acid formation – in large amounts and processed by
Streptococci and Lactobacilli from carbohydrates
● Streptococcus mutans – is considered the
dominant organism for the initiation of caries
OVERVIEW OF IMMUNOLOGY
● Study of the immune system & immune responses
● Deals with host defense reactions to foreign (non-self)
entities known as antigens
● Deals with antibodies & cell-mediated host defense
functions
● WBC of the immune system derive from precursors in the
bone marrow

In all, there are thought to be 300–400 bacterial species ❖ Immune System

present in mature dental plaque. ➢ considered to be a specific host defense mechanism
(springs into action to defend against a specific
How are caries controlled? pathogen) that has gained entrance to the body
➢ Physical removal of the plaque
➢ Limit sucrose intake ❖ Immunity
➢ Good nutrition (adequate protein intake) ➢ condition that permits innate and acquired resistance
➢ Reduce acid in the mouth (limit CHO, cleansing) to disease
➢ Fluoride – enhances acid resistance of the enamel
Primary Function
★ Control of periodontal disease: remove calcified ● Differentiate between self & non-self
deposits and good mouth hygiene. ● Destroy which is non-self

Stomach MAJOR ARMS

● Acidic pH
○ Low bacterial content
○ Only H. pylori present – located on the epithelial
side of gastric mucosa
○ Protects against infection of some enteric pathogens
(Vibrio cholera)
● Pyloric obstruction favor growth of gram-positive cocci and
bacilli
● Increase in pH (towards alkalinity) cause a great increase
in microbial flora (including fecal microbes)
1. Humoral Immunity
● “Antibody-Mediated Immunity”
● Always involves the production of antibodies in
response to antigen (Antibodies play a major role in
humoral immunity)
● After Production – circulating antibodies remain in
blood plasma, lymph, & other body secretions where
they protect against the specific pathogens that
stimulate their production
● A person is immune to a particular pathogen
because of the presence of specific protective
antibodies that are effective against that pathogen

2. Cell-Mediated Immunity
● Involves various cell types, including macrophages,
T- Helper cells, cytotoxic T cells, delayed
hypersensitivity T cells, NK cells, and
granulocytes
● Immune responses – the significant result is to make
a person resistant to certain infectious diseases
● When resistant – one is said to be immune

Intestinal bacteria play a role in IMMUNE RESPONSE

● Vitamin K synthesis
● Conversion of bile pigments and bile acids
● Absorption of nutrients and breakdown products (not
always protective, ie. ammonia)
● Antagonism of microbial pathogen
❖ Innate Immunity
➢ Non-Adaptive; Natural
➢ Preexisting
➢ Not acquired through contact with Antigen
➢ Non-specific immunity
➢ Characterized by physiologic barriers to entry of
pathogenic organism
➢ Includes barriers to infectious agents such as skin &
mucous membranes, phagocytic cells, inflammatory
mediators & complement components
➢ 1st and 2nd line of defenses
➢ Very fast host defense response
➢ Immediate response to a pathogen that does not
confer to long-lasting immunity.
➢ Response may vary with age and with hormonal or
metabolic activity

