Microbiology lecture note terminology

Microbial pathogenesis III: toxins

Cholera toxin

A:5B subunit toxin. Regulated by pH, temperature and osmolarity. Binds G-protein of adenylate cyclase complex causing stimulation block --> unregulated cAMP. Stimulates secretion of Cl- and H2O while inhibiting NaCl absorption --> severe fluid loss and electrolyte imbalance.

Toxin producing organisms

Bacillus anthracis, Bordetella pertussis, Clostridium botulinum, Clostridium tetani, Corynebacterium diphteriae, Escherichia Coli, Listeria monocytogenes, Pseudomonas aeurginosa, Shigella dysenteriae, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae

LPS toxins

Only act as toxins under certain circumstances. Endotoxins. LPS component of the outer membrane of G- bacteria. Released following bacterial cell death and lysis. Capable of activating almost every immune mechanism. One of the most effective immune stimuli known. Action of endotoxin is concentration dependent. Low concentrations canlead to fever, inflammation, vasodilation, increased antibody synthesis. Effect at high concentrations include shock and intravascular coagulation. Activation of complement, macrophages, and B-cells (via IL-1).

Protein toxins

Secreted into extracellular environment. Specificity varies. Exotoxins. Very potent

Vibrio cholerae

G- that produces an exotoxin.

Class I exotoxin

Superantigen toxins. Binds membrane of host cell surface. (TSST-1). Interact non-conventionally w/ immune cells. Results in direct stimulation of immune response (VERY POTENT). Can activate up to 20% of T-cells (2000X as many). Produced by staphylococcal and streptococcal species. Responsible for much of pathogenesis/toxicity

Class II exotoxin

Membrane damaging. (phospholipases, pore-formers).

Class III exotoxins

Intracellular (diphtheria toxin, cholera toxin). Entry by receptor binding, receptor mediated endocytosis (RME), and internalization. Composed of Active and Binding subunits. Common mode of action: ADP-ribosyltransferase.


Class II exotoxin. e.g. Lecithinase (clostridia). Causes enzymatic damage by utilization of phosphatidylcholine. Eliminates host defences and creates a nutrionally rich environment

Pore formers

Alpha-toxin of S. aureus. Pores are highly fortified protein structures. Resistant to protease and detergents. Cell death by osmotic lysis. Also called channel forming toxins (CFTs).

Diphteria toxin

Encoded by beta-phage. A:B subunit toxin. Must be proteolytically be cleaved to become activated. Single molecule sufficient for cell death. Inhibits protein synthesis by converting NAD+ + EF-2 --> ADPR-EF-2 + nicotinamide + H-.


Tetanus and botulinum toxins. Act intracellularly. Single polypeptide. Proteolysis and disulfide bond reduction. Binds to ganglioside receptors. Peptidases block release of neurotransmitters and inhibitory mediators.

Tetanus toxin

Clostridium tetani. Bacteria remains localized, but toxin spreadss. Binds presynaptic membranes of motor neurons. Migrates to spinal cord and brain stem --> degrades synaptobrevins. Inhibits release of inhibitory neurotransmitters such as GABA and glycine. Incubation of ~ 1 week prior to symptoms.

Botulinum toxin

Clostridium botulinum. Activated by intestinal proteases. Toxin carried in blood to neuromuscular junctions at peripheral nerve endings. Blocks acetylcholine relaxing muscles irreversibly. Can result in respiratory arrest. Symptoms include diplopia, dry mouth, pupillary abnormalities, ptosis, dysphagia, dysarthria. Usually occurs 4-36 hours after ingesting toxin


Produced by many group A beta-hemolytic streptococci. Plasminogen-->plasmin-->fibrin-->fibrin breakdown. Useful for treatment of pulmonary emboli and coronary thromoses

Indogenous pyrogens

IL-1 and TNF. Release can be caused by endotoxin.

High endotoxin concentrations

Systemic inflammatory response syndrome (SIRS). Hypotension, disseminated intravascular coagulation (DIC).

Limus test

Use amoebocytes from horseshoe crab. Endotocin --> degranulation and lysis of amoebocytes. Degree of reaction measured spectrophotometrically


Chemically modified toxin. Retains immunogenicity while losing toxicity


Antibody produced against toxin. Must be administered rapidly or will be ineffective

Serum sickness

Body producing antigens against forein antibodies (i.e. horse antibodies for tetanus)



Bacteria adhesed to a surface w/ a protective mucus layer. Resistant to antibiotics and WBC attack.


