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Flashcards in General Deck (151)
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1
Q

Colonizers

A

non-pathogenic organisms that live in gut/skin

prevent pathogenic organisms from overtaking systems and harming host

provide essential functions, eg. fermentation of carbs, Vit K

2
Q

OpportunistsOpportunists

A

Organisms that normalyl do not cause harm.

Can cause disease when “given the opportunity”; eg in catherizations for Staphlococci

3
Q

Pathogen

A

Organism that is always harmful to host; eg Ebola

4
Q

Methods of Identification of MIcrobes

A
  • naked eye
  • light microscope (w/ and w/o stains)
  • electron microscope
  • antigen recognition: flourescent dyes, serology
  • biochemical properties eg. testing of enzymatic activity
  • PCR or gene sequencing
  • protein detection
  • culture
5
Q

Differential Diagnosis

A

List of possible diagnoses for the signs/symptoms of the patient

–>involves figuring out infectious state, infectious agent (bacterial v viral)

–>takes into account pattern recognition, exposure risks, incubation times and epidemiology

–>confirmed by microbiological diagnosis

6
Q

Koch’s Postulates

Critique

A

Purpose: to identify the organism causing an infectious disease

  1. The microorganism must be found in abundance in all organisms suffering from the disease, but not in healthy organisms.

Some people are carriers

  1. The microorganism must be isolated from a diseased organism and grown in
    pure culture.

Viruses/prions don’t can’t be grown in pure culture

  1. The cultured microorganism should cause disease when introduced into a
    healthy organism.

Very difficult to test without animal models

  1. The microorganism must be re-isolated from the inoculated, diseased
    experimental host and identified as being the same as the original causative agent.

Some diseases can be caused by multiple organisms

7
Q

Koch’s Postulates–when they’re not met, what do you need to implicate a particular organism as the cause of disease?

A
  • biostatistical tests of association
  • serological surveys in human populations
  • epidemiologic studies (case controlled)
  • molecular pathogenesis postulates
8
Q

Molecular Koch’s Postulates

A

Purpose: to identify whether a factor produced by a pathogen is important for causing disease

–>Identify virulence factors

a) the phenotype or property encoeded by the virsulence gene should be associated with pathogenic strains
b) specific inactivation of the virulence gene encoding the suspected virulence strain should lead to measurable loss of virulence
c) addition of a cloned copy of the wild type gene to the mutant should restore virulence

9
Q

Microbiologic Testing Methods

A

a) Qualitative

Negative or positive

Negative result takes 5-42 days to process (growth rate dependent); high flase positive rate

Used for sterile body fluid analsysis

**b) Semi quantitative **

Specimen is directly stained w/ result expressed in a gradient (eg. low, med, high)

**c) Quantitative **

Specimen is direclty stained and known volume is pltated

CFU/mL calculated

10
Q

Blood culture collection

A

2 sets of 2 bottles are collected (one for aerobe, one for anaerobe)

different sites are used

Purpose: to differentiate between contamination and true bacteremia

**Blood should be sterile**

11
Q

Urine culture collection

A

Skin around urethral meatus may be contaminated. To check for true infection look for:

WBC, absence of epithelial cells, >100k bacteria/mL, one kind of bacteria in culture

12
Q

CSF Culture collection

A

CSF should be sterile; can be tested via lumbar puncture

–>look for WBC, high protein, low glucose as infection markers

13
Q

Virulence Factors

A

Factor produced by a pathogen that causes disease

eg. Toxins, adhesins, capsules

14
Q

General Infectious Life Cycle

A

Entry

Adherence/Colonization

Invasion

Evasion of host defenses

Damage

Dissemination

15
Q

Virulence

A

the degree of pathogenicity as indicased by case fatality rates and/or the ability of the organism to invade the tissues of the host

16
Q

Transposons

A

contain genes required for movement as well as additional genes such as antibiotic resistance, toxin production, etc.

