Microbiology lecture note terminology


Candida albicans

Part of normal human flora

Fungi properties

Eukaryotic. Aerobic or facultative. Will grow axenically. Can be easily isolated by their colony. Sacrophetic, heterotrophic, non-photosynthetic. Haplophase is dominant, transient diplophase. Have hyphae. True branching. ~10X the size of bacterium

Axenical growth

Growth w/o others (non-parasitic)

Fungi cell wall

Made of chitin (homo-poly N-acetylglucoseamine). Interlaced w/ glucans (glucosyl polymers). Peptidomannans


In fungi, serve in place of LPS (which is bacterial)


Recylce decomposed matter


A row of fungal cells. Can be septate or non-septate

Septate hyphae

Cells are divided with membrane between them, although communications between the cells may exist

Non-septate hyphae

No cell membrane diving septa into seperate cells

Fungal branching

Fungi have true branching w/ Y-shaped cell at fork. Bacteria have false branching w/ bent and partial cells at fork.

Fungal dimorphism

Same organism can exhibit two different forms. Mycelial or hyphal form and yeast form

Mycelial/hyphal forms

Usually @ sub-physiologic temperatures, reproduction may be asexual or sexual, distinct sexual forms are displayed

Yeast formed

Due mainly to physiologic temperature. Strictly asexual reproduction (budding). Oval morphology. Nothing distinct

Aspergillus sp.

Non-dimorphic. Always found in mycelial phase, even when in deep tissue infections

Torula sp.

Exist only as yeast. Most will at low temperature form pseudo-hyphae


Not permanent growing structures w/ regularly spaced nuclei. Can not differentiate furthar to form structures such as aerial hyphae/mycelia, fruiting bodies, and/or rhizoids. Branching does not occur and arthrospores and chlamydiospores are not found

Candida sp.

Thought to be monomorphic (only yeast), but will have mycelial stage at sub-physiologic temperatures. Grows in mycelial form in biofilms

Fungi staining

All fungi are strongly gram+, all fungi are non-acid fast

KOH preparation

Works because warm KOH hydrolyses proteins and fungi are protected by a carbohydrate cell wall. Background cells will lyse as integral membrane proteins. Procedure: take scraping from margins of lesion (not center), add 2-3 drops of 10% KOH, warm slide over flame, optionaly add 1 drop lactophenyl cotton blue stain, put cover slip over liquid and examine immediately under high dry microscope objective

Alkali stain

Alternative to KOH/lactophenyl cotton blue. Make stain w/ Use “Super Quink” permanent black-blue int for fountain pens. Add solid KOH, 10 grams/100ml of ink. Centrifuge to remove precipitates and store in plastic bottle. Use mixture as stain.

Fungus culture

Primary step: isolation of culture: sabouraud's agar.

Secondary step: culture and species identification: Corn meal agar incubated at 25 celcius.

Sabourand's agar

Made from simple peptone (protein hydrolysate) and agar. pH is adjusted to 5.6 to kill bacteria. Bacteria grow faster and would thus over take the fungi on the plate

Corn mean agar

When incubated at 25 degrees celsius, allows for the growth of characteristic sexual structures for the differentiation of fungi via visual techniques (morphology v. biochemical)


Antifungal drugs from streptomyces sp. Binds to sterols (ergosterol) in the fungal cell membrane. This will form channels through the membrane causing leakage and eventual cell death. Toxic because they can weakly bind cholesterol. Also nephrotoxic.


A topical insoluble polyene

Amphotercin B

Parenteral use only. Administered as a colloidal suspension


Antifungal drug from Penicillium griseus. Acts on microtubules and mechanism of the mitotic spindle. Poorly absorbed so can not reach therapeutic levels in blood, but is deposited in keratinous tissue and builds effective concentration there. Only effective against dermatophytes and superficial mycoses


Synthetic analog of cytosine. Gets incorporated into RNA after conversion to 5-flucouracil. Interferes w/ RNA formation and inhibits thymidylate synthetase. Toxic to bone marrow. Effective against Candida sp. Or Cryptococcus sp. No effect against molds. Oral administration

Synthetic azoles

Inhibit cytochrome enzymes. Also inhibit formtation of ergosterol from lanosterol precursor. Results in defective cell membrane. Fungistatic, not fungicidal. Used orally and parenterally. Effective against most systemic fungal infections. Some toxicity. Examples: ketoconazole, fluconazole, miconazole, itraconazole

Patassium iodide

Oral. Effective against Sporothrix schenkii


A napthiomate derivative. Topical: used only for dermatphytes

Undecalinic acid

A long chain fatty acid. Topical: used only for dermatphytes. Desenex


Contain napthalene ring


Oral: used only for dermatophytes


Topical: used only for dermatphytes

Penlac nail lacquer

Prescription nail polish. Active ingredient is ciclopirox. Used to treat onychomycosis and / or perinychia. Does not have side effects of terinafine or itraconazole. Limited effectiveness in clinical trials. Less effective than oral medication

Fungi classes

Class Ascomycetes

Class Basidiomycetes

Class Deuteromycetes

(Fungi imperfecti)

Asexual spores

Exogenous at ends or side of hypha

Exogenous at ends or side of hypha

Exogenous at ends or side of hypha

Sexual spores

Ascospores within sacs or Asci

Basidiospores on surface of basidium

Not yet found






Neurospora sp

Penicillium sp


Filobasidiella neoformans (Cryptococcus neoformans)

all mushrooms, Rusts, Smuts

Epidermophyton sp.

Microsporium sp.

Trichophyton sp.