Free floating bacteria


Bacteria on biofilm. Act as reservoir for planktonic form

Sessile killing dose

1000X planktonic killing dose


Refers to the formation and growth of bacteria on a surface. All synthetic implants can be colonized. Middle ear is normally colonized. Prostate by age 50 is colonized in 100% of males (in a trial),


Must be removed to resolve infection

Nosocomial sites

ICU pneumonia, sutures, exit sites, arteriovenous shunts, schleral buckles, contact lenses, urinary catheter crystitis, peritoneal dialysis peritonitis, IUDs, endotracheal tubes, Hickman catheters, mechanical heart valvles, vascular grafts, biliary stent blockage, orthopedic devices

Cystic fibrosis

Provides ground for biofilm growth in lungs

Natural biofilm infections

Dental carries/peridontits, necrotizing fasciitis, osteomyelitis, endocarditis, pneumonia Cystic fibrosis


Trials suggest that it may be effective in clearing biofilm infections


Acute infection

Brief/severe infection

Anchorage dependent

Can not grow in suspension. Tumor cells are anchorage independent


Virus that infects a bacterium


Branching off of cell. Slowly leaves cell taking part of cell membrane (envelope).


Protein coat or shell surrounding nucelic acid. Coded for by protemers


Noncovalent aggregations of protomers; usually visible by electron microscopy

Cell culture

The maintenance or growth of dispersed cells after removal from the body, commonly on a glass surface immersed in nutrient fluid. Primary cell line, directly from the animal. Secondary cells are adapted to gorwth medium (may be different).

Chronic infection

Long term low grade infection


Complex virus

Conditional lethal mutant

Deletion mutant

Mutation in which amino acids (nucleic acids) are lost. Can be used for attenuation

Disseminated infection

Eclipse phase

Infectious virus cannot be recovered from infected cells; uncoating has occurred and viral macromolecular synthesis is underway. Time from viral entry to production of mature virus in cytoplasm.



Substance surrounding a virus. Not naked (proteins/nucleic acid).

Extra cellular virus

Has no metabolism.


Things that will pass through bacterial filters


Complete set of genes for an organism

HeLa cell

Cervicle cancer cells isolated from a patient. Continuous immortalized cell line


Group of protomers grouped into 6 sided figure


A quantal assay. Infectious dose 50. What dilution will kill 50% of population.




Type of viral structure. 5-fold axis of symmetry through corners; 3-fold through center of each face; 2-fold through middle of edge (5:3:2 = pentagon:triangle:line)



Warning system for surrounding cell saying: “I'm infected”. Other cells will then be protected. Successful viri must have a way to overcome interferon.

Interference assay

Intracellular virus


LCM model infection

Latent infection

Viral genome can be detected but infectious virions are not produced except in certain conditions (Herpes, adenovirus). Herpes stays as DNA only

Latent phase

Progeny virus accumulates intracellularly or extracellularly. Can see free virus being released; different families have different time periods. Time from viral entry (mature virus) to production of mature virus

Local infection

Marker rescue

Mosaic envelope

Multiplicity reactivation

Nucleic acid

RNA/DNA. Genetic material


Enveloped virus. Capsid in a lipid bilayer


Reserved for structures found within complex: virion & typically is not used to describe helical nucleocapsid; (shell/capsid containing nucleic acid). Capsid in a protein coat

Oncogenic virus

Virus capable of transforming a cell

One step growth cycle


5 protomers grouped together.

Penton fibre

Long viral glycoproteins found in the adenovirus. Attachment protein. Specific to the virus (i.e. Coded for by the virus)


An area of clearing in a flat confluent growth of tissue cells. Plaque assay find regions of wholes in cell monolayer after virus has been added. (Virus particle enters and kills cells and neighboring cells). Non-permissive cells will not form plaques

Peplomer (spike)

Viral glycoproteins that produce or project from the envelope. Attachment protein. Can be used for viral identification. Can be used for diagnosis. H5/N2 strains are differentiated by peplomer structure


Embryonated agges. Used to distinguish pox. Chicken pocks will give many small hemorhages.


Infectious protein



Basic unit of viral capsid. Capsomeres are made of protomers. 3 protein subunits. Asymmetric.