“Jumping gene” –> can disrupt virulence gene thereby eliminating virulence factor production-

have interverted repeats

17
Q

Bacteria with sterols in plasma membrane

Bacteria w/o cell walls of peptidoglycan

Bacteria that do not make their own energy

Gram pos bacteria w/ endotoxin

A

Mycoplasma, H. pylori, Borrelia burgdorferi

Mycoplasma, Chlamydiae

Rickettsia, Chlamydiae

Listeria monocytogenes

18
Q

Transpeptidases

A

AKA pencillin binding proteins

Carry out peptidoglycan crosslinking (cell wall synthesis)

19
Q

Gram neg/gram pos

A
20
Q

O Antigen

A

Provides bile resistance

–>LOS lacks O antigen and is found in non-enteric Gram-neg bacteria

Provides resistance to lysis by complement

used for epidemiologic serotyping

21
Q

Porins

A

Allows movement of molecules across outer membrane in Gram neg bacteria

Alterations/loss of porins is a mechanism of antibiotic resistance

22
Q

Important Factors for Bacterial Growth

A

Temperature

pH

Oxygen (Redox) conditions

Nutrients (eg iron)

Osmolarity

23
Q

Why are some bacteria anaerobic

A
  • often lack catalase
  • often lack superoxide dismutase
  • often have sensitive enzymes that must be in a reduced environment to function properly

**IOW: anaerobes must be in a low redox environment

24
Q

Endospores

A

Resistant to destruction via heat, radiation, chemicals and drying

–> due to low water content and DNA stabilizing proteins

Sporulation is not a reproductive strategy: it’s survival

25
Q

Pharmacokinetics v Pharmacodynamics

A

Pharmacokinetics
–the ways the body manipulates a drugs:

absorption: bioavailabitlity
distribution: measured by Vd

metabolism

elimination: renal v hepatic

Pharmacodynamics
–the biochemical and physiologic effects of the drug and its mechanism of action: MOA, toxicities, dosing strategies for optimal kills, static v cidal activity

26
Q

Minimum inhibitory concentration

A

the lowest concentration of antibiotic that results in no visible growth

27
Q

Bacteristatic (5)

A

an antibiotic which only inhibits growth at usual achievable concentrations

eg tetracyclines, macrolides, clindamycin, linezolid, tigecycline

28
Q

Bactericidal (7)

A

An antibiotic which kills organism at usual achievable serum concentrations

eg: penicillins, cephalosporins, aminoglycosides, vancomycin, fluroquinolones, monobactams, daptomycin

*Critical for life threatening infections

29
Q

Antibiotic v Antimicrobial

A

TL;DR: Antimicrobials include antibiotics

Antibiotics
Produced by a microorganism
Kill or inhibit the growth of other microorganisms (usually bacteria)
Beta-lactams, aminoglycosides, etc.

Antimicrobials
Any product that kill or inhibit the growth of microorganisms (bacteria, fungi, viruses, parasites)
Includes all antibiotics
Some are fully synthetic, e.g. fluoroquinolones

30
Q

Types of Antimicrobial Therapy (5)

A

Prophylaxis: use of antimicrobial agents to prevent infection eg. before surgery

Pre-emptive antimicrobial therapy: starting antimicrobial therapy when lab markers indicate infection or ractivity but NO clinical signs of disease are present eg. bone marrow transplant patient with increasing CMV titer

Empric therapy: use of antibiotics in a patient w/ a suspected infection before the etiology of the infection is known; not usually done in chronic infections

Pathogen directed therapy: the organism is known but the antibiotic susceptibility is not

Susceptibility guided therapy: organism is known, antibiotic susceptibility is know: opportunity to streamline therapy o be most effective, least toxic, w/ narrowest spectrum, cheapest

31
Q

Disk diffusion

A

Clear zone size correlates with susceptibility

32
Q

MIC’s E test

A

combines disc diffusion methods w/ MIC methods through use of rectangle paper impregnanted w/ various doses of drug