Bacterial architecture

Spherical shape

Coccoid (coccus, cocci)

Cylindrical shape

Rod (bacillus, bacilli)

Curved shape

Vibrio. vibrates

Square shape

Not infectious

Chain arrangement

Strepto. Does not occur w/ bacilli

Cluster arrangement

Staphylo. Does not occur w/ bacilli

Pair arrangement

Diplo. Occurs w/ streptococcus pneumoniae

Gram stain

Purple/blue for gram positive. Red/pink for gram negative.

Place cells on slide, add primary stain (crystal violet), and mordant (Gram's iodine), add decolourizer (alcohol or acetone), add counterstain (saffranin)

Acid fast stain

Differential stain similar to Gram's. Used to differentiate Gram(-) bacteria. Mycobacterium

Ziehl Neelson staining

Acid-fast staining technique. Hot basic carbolfuchsin; decolourize w/ acid-alkali solutions; counterstain: methylene blue or malachite green. Acid fast red/pink; non acid fast: blue/green

Kinyou stain

Same as ZN but w/o heating

Fluorochrome stain

(auramine-rhodamine). Primary stain fluorescent dyes. Counterstain potassium permanganate. Organisms will fluoresce yellow/green against black background


Outer appendage; Organ of motility; not essential for survival; flexible; never for cocci; possible role in colonization. Compozed of 3 parts. Helical filament, hook and basal body. CW rotation is tumbling, CCW is smooth swimming. Propel at 20-90 um/sec


flagellum at one pole


Multiple Flagella at both poles


Multiple flagella at one pole


Flagella distributed around cell.

Helical filament

Inserted into hook. Composed of proteins (flagellin) (hauch, H antigen) 20nm diameter, 1-7 mm length


Short curved structure anchors filament into basal body

Basal body

Contains rod and 1 or 2 sets of double plates (rings). Located in cytoplasmic membrane and cell wall. 2 rings in Gram(+) and 4 rings in Gram(-) bacteria

H antigen

Helical filament of flagella.


Involuntary movement in response to stimulus. Chemotaxis, aerotaxis, phototaxis, magnetotaxis. + response is towards stimulus (up gradient), - response is away (down gradient). Non-response is random walk. Chemotaxic receptors in cell membrane


Protein component of pili and fimbriae


Sex pilus found in gram(-) bacteria only. Allows for entry of genetic material during conjugation


Attachment pili. Allows for adhesion to surfaces. Predominantly Gram(-) some Gram(+). Found in Corynebacterium renale, and Actinomyces maeslundii


AKA Capsule, slime layer or S-layer. External mucilaginous layer. EPS. Bacillus anthracis has a polypeptide instead of a polysaccharide. Surrounds cell and is non-vital. Shows degree of organisation. Has a capsule and slime layer. Functions in adherence to species members and to surfaces. Allows for antiphagocytosis. Neutrophil killing not possible because lysosome contents do not have access to cell interior. Protects anaerobes from oxygen.

Slime layer

Part of glycocalyx w/ poor organization, weak attachment to cell wall


Organized w/ adherence to cell wall (K antigen)

K antigen

Capsule. Cell wall antigen.

Streptococcus mutans

Responsible for dental carries via adherence of glycocalyx


Antigenic (K antigen). Found in S. pneumoniae, Haemophilus influenzae.

Streptococcus pneumoniae

Resists phagocytosis because of glycocalyx. Antiphagocytosis

B. fragilis

Capsule induces abscess formation

Quellung reaction

Swelling reaction that determines capsule presence. Antiserum + bacteria --> swelling. Specific antisera: capsular (K) antigens for typing


Backbone of eubacteria cell walls. Composed of NAM & NAG linked with beta 1-4 glycosidic bonds. Provides rigidity and strength prevents osmotic lysis in dilute environments

Gram- v. gram+ cell wall

L-lysine is replaced w/ D-aminopimelic acid in gram(-) bacteria. Gram(+) has no outer membrane and only in some instances a periplasmic space.

Staphylococcus aureus cell wall

L-alanine branches off of NAM followed by D-glutamate and L-lysine. Gram(+)

Teichoic acids

i.e. Lipoteichoic acid. Phosphate + alcohol (gycerol/ribitol). Binds proteins (maintain low pH), cations (Ca2+ and Mg2+). Act as adhesins, virus receptor sites.

Gram(+) bacteria

(50-60% of dry weight) Composed of thick peptioglycans. Teichoic acids and additional carbohydrates and proteins. M, T and R proteins of Group A streptococci; protein A of Staphylococcus aureus

Lipoteichoic acid role in disease

Dermal necrosis (Schwartzmann reaction); induction of cell mitosis at the site of infection; stimulation of specific immunity; stimulation of non-specific immunity; adhesion to the human cell; Complement activation; induction of hypersensitivity (anaphylaxis)

Gram(-) cell wall

Thin peptidoglycan (5-10% of dry weight). Outer membrane contians porins (protein channels) for nutrient transport. Contain lipopolysaccharide (LPS) and lipoproteins. Gaps in cell wall allow acetone to seap out. 2 major layers, 8-11nm thick, always have periplasmic space, and is less penetrable than gram(+)

Gram(-) outer membrane

Prominent outer layer peripheral to periplasmic & peptidoglycan sacculus. Similar to cytoplasmic membrane (bilayer). External layer (LPS), inner layer – phospholipids. Outer membrane proteins


Inner most lipid anchors LPS to outer membrane. Toxic. O-polysaccharide long repeating sequence of sugars (O-antigen). An endotoxin