❖ Adaptive Immunity
➢ Acquired
NORMALLY STERILE AREAS ➢ After exposure to Ag (the infectious agent)
❖ Cerebrospinal fluid ➢ Highly specific
❖ Blood ➢ Mediated either by Abs or lymphoid cells
❖ Middle ear (small bones — the hammer (malleus), anvil ➢ Can be antibody-mediated (humoral), cell-mediated
(incus) and stirrup (stapes)) (cellular), or both.
❖ Paranasal sinuses ➢ Has immunologic memory and can respond rapidly
❖ Tissues and vigorously to a second antigen exposure.
❖ Bladder ➢ 3rd line of defense
❖ Uterus ➢ 2 Types: Passive & Active
❖ Fallopian tubes
❖ Passive Immunity
➢ Transmitted by Antibodies or lymphocytes performed
in another host
➢ Excess antitoxin to neutralize the toxins
➢ Limit microorganism multiplication during the
incubation period
➢ Advantage: Prompt availability of large amounts of
antibody
➢ Disadvantage: Short half-life, hypersensitivity
reaction
➢ Examples: Rabies, hepatitis A & B, DPT
1. Natural passive acquired immunity
➔ acquired by a fetus when it receives maternal
Abs in utero or by an infant when it receives
maternal Abs contained in colostrums.
2. Artificial passive acquired immunity
➔ acquired when a person receives Abs
contained in antiserum or gamma globulin
❖ Active Immunity
➢ Induced after contact w/ foreign antigens
(microorganisms or their products)
➢ Consist clinical/subclinical infection
➢ Immunization w/ live or killed infectious agents or
their antigens
➢ Exposure to microbial products (toxins, toxoids)
➢ Transplantation of foreign cells
➢ Advantage: Long-term protection, capacity to
respond faster
➢ Disadvantage: Slow onset, need for prolonged or
repeated contact w/ the Ag
1. Natural active acquired immunity
➔ acquired in response to the entry of a live
pathogen into the body (i.e. in response to an
actual infection) – protective Abs
2. Artificial active acquired immunity
➔ acquired in response to vaccines
VACCINE
● Material that can artificially include immunity to an
infectious disease, usually after injection or ingestion of
the material
● A person is deliberately exposed to a harmless version of
a pathogen (toxin), w/c will stimulate the person’s immune
system to produce protective antibodies & memory cells,
but will not cause disease in the person
● The person’s immune system is primed to mount a strong
protective response should the actual pathogen be
encountered in the future
★ IDEAL VACCINE:
● Contains enough antigenic determinants to stimulate
the immune system to produce protective antibodies
● Contains antigenic determinants from all the strains
of the pathogen that cause the disease (Multivalent
or Polyvalent)
● Few or no side effects
● Does not cause disease in the vaccinated person
TYPES OF VACCINES
1. Live Attenuated Vaccine
● Avirulent (non-pathogenic) mutant strains of
pathogens that have been derived from the virulent
(pathogenic) organisms
● Growing for many generations under various
conditions or by exposing them to mutagenic
chemicals or radiation
● Should not be administered to
immunosuppressed individual
● Even weakened pathogens can cause disease in
these persons
● Adenovirus, chickenpox (varicella), measles, mumps,
german measles, polio, rotavirus, smallpox, yellow
fever
● BCG, cholera, typhoid fever (oral vaccine)
2. Inactivated Vaccine
● Made from pathogens that have been killed by heat
or chemicals
● Can be produced faster and more easily
● Less effective than live vaccines
● Antigens on the dead cells are usually less effective
and produce a shorter period of immunity
● Hep A, flu, Jap B, polio, rabies
● Anthrax, typhoid fever (subcutaneous vaccine)
3. Subunit Vaccine (Acellular Vaccine)
● Uses antigenic (antibody-stimulating) portions of a
pathogen
● Pili of N. gonorrhoeae
● Genes that code for hep B surface protein →
proteins are injected into people
● Hep B, Pertussis (whooping cough)
4. Conjugate Vaccine
● Conjugate bacterial capsular antigens (by
themselves are not antigenic) to molecules that
stimulate the immune system to produce Abs against
the less antigenic capsular antigens
● Hib, meningococcal meningitis, pneumococcal
pneumonia
5. Toxoid Vaccines
● Toxoid - exotoxin that has been inactivated by heat
or chemicals
● Injected safely to stimulate the production of antigens
that are capable of neutralizing the exotoxin of
pathogens
● Antitoxins – antibodies that neutralize toxins
● Antiserum – serum containing antitoxins
● Diphtheria, tetanus, and botulism
6. DNA or Gene Vaccine
● experimental, using lab animals
● Particular gene from a pathogen and inserted into
plasmids. Plasmids injected ID or IM, go inside the
host cells, and genes direct the synthesis of a
particular microbial protein (Ag). Copies are
produced then the body produces Abs directed
against the protein. Abs protect the person from
infection w/ the pathogen
● Malarial parasite antigen.