Mostly occurs w/ DNA viruses. Retroviruses w/ proviral DNA


Like recombination, but in RNA. Segments assembled in incorrect order.

Scanning Electron-microscope

Able to visualize characteristics of viri. Does not distuinguish between virus and virion. Gives total number of particles not all of which are infective.

Target tissue

Cells w/ receptors for virus (cells that will be infected by virus) and will result in clinical disease upon infection



Expression of certain viral genes in animal cells which alters morphological and biochemical properties characteristic of neoplastic cells or tumor cells. Transformed cells do not necessarilly produce tumors. NON-PERMISSIVE cell w/ DNA virus or RNA retrovirus

Transformation assay

detects “altered,” non-permissive cells. Morphology of transformed cells can change.


Genes from one virus, capsule from another virus

Viral hemagglutination

Allows u to get the viral concentration using adhesion to RBCs. Virus will cause RBCs to stick together. Virus must intrinsically be able to bind to RBCs. NON-Serological test.

Viral neutralization

Antibody binds to virus. Antibody is detected by attachment to the cell. Neutralization test tests only antibodies against a given species not the presence of that species. Serological test


Obligate intercellular parasites “filterable aents” which on their own are inert biochemical complexes. DO NOT GROW


Infective part of a virus. All parts needed to infect: protein/nucleic acid


Infectious agents composed exclusively of circular single stranded RNA w/ regions of double strandedness. Causes disease in plants

Von Magnus phenomenon

No proof reading of viral nucleic acid leading to production of large quantities of defective and modified viri and also antigenic shifting.

Vector borne

Carried by a “vector” such as an arthropod. Has a transmitting agent


Particles produced from assembly of preformed components. Process leading to synthesis of progeny viral genomes


dsDNA Naked, icosahedral virus. Penton fibers at vertices

Herpes virus

dsDNA enveloped icosaheddral virus. Projections or knobs on envelope


Class V. Has envelope and peplomer. Activity on one peplomer.. ssRNA, enveloped helical. Causes infections mainly in children


Segmented ssRNA, enveloped helical virus with peplomers (spikes)

Productive outcome

Infectious progeny are produced by permissive cells. 17 day old embryonic rat liver cell is susceptible to polio virus, but no 19 day old cell. 17 day old leads to productive outcome

Abortive outcome

No infectious progeny are produced; non-permissive cells may be susceptibile to infection but may not allow virion formation.


The only RNA viruses with demonstrated oncogenicity

Cis activating retrovirus

Have no oncogenes but activate cellular oncogene in situ

Trans acting retrovirus

Have no oncogene but carry a viral transactivating protein


Empty protein shell (not infectious)

Pox virus

Has thick protein coat.


Most common viral infection uder age of 5 (childrens infection). Double capsid. Characteristic capsid can be used for identification


Tissue affinity. Defines the capacity of a virus to infect a discrete type of cell. Used as classification until it was learned that viri can infect different tissues.

Hepatitis viruses

All infect liver and have same pathology


Family of viruses. e.g. Herpesviderae.


Sub-family. e.g. Lentiviriniae


Nucleic acid is the most important criteria for classifying bacteria. Enveloped/nonenveloped, size, shape, symmetry, capsid morphology

Hepatitis A

Is not destroyed by boiling water.

Small pox

Stable to radiation, thermal, pH.


Can cause eggs to smell by producing H2S. Black deposit in air sac of boiled egg

Cytopathic effects

Things you look for when trying to determine type of infection, pocks, plaques, and transformation assays. Lysis, necrosis (cell death but no lysis), syncytium formation (multinucleated giant cells), vacuolation or inclusion body formation.


Digests peplomer subunit. Can then detect digested components.

Serological test

Much more sensitive. Other tests may not detect virus. Primary highly specific, but may not be detected. Immunofluorescence can improve detection.

Hemagglutination inhibition test

Antibody test. Add antibody to virus, add RBCs. If no agglutination, antibody is for added virus. 4X increase in serological titier to serologically confirm a disease. Serological test

Host range

Defines the types of cells, tissues species that can be infected and in which the virus can multiply

Portal of entry

Cells initially infected where a virus enters a host

Target cells

Cells which, when infected results in clinical disease. May not be portal of entry

Syncytium formation

Herpes virus, HIV can cause this. Giant cell formation


Cell may become permissive, but virus must wait

Cytocidal infection

Infection that leads in cell death (lytic infection)

Persistent infection

Non-lytic. Host immune response must be avoided. Hepatitis B, Measles, HIV


DNA virus that do not transform cells


Do not need to integrate into host cell genome

Reverse transcriptase

Used by retro viruses to produce DNA. Necessary for transforming RNA viruses


Transfer of genetic material from one host to another by a virus.