O antigen

Surface antigen from outer membrane. Polysaccharide in LPS. endotoxins

Endotoxin effects

Fever, haemorrhagic necrosis (Schwartzman reaction), disseminated intravascular coagulation, production of TNF, activation of the alternate complement pathway, stimulation of bone marrow cell proliferation, and enhancement of the immune and limulus lysate reaction (clotting of horseshoe crab amoebocyte lysates)

Acid-fast bacteria

Genera Mycobacterium & Nocardia. Peptidoglycan + arabinose & galactose polymers. Arabinogalactan esterification --> mycolic acids (waxy)


Breaks beta 1-4 bonds between NAM & NAG. Present in body secretions (tear & saliva). Destroys all or part of cell. Leaves cells vulnerable to being lysed by osomotic pressure. Cell wall protects cells from swelling


Portion of cell wall remains after attack by lysozyme


Cell wall is completely removed. Gram(+) more sensitive


Penicillin prevents cell wall formation. Inhibits formation of normal cross-linkages in peptidoglycan (brick wall w/o cement). Binds irreversibly to penicilin binding proteins

Penicillin binding proteins

Enzymes of peptidoglycan synthesis

Periplasmic space

Found in gram(-) bacteria. Space between inner and outer membranes. Gel like area containing a loose network of peptidoglycan. Contains: nutrient transport proteins, nutrient acquisition enzymes (proteases), detoxifying enzymes (beta-lactamases), membrane derived oligosaccharides (MDO), osmoprotectants

Axial filaments

Found in mobile bacteria that lack flagella. e.g. Spirochetes – Leptospira. Flagella-like filaments (chemically and structurally). Long thin microfibril inserted into a hook. Entire structure enclosed in periplasmic space. Endoflagellum

Cytoplasmic membrane physical properties

Inner membrane. General structure: 2 densely stained layers seperated by non staining region. 4-5nm thick. Phospholipid 30-40% and protein 60-70%. semipermeable barrier

Plasma membrane function

Active transport of metabolites, oxidataive phosphorylation (ETC and ATP productions), biosynthesis and export cell wall components, phospholipid biosynthesis, secretion of extracellular enzymes and toxins, and anchoring DNA during cell division (mesosome), chemotactic receptors are also in membrane

Protoplasm appearance

Granular appearance due to ribosomes. Site of biochemical activity, 70-80% water acts as solvent (sugars, salts and aa's)


RNA/protein bodies (60% RNA, 40% protein). Composed of a 50S and 30S subunit. 70S in size. Sites of protein synthesis


Extensive invaginations of cytoplasmic membrane continuous w/ cytoplasmic membrane. Function is unknown. Mainly seen in Gram(+) bacteria. Corynebacterium parvum

Chromatin area

No distinct membrane enclosed nucleus and no mitotic apparatus.

Bacterial chromosome

Single circular DNA (chromatin body). Exception: Streptomyces & Borrelia sp. have linear DNA. Rhodobacter sphaeroides (2 seperate chromosomes). DNA aggregated in one area (nucleoid). All genes are linked


Extrachromosomal DNA. Circular DNA smaller than chromosome. Self-replicating. Antibiotic resistance, tolerance to toxic metals, production of toxins, mating capabilities.

Inclusion bodies

Storage granules. (seen under light microscope). Poly-beta-hydroxybutyrate (PHB) has role in carbon & energy store. Membrane bound. mw 1000-256000 and up to 50% cell dry wt Bacillus subtilis. Polymetaphosphate granules. Glycogen granules


Specialized structures produced in environmental stress. Resistant to UV, irradiation, chemical disinfection, drying. Requires specialized stains to see in light microscopy. Found in Bacillus and Clostridium spp. Contains complete nucleus, protein synthesis apparatus, energy-generating system (glycolysis), Ca-dipicolinic acid (10% dry wt, characteristic). Spore wall consists of peptidoglycan layer and cell wall germinating vegetative cell. The cortex consists of peptidoglycan w/ fewer cross-links. Coat: keratin-like protein. Impermeable layer (resistance to antibacterials)


Vegetative cell -> DNA condenses -> Transverse wall begins to form -> spore material seperated; formation of forespore -> vegetative cell grows around spore -> spore forms multilayered coating -> cell lysis frees spore


Outgrowth from spore gives rise to vegetative cell

Bacterial Growth and death


Continuous macromolecular synthesis

Lag phase

The part of the growth curve in which there is no actual population change. Cells are preparing to begin divisions.

Exponential phase

Period of exponential growth w/ geometric increase in population due to abundance of resources

Stationary phase

Population plateus with multiplication equalling cell deaths. Can induce formation of endospores

Death phase

Decline in population (reverse log phase). Death is in geometric fashion.


Minimum, optimum and maximum. Refering to temperatures allowing growth.


Optimimum growth at below 15 degrees celsius. Capable of growing at 0 degrees and no growth at 20

Faculatative psychrophile

Can grow at below 20, but that is not there optimal temperature. Contaminants of food/dairy products


Optimal temperature between 20 and 40. includes human pathogens.


Optimum temperature greater than 45. not involved in infection.


Converts hydrogen peroxide to water and oxygen


H2O2 + NADH + H+ --> 2H2O + NAD+

Superoxide dismutase

2O2- + 2H+ --> H2O2 + O2

Obligate aerobes

Totally dependant on O2 for growth. Require 20% oxygen. Possess catalase and superoxide dismutase.