7. Autogenous Vaccine
2ND LINE OF DEFENSE
● Prepared from bacteria isolated from a localized
infection (staph boil) → pathogens are killed &
1. Reticuloendothelial Cells
injected into the same person to induce the
● Mononuclear phagocytic cells
production of more antibodies
● Blood, lymphoid tissues, liver, spleen, BM, lungs
● Kupffer cells, macrophages
● Filtering microorganisms from the blood

2. Phagocytosis
● Migration, chemotaxis, ingestion & microbial killing
● PMN (granulocytes), phagocytic monocytes
(macrophages), fixed macrophages
● Stimulated to release cytokines that cause the
recruitment of more phagocytic cells to the site of
infection.

○ OUTCOME:
- kill ingested microorganisms
- permit their prolonged survival
- permit intracellular multiplication

3. Natural Killer Cells

● Role in antibody-dependent cellular cytotoxicity
(ADCC)
● Resemble large, granular lymphocytes
● Do not express antigen-specific receptors
● Lyse target cells that have undergone malignant
transformation
INNATE IMMUNOLOGIC MECHANISM ● Role in immune surveillance against tumor
establishment
PHYSIOLOGIC BARRIER AT THE PORTAL OF ENTRY ● Kill certain virus-infected cells
(1ST LINE OF DEFENSE)
➔ First line of defense
➔ Epithelial tissues that cover the whole surface of the body: ADAPTIVE IMMUNOLOGIC MECHANISM
● Acquired
A. Skin ● Innate immune response sets the scene for induction of
● Sweat & sebaceous secretions adaptive immune response
● Contain lysozyme – dissolves bacterial cell walls ● Has the capacity for long-term immunity
● Tears, respiratory & cervical secretions ● Key features: specificity & memory
● Cells involved: B lymphocytes, T lymphocytes
B. Mucous Membranes ● Humoral vs cellular immune response
● Respiratory – mucus/cilia/phagocytes
● GIT – saliva /acid pH/enzymes/phagocytes Antigen
● Normal Flora – oppose the establishment of ● molecules that stimulate the immune system to produce
pathogenic microorganisms antibodies
● After entering tissues, many pathogens are
recognized, ingested, & killed by phagocytes Features that determine IMMUNOGENICITY:
➔ Foreignness (difference from “self”)
Intrinsic Epithelial Barriers to Infection: ➔ Molecular size: MW less than 10,000 are weakly
1. Mechanical immunogenic
● Epithelial cells joined by tight junctions ➔ Chemical & structural complexity
● Longitudinal flow of air or fluid across epithelium ➔ Antigenic determinants (epitope) – smallest unit that is
● Movement of mucus by cilia capable of binding an Ab
➔ Dosage, route & timing of Ag administration
2. Chemical
● Fatty acids (skin)
● Enzymes: lysozyme (saliva, sweat, tears), pepsin CELLULAR BASIS OF THE IMMUNE RESPONSE
(gut)
● Low pH (stomach) B Lymphocytes
● Antibacterial peptides; defensins (skin, gut), cryptids ● Lymphocytes produced in the bone marrow
(intestine) ● Display Immunoglobulin (Ig) molecules on their surface →
serve as receptors for a specific Ag
3. Microbiological ● Surface receptors for the Fc portion of Ig & for several
● Normal flora compete for nutrients and attachment to complement components
the epithelium and can produce antibacterial ● Activated by an encounter w/ Ag to become Ab-secreting
substances. plasma cells
 Antibody
T Lymphocytes ● Proteins produced by the immune system in response to
● are lymphocytes produced in the bone marrow but antigen
require maturation in the thymus. ● Immunoglobulins (Ig)
● Utilized to activate B cells & to cope w/ intracellular ● IgG, IgA, IgM, IgE &IgD
pathogens
● They transform in the thymus to form T-cell subclasses
with specific functions

Cytotoxic T cells
● T cytotoxic cells, Tc cells & CD8+ cells Hypersensitivity Reaction
● Destruction of cells in tissue grafts, tumor cells, or cells ● Immune response results in exaggerated or inappropriate
infected by some viruses reactions
● Mainly utilized to activate B cell responses and to cope ● Harmful to the host
with intracellular pathogens. ● Typically occur after the second contact with a specific
antigen (allergen)
● First contact induces sensitization to allergen