33
Q

Concentration dependent killing

A

Maximal killing at maximal concentrations
Upper concentration limit is the concentration that will produce toxicity

aminoglycosides, fluoroquinolones

34
Q

Time-dependent killing

A

Do not achieve greater killing at high concentrations
Time above MIC is the important consideration

beta lactams (except those w/ long half life) and vancomycin

35
Q

Horizontal Gene Transfer in Bacteria

A

Genetic transformation: transfer of naked DNA between cells; Natural transformation occurs in bacteria that produce a protein called the “competence” factor. Homologus recombination of the DNA occurs via the RecA protein

Transduction: DNA transfer mediated by a bacterial virus (phage)

Conjugation: DNA transfer involving direct cell to cell contact mediated by conjugative plasmids

36
Q

Bacterial Plasmids

A

Extrachromosomal elements that exist in bacterial cells and have the ability to confer new genetic properties on the bacterial cell. They are usually circular, double stranded DNA molecules.

–l>inear plasmids are also found in nature

Often contain drug resistance genes

Very stable and rarely lost from bacterial cells

Carry genes that allow them to replicate independently of the bacterial chromosome

Require host proteins and enzymes for replication

37
Q

R plasmid

A

AKA Resistance factors

Conjugative

have a broad host range and can transer b/n different bacterial species

Structure: tra gene (sex pilus gene), drug resistance genes, replication region, inserstion sequences and transposons

is conjugative

38
Q

Virulence Plasmids

A

Carry genes that encode toxins and other virulence factors

eg. toxin proteins carried on plasmid (anthrax and tetanus)

39
Q

Structure of a Conjugative R plasmid

A

Initiate their own transfer from cell to cell
Contain tra genes that encode the sex pilus through which the DNA is transferred
Contain oriT which is nicked by a relaxase to initiate the transfer of a ss of plasmid DNA
Usually contain insertion sequences and transposons
Can also promote the conjugative transfer of mobilizable plasmids containing oriT
Are highly promiscuous

eg R plasmids

40
Q

Transposable Elements

A

Transposable (Tn) elements are specific DNA segments that can repeatedly insert at many sites in a genome. Carry one or more genes encoding drug resistant, toxin production, etc to a host cell. Normal contituients of bacterial plasmids and chromosomes. Are always part of a genome.

  • *Insertion sequences (IS):** Small elements (~ 750 bp-1.5 kb) which only carry genes that are required for movement
  • *Transposons (Tn):** contain genes required for movement as well as additional genes such as antibiotic resistance, toxin production, etc.

Replicative transposition involves replication of the Tn and results in duplication of the element
Conservative transposition involves simple cut-and-paste insertion of the Tn at the target site
Transposition can be Intermolecular (between two genomes) or intramolecular (within the same genome)

41
Q

Viruses

A
  1. Obligate intracellular pathogens (they require the host cell for replication)
  2. Have DNA or RNA, not both.
  3. No independent energy production or protein synthesis
  4. Usually show selectivity for infecting particular types and/or species of host cells 5. Not sensitive to antibacterial/antifungal antibiotics (e.g. penicillins)
42
Q

H antigen

A

found on flagella

43
Q

K antigen

A

capsular antigen

44
Q

Sterilization

A

all microorganisms are killed

45
Q

Disinfection

A

pathogens are killed but some other organisms may remain

46
Q

Pasteurization

A

brief exposure to heat, kills all pathogens

47
Q

Antiseptic

A

disinfectant that kills/inhibits microorganisms when applied topically

48
Q

Antimicrobial Chemicals

A

a. Agents that affect membranes:
i) 70% ethanol (bactericidal)
ii) Quaternary ammonium detergents (bactericidal)
iii) Phenols: used in disinfectant solutions (e.g., Lysol).

b. Agents that modify proteins:
i) Chlorine: water purification, active component of hypochlorite solutions used as disinfectants at hospitals. Cross-links cysteines to inactivate proteins. Bactericidal.
ii) Iodine: used as skin antiseptics prior to surgery. Often bactericidal.
iii) Hydrogen peroxide: weak antiseptic often used topically.
iv) Ethylene oxide: gas used extensively in hospitals to sterilize heat-sensitive items. Inactivates proteins.