Tolerate only 4% O2. Possess SOD, but enzyme system can be overloaded inhibiting growth

Obligate anaerobes

Grow in absence of oxygen only. O2 is lethal. Found in lower GI tract

Facultative anaerobes

Aerobic in the presence of oxygen and anaerobic only when oxygen is not available

Water activity

Index of amount of water. Same as relative humidity (i.e. 50% r.h. = .5 Aw). Most bacteria require Aw > .9 and grow optimally at Aw = 1.0


Survive at lower Aw. Fungi able to grow at Aw 0.60. salt tolerant bacteria (high solute, low water)

Trace elements

Mn, Zn, Co, Ni, Cu, Mo


K+, Ca2+, Mg2+, Fe2+, Fe3+


C, H, N, O, P, S. components of carbohydrates, lipids, nucleic acids and proteins


CO2 and soil primary C source


Reduced/pre-formed organic molecules or other organisms. pathogens


Light is used as energy source


Oxidation provides energy


Reduces inorganic molecules for H/e-.


Orgranic molecules are reduced

Complex medium

AKA non-synthetic medium. Composition unknown

Defined medium

Aka Synthetic medium. Chemical contents are known

All purpose medium

Supports the growth of most microorganisms.

Enriched medium

Basal support growth media + nutritive supplements added

Reduced medium

Addition of a reducing agent

Transport medium

Preserve microorganisms in transit following isolation from patient until cultivated

Selective medium

Allows one species to grow and suppresses others

Differential medium

Causes changes in medium that allow one to distinguish between species


Killing of bacteria


Inhibition of growth of bacteria


All living cells, viable spores, viruses are destroyed or removed from object of environment


Chemical agent causeing sterilization


Killing, inhibition or removal of microbes that may cause disease


Agent that disinfects. Inanimate objects only. Chlorine, hypochlorites, chlorine compounds, copper sulphate, quaternary ammonium compounds.


Reduction of microbial population to that deemed acceptable


Prevention of infection or sepsis


Chemical applied to prevent sepsis. Not toxic, applied to living organism. Mercurials, silver nitrate, iodine solution, alcohols, detergents


Kills pathogens and non-pathogens, but not endospores


Disinfectant/antiseptic effective against specific species. Also fungicide, algicide, viricide


Burns/physically destroys. Needles, inoculating wires, glassware, etc.Vaporizes organic material, but can destroy substances


100 degrees. Kills everthing but endospores


Everything will die! Steam under pressure at 121 degrees for 15 mins. 15Lbs/in2 but heat labile substances will be denatured or destroyed (plastics). Must do full time for sterilization

Dry heat

160 degrees for 2hrs. Used for glassware or metal. Usefull for materials that must remain dry

Intermittent boiling

3x30 min intervals will kill off endospores


72 degrees/15 secs. Similar to batch method. For milk conductive to industry. Fewer undesirable effects on taste and quality


Destroyes/distorts nucleic acids. UV common object surfaces. X-rays and microwaves


Physical removal from liquid or gas. Sterilize solutions denatured by heat. i.e. Antibiotics, injectable drugs, amino acids, vitamins, etc.


Formaldehyde, glutaraldehyde, ethylene oxide. Toxic chemicals (require gas chamber)


Denatures proteins and solubilizes lipids. Antiseptic used on skin


Denatures proteins and solubilizes lipids. Antiseptic used on skin


Reacts with NH2, SH and COOH groups. Disinfectant, kills endospores

Tincture of iodine

Inactivates proteins. Antiseptic used on skin

Chlorine gas

Forms hypochlorous acid (HCLO) – strong oxidizing agent. Disinfectant, drinking water, general disinfectant

Silver nitrate

Precipitates proteins. General antiseptic. Used in eyes of new borns

Mercuric chloride

Inactivates proteins by reacting w/ sulphide groups. Disinfectant, occasionally used as antiseptic on skin endospores


Inactivates proteins by reacting w/ sulphide groups. Skin antiseptic and disinfectant

Phenolic compounds

Denature proteins and disrupts cell membranes. Antiseptic at low concentrations and disinfectant at high concentrations

Ethylene oxide gas

Alkylating agent. Disinfectant used to sterilize heat-sensitive objects

Chemotherapeutic agents

Synthetic agents that treat microbial or viral disease


Chemical of natural origin that kills or inhibits growth of other cell types

Biology of atypical bacteria


Smallest known free-living organisms. 0.15-.03um. No cell wall. Shape varries from coccoid to long filaments. No peptidoglycans. Resistant to drugs that attack the cell wall. Cell wall contains sterols. Membrane proteins are structural, catalytic and immunological. Cytoplasm only contains ribosomes. Genome is 0.5-1x109 Daltons. Smallest capable of self reproduction. Binary fission or filamentous process of reproduction. Looks like fried eggs under microscope (except M. pneumoniae). Colonies are small 600um in diameter. Require a rich growth medium w/ sterols and serum proteins. Has a unique attachment organelle

Filamentous reproduction process

Process in Mycoplasma sp in which genomic reproduction occurs at a pace exceeding cytoplasmic replication. Cell elongates and eventually fragments into many cells.

Primary atypical pneumonia

M. pneumoniae

Non-gonococcal urethritis

M. genitatlium


U. urealyticum

M. hominis

Stillbirth, Spontaneous abortion, infertility


Cell that has lost ability to produce cell wall, but that had a cell wall in at least one stage of life. NOT MYCOPLASMA. No sterols are present.


Obligate intracellular pathogens. Zoonotic except for Coxiella burnetli. 0.3-.05um in diameter. 0.8-2um long. Closely related to Gram(-). Have two membranes (CM and OM). Have D-aminopimelic acid. Part of arthropod intestinal flora. Not all have O-antigen (no LPS). Can not be cultivated on agar since they need host cells. Multiplication is slow. Binary fission, growth leads to host cell lysis.