FOUR TYPES OF HYPERSENSITIVITY REACTIONS

• Types I, II, and III - antibody-mediated
• Type IV - T-cell mediated

Helper T cells
● T-helper cells, TH cells, and CD4+ cells
● Stimulate B cells to produce antibodies
● Defense against intracellular agents
● Primary function is the secretion of cytokines (proteins w/c
facilitate chemical messages among various cells in the
body)

ANTIGEN RECOGNITION MOLECULE

● In order for the immune system to respond to nonself
(antigen), a recognition system capable of precisely
distinguishing self from nonself had to evolve
 ❖ Coagulase
➢ accelerates the formation of a fibrin clot coating the
organisms with a layer of fibrin

❖ Immunoglobulin A (IgA) protease

➢ cleaves IgA → allows adherence to mucous
membranes
➢ seen in SHiN organisms – S. pneumoniae, H.
influenza, type b, Neisseriae spp. (gonococci and
meningococci)

INFECTION BIOLOGY
TERMS:

Pathogenicity
● Describes the ability and strength of a pathogenic
substance to cause pathologic changes

Infectivity
● The capability of the pathogen or agent to enter, survive,
and multiply in the host.

Virulence
● The capacity and strength of the disease to produce
severe and fatal cases of illness
❖ Leukocidin
Antigenicity ➢ destroys both neutrophilic leukocytes and
● The ability of the agent to induce antibodies in the host. macrophages (e.g. Panton-Valentine Leucocidin or
PVL)

INFECTION BIOLOGY
VIRULENCE FACTORS
MECHANISMS OF BACTERIAL DISEASE
★ production of toxins ❖ Polysaccharide Capsule
★ induction of inflammation ➢ protect against phagocytosis

MODES OF TRANSMISSION ❖ Cell Wall Proteins

➔ Human to Human ➢ M protein of S. pyogenes (group A Streptococcus) of
◆ direct (sexual, transvaginal), fecal-oral, inhalation, antiphagocytic (via molecular mimicry – it can cause
transplacental, bloodborne the autoimmune response seen in acute rheumatic
fever)
➔ Nonhuman to Human
◆ soil, water, direct animal source, vector-borne,
animal excreta, fomites

BACTERIAL ADHERENCE
● pili mediate attachment of bacteria
● glycocalyx mediates strong adherence to surface of
human cells → allows adhesion to prosthetic devices

ENZYMES IN BACTERIAL INVASION

❖ Hyaluronidase (a.k.a. spreading factor)
➢ spread through subcutaneous tissue
EXOTOXINS BACTERIOLOGY
● polypeptides secreted by certain bacteria that alter specific Staphylococcus spp.
cell functions resulting in the symptoms of disease
● have an A–B subunit structure:

★ A subunit is the active (toxic) subunit

★ B subunit is the binding subunit

★ Streptolysin O (Streptococcus pyogenes)

★ Botulinum toxin (Clostridium botulinum)
★ Enterotoxin (Staphylococcus aureus)
★ TSST-1 (Staphylococcus aureus)
★ Exfoliative toxins A, B (Staphylococcus aureus)
★ Shiga toxin (Shigella dysenteriae)
★ Tetanus toxin (Clostridium tetani)
★ Cholera toxin (Vibrio cholerae)

ENDOTOXIN
● is a component of Gram (-) bacteria and plays an
important role in the pathogenesis of septic shock when it
is recognized by the immune cells.

➔ Lipopolysaccharides (LPS) located in the outer

membrane of gram-negative bacteria
➔ Lipid A is the toxic component of LPS

STAPHYLOCOCCUS AUREUS
● gram-positive cocci in grape-like clusters
● yellow or golden colonies on blood agar
● catalase-positive
● coagulase-positive

HABITAT
● human nose (anterior nares) and skin

TRANSMISSION
● direct contact (hands)
● fomites - objects or materials that are likely to carry
infection, such as clothes, utensils, and furniture.
● contaminated food
Toxins
● Exofoliatin A and B: superantigen causing epidermal
separation in Staphylococcal Scalded Skin Syndrome
● Enterotoxins (heat-stable): superantigens causing food
poisoning
● Toxic shock syndrome toxin (TSST-1): superantigen
leading to toxic shock syndrome