49
Q

Antimicrobial Physical Agents

A

a. Heat
i) Autoclaving: sterilizes using heat under pressure to achieve high temperatures.
ii) Pasteurization: removes most pathogens by heating to 60-65°C.
iii) Dry heat: can be used to sterilize objects sensitive to moist heat.

b. Radiation
i) Ultraviolet: can be bactericidal but doesn’t penetrate well; sometimes used to disinfect hospital rooms.
ii) Ionizing: bactericidal; used to sterilize disposable surgical/medical supplies.

c. Filtration
i) Used to sterile very heat-labile substances
ii) Bacteria are too large to pass through filter pores and are thus remove from the filtered solution.
iii) Filters do not remove viruses.

50
Q

Conjugative Plasmids

A

Found in both Gram negative and gram positive bacteria

51
Q

Plasmid Replicon

A

A plasmid replicon consists of:
a. Origin - the site of initiation of replication.
b. rep gene - encodes an initiator protein that is required for
plasmid replication.
c. Copy control gene (cop) - involved in controlling the
replication and copy number of a plasmid.

52
Q

Copy Number

A

the number of plasmid molecules per chromosome in a cell; the copy number for a given pladmi is fixed

–>large plamids usually have a low copy # and small plasmids a high copy #

53
Q

Tn3–the typical transposon

A

trpA gene: encodes the transposase protein required for transposition

tnpR gene: encodes repressor of transposition

Amp gene: beta lactamase which makes bacteria resistant to ampicillin

interverted repeasts

54
Q

NDM-1: New Delhi metallo-beta-lactamase 1

A

refers to a transmissible genetic element encoding multiple resistance genes

intrinscic ability to destroy most beta lactams including carbapenems

55
Q

Sources of Antibiotic Resistance

A

Introduction of resistant strains from outside the “community”
Acquisition of resistance from another strain
Emergence of resistance as a result of mutation
Selection of resistant strain by antibiotic pressure

56
Q

Mechanisms of Antibacterial Resistance: Enzymes That Destroy or Inactivate Antibiotics

A

beta-lactamases:

  • can have a narrow or extended spectrum
  • gene acquired from plasmid or bacterial chromosome
  • does not result in a “fitness cost” to organism
  • enzymatically hydrolysis the beta-lactam ring of antibiotic–>inability of hydrolyzed product to bind to PCP–>resistance

EXAMPLES:

ESBL: extended spectrum beta lactamase–>notable for ability to affect advanced gens of Beta lactams including 3/4th gen cephalosporins

AmpC: tend to be inducible and can coade for broad spectrum beta lactamase activity (does not act on cefepime) and are not fully inhibited by beta lactamase inhibitors

carbapenemase

57
Q

Mechanisms of Antibacterial Resistance:Development of Altered Targets

A
  • Diminished ability of antibiotics to attach to bacteral target
    eg. PCP and beta lactam: PBPs are responsible for cross-linking of the cell wall; they bind beta-lactams which leads to inability of cell wall to form–>death. If a PBP has low afinity for beta-lactams, then the bacteria will be able to make the cell wall in the prescense of beta lactam antibiotics
    eg2. mutant peptidoglycan precursors and vancomycin-resistance
    eg3. alteration of ribosome and macrolide resistance
    eg4. quinolone resistance and alterations in DNA Gyrase: quinolones extert antibacterial effect by binding to DNA gyrase and preventing normal function–>mutation of DNA gyrase gene selected by exposure to quinolones–>alterations of DNA gyrase prevents binding of quinlones and conveys resistance
58
Q

Mechanisms of Antibacterial Resistance:Alterations in permeability of bacterial cells

A

Modification of porins may prevent or slowantibiotic entrance into cell

eg. Porins and P. aeruginosa

Quinolones/other antibiotics enter P. aeruginosa via the porin “OprD”–>decreased OprD expression–>altered permeability

59
Q

Mechanisms of Antibacterial Resistance: Prescence of Pumps which remove antibiotics

A

“Efflux” pumps: remove antibiotics from cell cytoplasm before it is able to bind the target

increased importance of pumps if there is already decreased susceptibility

60
Q

Mechanisms of Antibacterial Resistance: Highlights

A
  • there are 4 mechanisms
  • more than one mechanism can be working at the same time
  • multiple mechanisms are synergistic
61
Q