Ricketsiae diagnosis

Macchiavello stain and Castaneda stain both stain organism against background, Giemsa stain just stains organism. Confirmative test is serological Weil-Felix reaction. Agglutinins in serum against proteus strains. Shared antigens: alkali stable polysacc haptens. Complement fixation test gives positive results 14 days into infection. Indirect fluorescent antibody test (Ehrlichiosis) detect IgM and IgG against Rickettsia


0.2-0.7um in diameter. Non-motile, coccoid. Originally thought to be viruses. Obligate intracellular pathogens. Can not generate ATP. Zoonotic infections between birds and men. Acquired via direct contact or via respiratory tract. Have two membranes, but no muramic acid/peptidoglycan

Chlamydia trachomatis transmission

Diseaase: trachoma, inclusion conjunctivitis, urethritis, cervicitis, ophtalmia neonatorum, Myocarditis, Lymphogranuloma venereum, Atherosclerosis, Neonatal pneumonia

C. penumoniae

Bronchitis/pneumonia/sinusitis via bird to human transmission. Can also cause atherosclerosis

C. psittaci

Meningopneumonitis, hepatic and renal dysfunction, conjunctivitis, abortion, and endocarditis. Transmitted from birds to humans

Chlamydia developmental forms

2 forms: elementary bodies and reticulate body/initial body. Dormant phase (EB)--> elementary body enter cell and metabolize --> reticulate body formation (8 hrs) --> reticulate bodies mature --> form EB in 24-48 hrs --> release from host cell as EB

Lab diagnosis

Isolation from infected tissue: cytoplasmic inclusion bodies in infected cells. Serological: microimmunofluorescent tests (anti-chlamydia Antibodies). Direct immnofluorescence: conjugated monoclonal Ab, complement fixation/fluorescent antibody test: rising titer Ab. Frei test: delayed type skin reactiojn (type IV hypersensitivity)

Diseases according to arthropod vector




Weil-Felix response


European epidermic typhus

R. Prowazekii


Brill's disease

R. Prowazekii


Trench fever

Bartonella quintana



Endemic murine typhus

R. typhi

Wild rodents


Cat scratch fever/Bacilliary angiomatosis

Bartonella henselae

Domestic cat


Mite borne

Scrub typhus

R. tsutsugamushi

Wild rodents


Rickettsial pox

R. akari

House mice


Fly borne

Oroyo fever/Verruga peruana

B. bacilliformis


Tick borne

Rocky mountain spotted fever

R. rickettsii

Dog, rodents

OX-19, OX-2

North asian tick typhus

R. siberica

OX-19, OX-2

Fievre boutonneuse

R. conorii

Dog, rodents

OX-19, OX-2

Queensland tick fever

R. australi

Marsupials, rodents

OX-19, OX-2


Coxiella burnetii

Cattle, sheep, goats


Spotted fever

R. rhipicephali




E. canis

E. chaffeensis





Comparative properties













Obligate intracellular pathogen






Peptidoglycan in cell wall






Growth on agar plate






Contain ribosomes






Sensitivity to antiB/interferon






Binary fission






Microbial genetics

Bacterial chromosomal replication

Initiation, elongation and termination. Bi-directional and semi-conservative. Helicase unzips DNA, RNA primer synthesized, RNA primer gives initiation site of synthesis, formation of replication fork, DNA Polymerase III attaches at origin, DNA synthesized 5'->3', now have 2 strands, DNA Polymerase I replaces primer w/ DNA

Okazaki fragments

Short fragments made on lagging strand

Non-chromosomal replication

1 strand nicked and it forms a unidirectional point of origin for replication


A set of genes grouped together for regulation purposes. IPOABC where I=initiator, P=promoter, O=operator and ABC are genes. Regulate genes include diphteria toxin, cholera toxin, fimbriae of uropathogenic E. coli

Chromosomal CtxR

Controls operon for diphtheria toxin (beta-phage encoded)

Lac operon

Lactose binds to repressor causing it to fall off. Repressor bound to operator region otherwise. Low cAMP levels no binding with CAP, so no transcription. High cAMP will bind w/ CAP leading to transcription.

Trp operon

Low level of trp, no binding to repressor, gene transcribed.


Permanent, heritable change in genetic information. Can be natural (mistakes in replication) or chemical (chemical acting to force change)

Wild type

Non-mutated form of a gene

Missense mutation

Mutation changes AA sequence.

Nonsense mutation

Mutation causes AA gene to be changed to stop codon

Silent mutation

Mutation has no effect on AA sequence

Back mutation

A mutant form reverts back to original wild-type

DNA polymerase III

Responsible for DNA replication. Can remove and replace defective genes.

Acquisition of genes

Plasmids via conjugation, loose DNA via transformation, bacteriophage via transduction, jumping genes

Conjugative plasmid transfer

F-factor encodes F-pilus needed for conjugation. F-factor gene is encoded for on a plasmid. This plasmid also contains transfer genes.

F+ cells

Cells possessing f-factor gene

Hfr cell

High frequency of recombination cell. F factor is on chromosome.


Can be discriminatory (species specific) or indiscriminatory. Haemophilus is discriminatory and pneumococcus is not. Uptake by DNA binding proteins on cell wall. Cells w/ binding protein are considered competent


Bacteriophage genes integrated into host cell DNA. Phage encorporates the wrong part of host DNA into phage head. Generalized if any part of host chromosome is packaged. Specialized if a certain area is selected for (those around prophage genes).