CLINICAL SYNDROMES

PYOGENIC:
➔ Skin and Soft Tissue Infections – bullous impetigo
➔ Acute Endocarditis - most common cause of acute
endocarditis
➔ Pneumonia – most common cause of bacterial STREPTOCOCCUS PNEUMONIAE
pneumonia post-viral infection ● Alpha-hemolytic streptococci

TOXIGENIC:
➔ Gastroenteritis - due to ingestion of heat-stable
enterotoxin
➔ Scalded Skin Syndrome (Ritter Disease)
◆ separation of skin at stratum granulosum
➔ Toxic Shock Syndrome
◆ fever, hypotension, sloughing of filiform papillae -
strawberry tongue, desquamating rash and
multi-organ involvement (>3)
◆ Tampon - using menstruating women or in patients
with nasal packing for epistaxis

STAPHYLOCOCCUS EPIDERMIDIS
● low-virulence organism
● glycocalyx adheres well to foreign bodies and form METABOLISM
biofilms ● Bile and optochin-sensitive: OVRPS (overpass)
○ prosthetic heart valves ○ Optochin sensitivity differentiates Strep pneumoniae
○ prosthetic joints from Viridans strep (since both are alpha-hemolytic)
○ indwelling catheters
RESERVOIR
● Upper respiratory tract
STAPHYLOCOCCUS SAPROPHYTICUS
● gram-positive cocci in clusters TRANSMISSION
● catalase-positive ● Respiratory droplets
● coagulase-negative
● novobiocin-resistant (S. epidermidis is VIRULENCE FACTORS
novobiocin-sensitive) ● Polysaccharide Capsule: stops phagocytosis; major
● whitish, non-hemolytic colonies on blood agar virulence factor

EPIDEMIOLOGY CLINICAL SYNDROMES

● 2nd most common cause of UTIs in sexually active ● Pneumonia: most common cause of CAP in adults;
women rust-colored sputum
● Otitis Media: most common cause in children
CLINICAL FINDINGS ● Bacterial Meningitis: most common cause in adults
● dysuria, pyuria, and bacteriuria ● Sinusitis

DIAGNOSIS
BACTERIOLOGY ● Gram-positive "lancet-shaped" cocci in pairs or
Streptococcus spp. chains
● Alpha-hemolytic
● Positive Quellung reaction: capsular swelling when
mixed with a small amount of antiserum (serum with
antibodies to the capsular antigens) and methylene blue
 STREPTOCOCCUS PYOGENES
• Group A Beta-hemolytic streptococcus RESERVOIR
● Vagina

TRANSMISSION
● Transvaginally
● Transplacentally

CLINICAL SYNDROMES
● Neonatal Pneumonia and Meningitis:
○ Group B Streptococcus is the most common
cause; predisposing factors include:
- Intrapartum fever >38°C
- PROM
- Vaginal colonization

TREATMENT/PREVENTION
● DOC: Penicillin G
VIRULENCE FACTORS ○ Penicillin G + Aminoglycoside for serious infections
● Hyaluronidase: degrades hyaluronic acid (spreading ● All pregnant women should be screened for GBS
factor) colonization at 35-37 wks AOG; if (+), chemo-prophylaxis
● DNase (streptodornase): degrades DNA in exudates or with IV penicillin or Ampicillin 4 h prior to delivery
necrotic tissue
○ Anti-DNAse B to document antecedent Skin
infection VIRIDANS STREPTOCOCCI

TOXINS
● Erythrogenic toxin: produces scarlet fever
● Streptolysin O: highly antigenic, causes Ab formation;
destroys RBCs and WBCs; and is the reason for the beta
hemolysis
○ ASO Titers to document antecedent Pharyngitis

● Exotoxin B: protease that rapidly destroys tissue →

necrotizing fasciitis

CLINICAL SYNDROMES

PYOGENIC:
● Impetigo Contagiosa:
● perioral blisters with honey-colored crust
● Cellulitis: deeper infection involving subcutaneous/dermal
tissues; facilitated by hyaluronidase (spreading factor) METABOLISM
● Pharyngitis: most common bacterial cause of sore throat • Catalase-negative
• Bile and optochin-resistant
TOXIGENIC:
• Scarlet Fever: VIRULENCE FACTORS
due to erythrogenic toxin; fever strawberry tongue, • Glycocalyx enhances adhesion to damaged heart valves
sandpaper-like centrifugal rash • Protected from host defenses within vegetations