Mechanisms of Antibacterial Resistance: biofilms

A

in vivo mechanism of resistance

–>channels, quorum sensing, etc

62
Q

Vancomycin-intermediate S. aureus (VISA)

A

Mechanism is synthesis of unusually thickened cell wall containing dipeptides (D-Ala-D-Ala) capable of binding vancomycin which reduces availability of drug to reach intracellular target molecules

63
Q

Heterogenous vancomycin-intermediate S. aureus (hVISA)

A

subpopulations display variable rather than uniform susceptibility to vancomycin
hVISA populations withstand vancomycin by means of an unusually thickened cell wall

64
Q

High-level vancomycin-resistant S. aureus (VRSA)

A

Mechanism due to transfer of plasmid-mediated transfer of VanA gene cluster on transposon

65
Q

Fungi 101

A

Eukaryotic organisms w. more than one chromosome, mitochondria, ER, and 80S ribosomes.

Chemotrophic: secrete enzymes that degrade a wide variety of organic substrates into soluble nutrients which are then passively absorbed or taken into the cell by active transport

Reproduce sexually

non-motile

May produce spores

Rigid cell wall: chitin and glucan composition; also contains sterols and mannan

Stain blue w/ calcoflour, green with silver stains (cell wall), pink with PAS (only on living fungal cell walls)

Dimorphic in some species

66
Q

Fungal growth forms

A

Molds aka filamentous fungi

  • multicellular forms composed of hyphae (mycelium=many hyphae)
  • hyphae grow by branching and longitudinal extension; they are branched/tubular
  • fuzzy colonies
  • hyphae may be septate or non septate
  • speciated based on colonial morphology, color and microscopic appearance
  • saprophytic stage of dimorphic fungi

Yeast

  • independent single cells–>round to oval
  • form smooth flat colonies
  • Propagate by budding
  • speciated by biochemical test
  • parasitic stage of dimorphic fungi

Pseudohyphae

  • several elongated yeast cells chained together and resembling true hyphae

Dimoprhic Fungi

  • can grow either the yeast (in tissue) or mycelium (in environment) forms depending on environmental conditions
67
Q

Fungal disease

A

Overview

AKA mycoses–>superficial, cutaneous, subcutaneous, systemic and opportunistic variants

important resistance factor: phagocytosis by neutrophils and macrophages

non specific resistance: mechanical, humoral and cellular factor

specific resistance: cellular immunity

Allergies

due to spores

allergic rhinitis, bronchial asthma or allergic alveolitis

Toxicoses

due to mycotoxins

effect is indepenent of infection or viability

i.e. aflatoxins–>Aflatoxin B1: most potent carcinogen known to man (hepatocellular carcinoma)

68
Q

Types of Parasites

A

Endoparasites

live inside host; protozoa or helminths

Protozoa

unicellular, free living organisms

motile w/ flagella, cilia, pseudopods or apical microtubule complex

Helminths (worms): cause disease based on mechanical effects (intestinal obstruction), competition for nutrients or invasion of host tissues

1) Roundworms

intestinal nematode

tissue nematode (filaria)

2) Flatworms

flukes (trematodes)

tapeworms (cestodes)

Ectoparasites

arthropods or arachnids that fuilfill a life cycle requirement by being on the skin or hair of the host

sometimes disease is simply due to ectoparasite prescense, other times, the ectoparasite serves as a vector for bacteria/virus/protozoa

69
Q

Parasite Life Cycles

A

Parasites can take different forms (eggs, larvae, mature organisms, etc)
Parasites may require more than one host species within which they complete their life cycle

  • *Definitive host:** where the parasite reproduces sexually
  • *Intermediate host:** where the parasite reproduces asexually/larval stage
70
Q

Parasitism

A

type of symbiotic relationship where one organism depends on the other for survival at some expense to the host

71
Q

Common modes of parasitic transmission

A
  • fecal oral route
  • skin penetration
  • insect vectors
  • vertical transmission
  • inhalation of eggs
  • sexual intercourse
72
Q

Viral Diagnosis

A

incoculation of cell culture: plaque assay, transformation assay

immunohistochemical staining for antibodies

ID of virus particle or antigens–>eg through ELISA

detection of viral nucleic acids->PCR

Detection of viral (CPE) cytopathic effect (e.g. rounding of cells, cell lysis, syncytia formation = fused cells).