Jumping genes. Contain sequences for excision and reinsertion into the chromosome. If inserted into other gene, inactivate that gene.


Homologous (between similar DNA sequences), can result in drug resistance, virulence factors. Can occur w/ transposons.

Pathogenicity island

Virulence genes usually localized on chromosome

Beta phage

Gives virulence to C. diphtheria

Antisense DNA

Binds specific sites on mRNA that are therapy targets and block translation. Can not be used for non-functional genes (CF, sickle-cell)

Triplex DNA

Insert third strand to prevent transcription. Early stages of technology


Quarternary ammonium compounds

Found in mouth wash. Cetylpridinium chloride. Antiseptic

Resistance mechanisms

Drug inactivation, altered uptake, altered target

Krby-bauer method

Disk diffusion method. Plate is incubated and zone of inhibition measured. Inhibition zone is compared against a standard.

Inhibition zone

Area of no bacterial growth

Broth dilution method

Dilution of drug in liquid medium and inoculated w/ organism. Determine minimum concentration (MIC) of drug needed to suppress growth and minimum bactericidal concentration (MBC). Agent is bactericidal if MBC < 4MIC


e.g. Chloramphenicol. Block attachment of amino acids to 50S subunit. Bacteriostatic. Resistance by modifying drug via enzymes. Limited applications.


e.g. Erythromycin. Prevent peptide elongation by binding 23S subunit of 50S subunit. Bacteriostatic. Good intracellular penetration. Resistance by rRNA methylases


Inhibit 30S subunit to make ribosome unavailable. Bactericidal. Useful against Gram(-) infections. Resistance by modifying enzymes and altered uptake.


Block access of tRNA to mRNA-ribosome complex. Bacteriostatic. Treatment of choice for Rickettsial infections because it can enter cells. Resistance to drug by rapid drug efflux, altered target and modifying enzymes


Bacteriostatic. Binds 50S subunit to interfere w/ peptidyl transfer. Lincomycin, clindamycin (chlorinated derivative of lincomycin). useful in treating severe anaerobic infections.


e.g. Rifampicin (sweat and saliva turns orange). Binds to RNA polymerase and blocks mRNA synthesis. Broad spectrum including M. tuberculosis. Bactericidal. Restricted use to mycobacterial infections. High affinity for bacterial polymerases v. human polymerase. Affinity for plastics. Useful in treatment of infections involving prostheses. Resistance via altered RNA polymerase


Treat anaerobic bacteria and some protozoa (Giardia lamblia, Entaemoeba coli). Bactericidal. Forms toxic metabolite w/ anaerobic metabolism. Resistance rare: altered uptake or decreased cellular uptake


Colistin (polymyxin E), polymyxin B. limited spectrum (gram(-) bacteria); bactericidal. Free aa act as cationic detergents to destroy integrity of phospholipid bilayer. Nephro and neuron toxic. Applications include wound irrigation and bladder wash-out. Resistance via altered uptake/membrane structure


Structural analog of D-alanine. Blocks D-alanyl D-alanine peptide synthesis. Inhibits peptidoglycan subunit synthesis. Active against all mycobacteria. Second drug for TB


Prevents dephosphorylation of phospholipid carrier (bactoprenol): no regeneration of carrier. Active against Gram(+), Staphylococci, Streptococci. Only topical use


Vancomycin and teicoplanin. Large molecules; have difficulty penertraing Gram(-) cell wall. Narrow spectrum bactericidal. Complex w/ D-alanyl-D-alanine residues of cell wall precursor; inhibit transglycosylation. Incorporation into peptidoglycan precented. Will not work againt G- or mycobacteria. Use against G+ and rods resistant to beta-lactams. Resistance in staphylococci is rare. Applications restricted to severe life-threatening infections


Contain beta-lactam ring in structure. Penicllins, cephalosporins, monobactams, carbapenems. Active only on growing cells. Bactericidal. Do not work on intracellular species or on species w/o cell wall. Less active against G- bacteria. Resistance via altered target, altered uptake and drug inactivation.


Structurally similar to D-alanine D-alanine. Inhibits activity of transpeptidases (penicillin binding protein) preventing the formation of cross-links. Cell wall can not hold cells and cell will burst


Cephalxin, cefaclor. A Beta-lactam. Similar to penicillin but resistant to penicillinases. More effective against G- organisms. Different generations w/ each subsequent generation more resistant to bacterial resistance and more active against G- bacteria


Destroys beta-lactams thus protecting bacteria from drug activity. Staphylococci and other G+ bac. Excrete them extra-cellularly. More drug, more B-lactamase produced. G- bacteria have constitutive production of B-lactamase thus enough drugs will overwhelm B-lactamase

Beta-lactamase inhibitor

Clavulanic acid, sulbactam, tazobactam. Synergizes w/ beta-lactams to kill bacteria


Aztreonam. Synthetic. Single ring. Inhibits transpeptidase. Bactericidal. Only useful in G- bacteria. Pseudomonads and E. coli. Low toxicity


Primaxin. Penicillin-like. Inhibits transpeptidase. Bactericidal. Resistant to most beta-lactamases. Causes cell elongation and lysis. Most potent beta-lactam against anaerobes.


Sulfa drugs. Completely synthetic. Sulfamethizole. Sulfamethoxazole. Structure mimics PABA. Used by bacteria to synthesis folic acid. Faulty folic acid made. Competes for active spot of THFA which is needed to make purines and pyramidines. High affinity for bacterial enzymes. P. aeruginosa, enterococci, anaerobes are resistant. Plasma encoded gene transfers resistance.