IMMUNOLOGIC: CLINICAL SYNDROMES

• Acute Rheumatic Fever • Dental caries: S. mutans
- Post-pharyngitis • Subacute Bacterial Endocarditis:
- Joint, heart, and brain tissue - S. sanguis – most common cause of subacute and
native valve endocarditis
• Post Streptococcal Acute Glomerulonephritis (PSAGN)
- Post-pharyngitis OR post-impetigo
- M protein
- S/S: Hypertension, periorbital edema, hematuria BACTERIOLOGY

BACILLUS ANTHRACIS
STREPTOCOCCUS AGALACTIAE
CHARACTERISTICS
• Group B beta-hemolytic streptococcus
• aerobic, gram-positive box-car like rods
• non-motile
• spore-forming
• Medusa head morphology
- dry "ground glass" surface and
irregular edges with projections
along lines of inoculation

HABITAT AND TRANSMISSION

• habitat is soil
• transmission by contact with infected
animals or inhalation of spores from animal hair and wool
(woolsorter’s disease)
SPECTRUM OF DISEASE: PATHOGENESIS
• Cutaneous Anthrax • spores germinate under anaerobic conditions in the wound
- direct epidermal contact with spores causes formation • tetanus toxin (tetanospasmin)
of a malignant pustule with subsequent central - Rigidity: trismus, risus sardonicus, opisthotonos,
necrosis apnea/laryngospasm, dysphagia, ↑DTRs
- 20% mortality rate - Weakness or paralysis

• Inhalational Anthrax TREATMENT

- inhaled spores from animals (woolsorter’s disease)
or from weaponized preparations (bioterrorism)
- prolonged latent period (2 mos) before rapid
deterioration
- pulmonary hemorrhage
- 100% mortality rate without immediate treatment
• Debridement of primary wound
• Metronidazole or penicillin
• Tetanus Immunoglobulin (at the wound site)
• Vaccination with tetanus toxoid
- given in childhood and every 10 years thereafter

• Gastrointestinal Anthrax
- ingestion of live spores leads to UGI ulceration,
edema and sepsis (rapidly progressive course)
- mortality rate approaches 100%

TREATMENT:
• Cutaneous anthrax
- DOC is ciprofloxacin

• Inhalational/gastrointestinal anthrax
- DOC is ciprofloxacin or doxycycline with one or two
additional antibiotics (rifampin, vancomycin,
penicillin, imipenem, clindamycin, clarithromycin)
CLOSTRIDIUM BOTULINUM
Most common cause of death is pulmonary hemorrhage in the
ff: CHARACTERISTICS
• Anthrax (pulmonary) aka wool sorter’s disease • anaerobic, gram-positive,
• Leptospirosis, severe (Weil’s syndrome) spore-forming rods
• Congenital syphilis
HABITAT AND TRANSMISSION
• habitat is soil
BACILLUS CEREUS • organism and botulinum toxin
transmitted in improperly preserved food
CHARACTERISTICS - alkaline vegetables such as
• aerobic, gram-positive spore-forming green beans, peppers, and mushrooms
rod - smoked fish
• motile - canned goods (bulging)
- honey
HABITAT AND TRANSMISSION
• spores on grains such as rice survive PATHOGENESIS
steaming and rapid frying • botulinum toxin blocks acetylcholine release causing flaccid
• spores germinate when rice is kept paralysis (descending pattern)
warm for many hours (e.g. reheated
fried rice) • Botox is a commercial preparation of exotoxin A
- uses: wrinkle removal, torticollis

Food-Borne Botulism
● eye symptoms: blurring of vision, diplopia, ptosis,
mydriasis
● dry mouth, constipation, abdominal pain
● bilateral descending flaccid paralysis
● respiratory paralysis