EM for detection of viral paricles

hemagglutination assay for erythrocyte lattice formation

73
Q

Viral Structure

A
  • Genome (DNA or RNA) enclosed within a protein shell called a capsid
  • Capsid symmetry: helical/rod shaped, spherical w/ icosahedral symmetry (w/ 2, 3 or 5 points of symmetry)

Note: helical viruses are always enveloped except TMV

  • Capsid composition: may or may not have capsomeres
  • Virus can be:
    1) enveloped-composed of a nucleocapsid surrounded by a lipid containing envelope
    2) non-enveloped- composed of a viral genome enclosed within a capsid (nucleocapsid)
74
Q

Virion

A

the intact infectious particle

75
Q

Viral genome

A

the viral nucleic acid (either DNA or RNA)

76
Q

Capsid

A

the protein shell surrounding the viral nucleic acid

77
Q

Capsomere

A

a clustering of capsid proteins discernible by electron microscopy

**capsomeres are basically building blocks that come together to make a capsid; not all capsids are composed of capsomeres

78
Q

Nucleocapsid

A

the viral genome + the capsid

79
Q

Non-enveloped virus

A

AKA naked nucleocapsids

have only the viral genome and capside

eg. Adenovirus

Stable against: temperature, drying, acid/detergents

Flourish in GI tract

80
Q

Enveloped viruses

A

have a lipoprotein membrane external to the nucleocapsid

eg Herpesvirus

**the envelope is an essential part of the infectious virion for these sorts of viruses–>w/o it, the viron is not infectious. This means that enveloped viruses are easier to destroy than non-enveloped viruses

Environmentally unstable–>need moisture to transmit (wet hands, snot, sexual transmission)

do not survive in GI tract

81
Q

Viral tropism

A
  • what cell types a virus can infect
  • determined by proteins on the viral surface–>iow, often the cell surface proteins that a specific virus binds is restricted to a specific cell type:

• Factors affecting viral tropism.

 - The proteins on the cell surface (presence of a viral receptor).
  - The proteins on the virus surface that interact with the cell surface receptor.  - capsid protein (non-enveloped virus) or glycoprotein (enveloped virus).
82
Q

Nuetralizing antibodies for viruses

A

can recognize and bind to proteins on the viral surface and interefere with the ability of a virus to enter a cell, thus nuetralizing the infectivity of a virus

  • Enveloped: neutralizing antibodies recognize the outer envelope proteins, typically glycoproteins that stick out from the lipoprotein membrane
  • Non-eveloped: nuetralizing antibodies recognize the capsid proteins
83
Q

DNA viruses: General Characteristics and Exceptions, and diseases caused

A

HHAPPPI: hepadna (HBV), herpes, adeno, pox, papova(HPV), parvo(B19, AAV), irido

  • double stranded DNA
  • linear genome
  • icosahedral capsid
  • replicate in the nucleus

-Enveloped: hepadna, pox, herpes, irido

-Naked: parvo, adeno, papova

Exceptions

Parvovirus–>single strand DNA

Papovavirus and Hepadnavirus–>circular genome

Poxvirus–>not icosahedral and replicates in the cytoplasm

Iridoviridae–>no known human diseases

84
Q

Reovirus

A

Double stranded RNA virus

naked (non enveloped)

segmented genome

cause of rotavirus

85
Q

RNA viruses that replicate in the nucleus

A

Influenza

Retroviruses

86
Q

Naked RNA viruses

A

Calicivirus

Picornavirus

Reovirus

87
Q

ssRNA + viruses

–>enveloped/naked, diseases caused, segmented genomes?

A

None segmented!