Acts synergistically w/ sulfonamides. Bacteriostatic. Pyramidine analogue. Active against UTI and Salmonella typhi


Analog of nalidixic acid. Inhibits gyrase activity. 3 generations. Specific to bacteria. Mammalian topoisomerases unaffected. Can cause toxic effects on cartilage decelopment, so can not be used on children. Resistance is chromosomally-mediated. Altered DNA gyrase subunit structure. Can permeate intracellularly.


Isonicotinic acid hydrazide. Only effective against mycobacteria. Inhibts mycolic acid synthesis. Usually used in combination w/ other antimycobacterials


Used against Mycobacterium tuberculosis. Interferes w/ RNA synthesis. Mycostatic. Resistance develops quickly, so used w/ other drugs.

Microbial pathogenesis (Bacteria and Viruses)

Acute infection

Symptoms develop rapidly, but last only for a short time


Molecule present on a microbial cell that is responsible for enabling adhesion of organism to a host cell or to a surface

Antigenic variation

Alteration of the antigen surface components in order to evade the immune responses of the host.

Chronic infection

Symproms develop slowly and illness is likely to reoccur or continue for long periods. Symphilis, tuberculosis


The multiplication of an organism following adhesion to a tissue or a surface

Compromised individual

Individual w/ one or more defects in there natural defenses

Neutropenic patients

Highly susceptible to aspergillosis

Aspergillus fumigatus

Oppurtunistic parasite. Infects immunocompromised individuals

Exogenous infection

An infection due to an organism acquired from an external source such as food, water, animals or sexual contact.

Endogenous infection

An infection due to a member of the normally non-pathogenic microflora. E. coli cystitis and Candidiasis


Invasion/colonization by pathogenic microorganisms


Those organisms present at a particular anatomical site


Acquired in a hospital


A disease causeing organism


Ability of a microorganism to cause disease by overcoming the defenses of the host

Primary infection

Acute infection that causes the initial illness

Secondary infection

Caused by opportunistic pathogen after primary infection has weakened defenses. Influenza followed by Streptococcal pneumonia

Systemic infection

Infection that spreads throughout the body of the individual


Degree of pathogenicity of an organism.

Sterile locations

Blood, spinal fluid, organs

Acquisition of normal flora

Exposure at birth (changes w/ diet); environment (air, dust, food, water, human contact)

Survival of flora

Receptor availability; existing flora; evasion/survival of extreme unfavorable conditions

Normal flora pathogenicity

Microflora spreads to other body site (intestinal perforation, tooth extraction)

Non-normal flora pathogenicity

Changes in normal flora, changes in local environment, or deficiencies in immunity can lead to infection w/ non-normal flora pathogens

Ininfectious process

Entry, adhesion, invasion, dissemination, growth/multiplication, dissemination, release/transmission

GI tract infections

Faecal oral transmission; localised (diarrheal disease) or systemic (Hepatitis A)

Genital tract

Local lesions (HSV) or may spread e.g. Meningitis due to HHV

2ndary sites of infection

Delayed symptoms, incubation period, viral tropism for specific cell types and tissues


Rash due to infection of epithelial cells (contains infectious virus)

N. meningitidis

Blood borne organism that infects edothelial cells fo cerebral vessels and crosses blood brain barrier. Can be released from endothelial cells into CSF at choroid plexus


Axonal migration from peripheral nerve endings to CNS

Fetal infections

Virus from maternal circulation can infect placental cells, fetal circulation and tissues. This can lead to death or developmental abnormalities


Highly specific molecular interactions. Causes changes in bacterial phenotypes and host cell behaviour. Can adhere to skin, blood vessels and artifical surfaces such as titanium hip joints. Can occur via hydrophobic interactions, cation bridging, receptor-ligand binding. Can be directly to bilayer or surface receptors, or indirect via host molecules bound to cell. Receptors and ligands can be composed of proteins, polysaccharides, glycoproteins, glycolipids.


Bacterial structure involved in adhesion. All bacterial cell surface molecules can be involved in adhesion, but some molecules may exist specifically for that purpose


Multisubunit appendage involved in adhesion. Pili are composed of protein and carbohydrate


Infection of oral epithelium caused by C. diphteriae. Tissue specific


Urogenital epithelium. N. gonorrhoeae. Tissue specific

E. coli

Type I pili interact w/ mannose receptors on epithelial cells

Streptococcus pyogenes

M protein aa sequence overlaps w/ host components. Mediates attachment to host epithelial cells and resistance against phagocytosis (important in pathogenesis). M protein binds to C4BP (a regulatory of complement activation) w/ RCA still active. Bacteria is covered by compliment inhibitor thus blocking phagocytosis. Produces hyaluronic acid capsule that is antigenically identical to ground substance

Vibrio cholerae

Specific adhesion pilus (toxin coregulated pilus TcpA). Enables colonization of intestinal mucosa. Synthesis controlled by same regulatory system as for cholera toxin. Mutants lacking TcpA are avirulent

Viral adhesion

Receptor specificity narrowing target organs (increased specificity)

Hepatitis B

Increased tropism for liver. Chronic infection w/ virus continually detectable at low levels. Mild or no clinical symptoms


Adhesin: Haemagglutinin; receptor neuramic acid. Tropism for upper respiratory tract. Antigenic switching occurs with haemagglutinin and neuraminidase


Adhesin: envelope of gp120 proteins. Receptor CD4 proteins


Adhesin: Capsid protein; receptor intercellular adhesion molecules (ICAM-1)

Auto-immune disorders

Immune system is unable to distinguish clearly between self and non-self. Loss of tolerance.