Cellular sequences acquired by a retrovirus and can be transferred to host cells (the source gene)


(attachment) Specific binding of a host virion protein to a host cell surface (receptor). Can take 6 steps before penetration can occur.


Energy dependent stage that occurs rapidly after attachment leading to the introduction of viral genetic material, usually accompanied by at elast some viral proteins, into the interior of the cell

Membrane-envelope fusion

Viral envelope fuses w/ host cell membrane


Used by a naked virus

Receptor-mediated endocytosis

Method of viral entry. Used by a virus with a capsid


Term applied to events that occur after penetration and that set the stage for the viral genome to express its functions. Usually involves removal of certain viral proteins

Viral locations

RNA viruses stay in cytoplasm, DNA viruses go into nucleus

Pox virdaes

DNA virus that stays in cytplasm

RNA virus that goes into nucleus


Assembly of virion components into virions; maturation events involve structural changes that occur during or following assembly.


Release of virus from cell

Baltimore classification

Based on relationship between the viral genome and the mRNAs used for translation of viral proteins.

Positive sense

Positive polarity. mRNA sense of RNA. RNA that is transcribed directly

Negative sense

The complimentary strand of positive sense RNA. No enzymes exist to turn negative sense RNA in cell. Virus must bring RNA-dependent RNA polymerase w/ it.

Virus associated enzyme

Virus brings pre-made enzyme with it

Class I virus

DNA virus used to synthesize mRNA to make immediate early proteins, then early proteins which can make progeny DNA which can then make late proteins which will make the progeny VIRUS.


Class I ds, circular DNA


Class I ds, linear DNA + 55S protein


Class I ds, linear DNA


Class I ds, linear DNA w/ closed ends. Does NOT go into the nucleus. Brings its own enzymes.


Class II ss, linear DNA. 50% of viral progeny are positive strand and 50% are negative strand


Class II ss, circular DNA. Can cause tt hepatitis.

Class II virus

Single stranded DNA. Virus DNA (+strand) --cellular proteins--> double stranded DNA --> mRNA --> virus proteins. dsDNA + virus proteins --> progeny virus.

Class III

Double stranded RNA. Double capsid virus. Virus RNA –virion enzyme--> mRNA --> virus proteins. viral RNA --> progeny RNA. Viral protein + progeny RNA --> progeny virus


Class III, linear RNA. Induces interferon.


10 segments.


11 segments. Most common viral diarrhea under the age of 5.

Class - IVa

Virus RNA --> poly-protein --> protein cleaved --> structural and enzymatic components. Virus Enzymatic proteins duplicate RNA. Only positive strand is encapsulated. Must become double stranded to replicated; therefore, interferon can be triggered.


Class IVa, +, ss, linear RNA


Class IVa, +, ss, linear RNA. Hepatitis E


Class IVa, +, ss, linear RNA. Yellow fever, dengae, hepatitis C

RNA dependent RNA polymerase

Makes complement strand which can then make more original strands.

Class IV b

Original virus RNA codes for enzymes to make complement strand which can then make mRNA to make viral structural proteins to make progeny virus.


+, ss, linear RNA


+, ss, linear RNA

Class V

Negative polarity RNA. Virion enzymes make mRNA which codes for viral proteins that can then make more -pol RNA to be packed.


-, ss, linear, 8 segments. influenza


-, ss, linear, Vaccination possible


-, ss, linear Rabies


-, ss, Ebola, marberh, ambisense


-, ss, 3 segs. Hanta virus


-, ss, 2 segs, ambisense

Class VI

Retro-viri. Positive polarity. Reverse transcriptase converts RNA to ddDNA --> mRNA --> viral proteins --> mRNA --> progeny virus (contains viral proteins, reverse transcriptase and mRNA).