TREATMENT
• food poisoning (emetic/diarrheal)
- symptomatic treatment only
TREATMENT
• adequate ventilatory support
CLOSTRIDIUM TETANI • elimination of the organism from GIT
- judicious use of gastric lavage and metronidazole or
CHARACTERISTICS penicillin
• anaerobic, gram-positive, spore-forming • botulinum antitoxin
rods
• spore is at one end (terminal spore) so PREVENTION
organism looks like a tennis racket • proper sterilization of all canned and vacuum-packed foods
• adequate cooking
HABITAT AND TRANSMISSION • discard bulging/swollen cans
• habitat is soil
• entry through traumatic implantation into tissues with low
oxygenation leads to spore formation, growth, & toxin
production
 CLOSTRIDIUM PERFRINGENS CORYNEBACTERIUM DIPHTHERIAE

CHARACTERISTICS CHARACTERISTICS
• anaerobic, gram-positive, spore-forming rods • aerobic, non-spore-forming, non-motile gram-positive rods
• nonmotile but with rapidly spreading growth on culture • club or comma-shaped rods arranged in V or L shape
media • looks like Chinese characters

HABITAT AND TRANSMISSION

• habitat is soil and human colon
• myonecrosis results from contamination of wound with soil or
feces
• food poisoning is transmitted by ingestion of contaminated
food

PATHOGENESIS
• Gas Gangrene
- alpha toxin destroys cell membranes
- Gas produced by anaerobic metabolism HABITAT AND TRANSMISSION
• habitat is human throat
• Food Poisoning • transmission via respiratory droplets
- production of enterotoxin
SPECTRUM OF DISEASE
SPECTRUM OF DISEASE • prominent thick, gray, pseudomembranes over tonsils
• Gas Gangrene and throat
- pain, edema and cellulitis with crepitation
TREATMENT
• Food Poisoning • antitoxin and penicillin G
- 8- to 16-hour incubation period
- characterized by watery diarrhea with cramps & vomiting PREVENTION
- resolves in 24 hours • toxoid vaccine, usually in combination with tetanus toxoid and
pertussis vaccine (DTaP)
TREATMENT
• wound debridement and penicillin for gas gangrene
• supportive management for food poisoning LISTERIA MONOCYTOGENES

PREVENTION CHARACTERISTICS
• proper wound care • aerobic, non-spore-forming, gram-positive rods
• adequate cooking • arranged in V- or L-shape
• tumbling motility
• cold enhancement: paradoxical growth in cold temperature
CLOSTRIDIUM DIFFICILE (CLOSTRIDIUM DIFFICILE)

CHARACTERISTICS
• anaerobic, gram-positive, spore-forming rods
• exotoxin in stool

HABITAT AND TRANSMISSION

• carried in the colon
- 3% of the general population
- up to 30% of hospitalized patients
• transmitted by the fecal-oral route
HABITAT
• hands of hospital personnel are important intermediaries
• colonizes GI and female GUT
• widespread in animals, plants, and soil
PATHOGENESIS
• antibiotics suppress normal flora, allowing C. difficile to
TRANSMISSION
overgrow
• across placenta or by contact during delivery
- Clindamycin
• ingestion of unpasteurized milk products, e.g., cheese
- 2nd & 3rd gen Cephalosporins
- Ampicillin
SPECTRUM OF DISEASE
• pseudomembranes are the visual result
• Early-Onset Neonatal Listeriosis
- transplacental transmission
SPECTRUM OF DISEASE
- characterized by late miscarriage or birth
• Pseudomembranous Colitis
- Non-bloody diarrhea associated with
• Late-Onset Neonatal Listeriosis
pseudomembranes (yellow-white plaques) on the
- transmitted during childbirth and manifests as meningitis
colonic mucosa
or meningoencephalitis
- toxic megacolon can occur
TREATMENT
TREATMENT
• ampicillin with or without gentamicin
• causative antibiotic should be withdrawn
• oral metronidazole or vancomycin should be given
PREVENTION
• surgery if toxic megacolon develops
• pregnant women and immunocompromised patients should
not ingest unpasteurized milk products or raw vegetable
★ Clostridium TETani = TETanic paralysis
★ Clostridium BOTulinum = BOTulism from bad
BOTtles of food
★ Clostridium PERFringens = PERForates a
gangrenous leg (gas gangrene)
★ Clostridioides DIfficile = DIarrhea