Reiter's syndrome

Complication of shigella infection that leads to joint inflammation

Post-streptococcal rheumatic fever

Caused by certain strains of Group A Streptococci (GAS). Streptococcal pharyngitis can be followed by acute rheumatic fever. Streptococcal antigens cross react with heart muscle and valvular connective tissue. Evoke cross reactive T cells

Post-streptococcal glomerulonephritis

Can occur following pharyngitis, impetigo, and some other streptococcal infections. Characterized by hypoalbuminemia and salt retention. If antigen is in excess, formation of antibody-antigen complexes. Cross reaction between complexes and glomerular tissue. Results in inflammation and tissue damage

Systemic inflammatory response syndrome

The cross-reaction between antibody-antigen complexes and glomerular tissue

Systemic inflammatory response syndrome

Endotoxic shock, septic shock, sepsis. Infectious and non-infectious causes. In response to G- bacteria endotoxin or in response to peptidoglycan, teichoic acids, exotoxins, e.g. TSST-1, fungal cell wall components


Invasive organisms usually have longer incubation period. Invasion facilitated by enzymes (collagenase and hyaluronidase). Invasins induce endocytosis by host cells

M. Tuberculosis

Survives within phagocytic cells

S. typhimurium

Causes gastroenteritis. Can survive in phagocytic cells

B. burgdorferi

Causes lyme disease. Can invade epithelial cells


Produces lytic infection. Virus overruns cells and kills them off. Crosses blood-CSF junction (meninges or choroid plexus)


Oncogenesis. Irreversible. Stable intergration of viral DNA into host DNA. Host cells exhibit altered cell surface, metabolic functions and growth and replication patterns.

Cell fusion

Results in large multinucleate cells. Herpes viruses and paramyxoviruses.

Salmonella typhi

GI tract epithelia is site of epithelial invasion

Treponema pallidum

Urogenital tract is site of epithelial invasion

Mycobacterium tuberculosis

Respiratory tract is site of epithelial invasion. Forms granuloma that is immunosuppressive

Staphylococcus aureus

Skin is site of epithelial invasion. Protein A binds antibodies for evasion of acquired immunity.

sIgA evasion

By production of glycosidases or sialidases. Proteases. IgA-binding proteins

Lactoferrin-binding protein

Binds antibacterial protein allowing for evsion.

Efflux pumps

Removes antibacterial peptides from bacterium.


Protein or glycoprotein acting as an intercellular signal. Overproduction can overwhelm system with multiple signals.


Molecules capable of stimulating cytokine production. LPS, PG, LTA, lipoproteins of mycobacteria


Cytokine-like proteins. Affect IL-10 (imp. In controlling inflammatory response)


Viroreceptors = receptors for cytokines

Cholera toxin

Inhibits cytokines. Inhibits IL-12 secretion by APCs


Protein or polysaccharide that impairs phagocytosis. Adhesion by phagocytes is prevented. Capsule produces are Streptococcus pneumoniae and Haemophilus influenzae


An exotoxin that kills neutrophils and macrophages. Produced by Staphylococci and Group A streptococci (including beta-hemolytic strep). Can be released into surrounding environment or into phagocyte


exotoxins that acts to kill neutrophils and macrophages


Degrade sIgA. May also inhibit/inactivate complement

Psuedomona aeuruginosa

Produces an elastase that inactivates C3b and C5a


Capable of blocking MHC Class I/II-dependent antigen processing

Listeria monocytogenes

Listeriolysin can impair antigen processing


Highly potent protein exotoxins. Toxic shock syndrome toxin


Long term infection of cells (persistant, latent infections). No adverse effects on cell viability.

Pseudomembranous colitis

Results by the colonization of pathogenic organisms when the normal microflora has been disrupted


Granulocyte abnormalities that leads to an innate immune deficiency

Specific immune deficiency

Cell mediated immunity abnormalities as with AIDS


A toxin that allows for the spread of a pathogen


Spreads via nerves. Occult persistence. Intermittent flare-ups

Haemophilus influenzae

Spreads via CSF. Crosses blood-CSF barrier through meninges or choroid plexus

Blood dissemination

Hepatitis B and B. anthracis spread via plasma. HSV, listeria spread via mononuclear cells

Lymphatic dissemination

Spread from tissue fluid into lymphatic capillaries. Yersinia pestis, measles, polio and HIV


Pilin subunits undergo antigenic switching


Someone who can harbor and transmit a pathogen. May be asymptomatic. i.e. Women w/ Gonorrhea and early HIV

Francisella tularensis

10 to 50 cells is enough to establish infection --> tularemia


Need 106 cells to establish foodborne infectious disease

Host factors influencing infection

Age, sex, nutritional status, immune status, receptor sites (genetic)

Sites for shedding

Skin: from lesions such as warts, vesicle fluid (impetigo). Respiratory tract: infected droplets (influenza, tuberculosis). GI tract: faecally (salmonellosis, Norwalk virus). Body fluids: blood, milk (HIV, listeriosis)

Transformed cell

Viral DNA is integrated into host cell


Sepsis due to fungal infection

Angioinvasive aspergillus

Causes necrosis of the lung walls and bleeding

Fungal infection consequences

Mild to asymptomatic. Limited by immune responses. Delayed type hypersensitivity reaction. Chronic infection more common than acute. Often difficult to treat

Fungal virulence factors



Toxins (e.g.) aflatoxin

Keratin-digesting enzymes

Ability to grow at > 37 degrees

Candida albicans

Cryptococcus neoformans

Aspergillus flavus


Systemic fungi