Class VII

Virus DNA partially ds circular DNA. Becomes supercoiled DNA upon entry into cell. Makes pregenomic mRNA and mRNA. Pregenomic mRNA makes progeny virus. Normal mRNA codes viral proteins that assist in making the pregenomic mRNA and put it into the capsid. Hepatitis B. reverse transcriptase activity makes progeny DNA.


Class VI, ss RNA, diploid


Class VII

DNA virus evolution

Low rate of mutation. DNA polymerase has proof reading

RNA virus evolution

High rate of mutation, highest variablility, instability of RNA polymerase and lack of proof reading, reassortment of segmented RNA viruses. Antigenic shift and drift

Antigenic shift

A sudden change in antigenic type. RNA-reassortment. RNA polymerase may shift segments, so order of RNA is different. Known to occur in influenza Type A. change occurs in one generation.

Antigenic drift

Gradual accumulation of mutations. Usually a one point mutation. Known to occur in influenza viruses. Over many generations, virus is of a different type.


A mutant virus w/o virulence. Danger of back mutation. All live virus vaccines are based on attenuated viruses. ***Stimulated IgM, IgM and IgA***. Limited need for boosters. danger of reversion to “wild type”. Less stable (labile), risky in compromised host, contraindicated in pregnancy. Long term immunity, local immunity (IgA). Cost

Conditional lethal mutants

Select for viruses that dies under certain condition

Phenotypic mixing

Transcapidation, mosaic envelopes. Same genotype of virus, but phenotype is changed.


Takes more than one copy of a given segment is put into a capsule. HIV requires polyploidy. 2 positive strands must be put into the capsule

Mosaic envelopes


Both viruses are put into capsule

Defective interfering genomes

A defective virus requires a homologous helper virus in order to replicate. The defective virus then suppresses the original virus. Coxaki, parovirus. Adenovirus needs to be there for some parovirus to replicate. Class IVa can be problem with RNA polymerase. Can contain multiple origins of replication. May attenuate virulence, cause persistent infections, cause chronic disease. May be used in vaccines



Carriers that inocculate people with viri. Mosquitoes, arthropds, rats. Most hemorrhagic fevers transmitted by vectors (mainly rats). Control of vectors --> control of disease

Public education/awareness


Immunological therapy

Usually high effacacy, narrow spectrum, relatively long duration


Moderate efficacy, narrow spectrum, very short duration

Interferon therapy

Moderate to high efficacy, broad spectrum, short duration

Inactivated/killed vaccines

May not get complete inactivation, may not confer complete immunity. Works mainly against peplomers. Safe, stable, can be used in compromised hosts. DO NOT PRODUCE IgA. Produces IgM, IgG. Needs boosters. Limited epitope recognition. No local response.

DNA genetic vaccines

Non-replicative in vivo. Easy to prepare. Low level and long term expression of antigens. Ability to modify vectors. Inherent adjuvant activity. foreign DNA may integrate into host DNA disruptine normal genes, causing malignant transformation. Immunologic tolerance may be lost --> Autoimmune disease may be triggered.

Passive immunization

Immune globulin prepared from donors recently recovered from the disease. Used in the immunocompromised or with another vaccine. Used for rabies and tetanus.

Antiviral chemotherapy

Should be specific, nontoxic and selective. Protease inhibitors. Glycosidase inhibitors. Bacteriostatic. Reverse transcriptase is unique to viri, so a good target.

Combination therapy

Synegisic effects. May decrease development of mutants. Acts at multiple points along line of viral replication.

Herpes virus

Shows resistance to chemotherapy


Small glycoproteins. Can be released in response to viruses (dsRNA), bacteria, cytokines, mitogens, tumor promoters. Non-specific defence mechanism. Non-toxic, short acting

Interferon Type I

Human type I specific to humans. General acting against viri. IFN alpha: leucocytes; IFN beta: fibroblast; IFN omega: trophoblast

Interferon Type II

Viral specific. IFN gamma: effector T-cells.

2,5-oligoA system

RNase L

IFN gamma

Used against hepatitis C. triggers inflammation

Nucleoside analogues

Defective nucleoside inserted into viral genome preventing the spread of the disease

IFN alpha

Activates natural killer cells

Additional random material

MacConkey agar

Enterobacteriaceae. Differential agar.

Eosin-methylene blue (EMB)

E. coli and Enterobacter aerogenes. Differential agar

Salmonella-Shigella agar

Selective media

Manitol salt agar

Selective media