Enveloped

Togaviridae–Rubella

Coronaviridae–SARS

Flaviviridae–HCV, West Nile, Dengue

Retroviridae–HIV, HTLV

Note: retroviruses bring in RT, integrease and protease in virion

Naked

Picornaviridae–Polio, Hep A, Rhinovirus

Caliciviridae–Norovirus, Hep E

88
Q

ssRNA - viruses

–>enveloped/naked, diseases caused, segmented genomes?

A

–All enveloped!

-bring in a RNA polymerase in the virus particle

Segmented

Arenaviridae–Lasa Fever virus

Bunyaviridae–Hantavirus

Orthomyxoviridae–Influenza

Non-segmented

Filoviridae–ebola, marburg

Paramyxoviridae–RSV, PIV, measles, mumps

Rhabdoviridae–rabies

89
Q

Viral Life Cycle

A

1) Attachment
- involves finding the appropiate host cells, adsorbing/sticking to charged molecules/charged lipids on host cell surface and binding to other cell surface receptors that faciliate entry across the membrane
2) Penetration
- fusion of viral evelope and plasma membrane
- receptor mediated endocytosis (can occur w/ both naked and enveloped viruses)
3) Uncoating

can occur at the plasma membrane or within endosomes

4) Gene expression–>transcription and translation
5) Replication

Involved transcription (viral mRNA synthesis) and translation (viral protein synthesis)

Some DNA viruses have early and late phase of gene expression

Viruses encode their own polymerases (except parvovirus) to do this

6) Assembly / Maturation

Concerted Assembly: the nucleic acid is incorporated into the capsid as it’s being assembled; mechanism used by majority of viruses

Sequential assembly: the nucleic acid is interested into a preformed capsid shell.

7) Release
- infected cell may or may not die
- enveloped viruses may exist through budding or fusion of secretory vesicles

90
Q

Viruses that use host cell polymerase for replication

A

Parvovirus

single stranded DNA virus

91
Q

RNA to RNA enzyme

RNA to DNA enzyme

A

RNA dependent RNA polymerase; used by RNA viruses

RNA dependent DNA polymerase; used by retroviruses

92
Q

—Plus v Minus Strand—

What is a Plus strand?

What is a Minus strand?

A

mRNA is defined as the plus (+) strand because it contains immediately translatable infromation

A strand of DNA of equaivalent polarity is also a plus strand–>iow, if this DNA was RNA, it would be translated into protein

5-3 polarity

the RNA and DNA complement of the + strand is the - strand

the - strand CANNOT be translated; it must first be copied into a + strand

3-5 polarity

93
Q

“Early” v “Late” viral proteins

A

**Early Viral Proteins: **

important for altering the host cell and for viral genome replication (eg polymerase)

Made BEFORE genome replication

**Late Viral Proteins: **

important for virus structure and assembly (eg nucleocapsid and structural proteins)

made AFTER genome replication

**some large DNA viruses also have an “immediate early” phase before the early phase

94
Q

Hepatitis B virus

A

Hepadnavirus

incompletely double stranded DNA virus

unique DNA virus in that it uses RT for replication:

Gapped DNA repaired in the nucleus – covalently closed circle
Viral mRNA and Pregenomic RNA are made using host cell machinery.
Pregenomic RNA is exported to the cytoplasm where it serves as template for RT to form dsDNA within newly formed viral particles.
If enough envelope proteins available the particle is released from the cell if not the particle is directed back to the nucleus.

95
Q

Stages of Viral Pathogenesis

A

1) Entry into human host
2) Primary replication
3) Primary viremia (spread throughout the bloodstream)
4) Secondary replication
5) Spread to target organisms
6) Further replicaiton, cell injuary and clinical disease

96
Q

Routes of viral acquisition

A
  • Fecal/Oral: localized/systemic
  • Respiratory: upper/lower localized or systemic
  • Urogenital/sexual: localized or systemic

Eyes: systemic

Parenteral

Insect vector/animal bite

**Entry may be through one method but it may cause disease elsewhere/systemic disease

97
Q

Routes of Viral Dissemination

A
  1. -Hematogenous spread: viremia–>BLOOD
  2. -Localized spread: remain in close proximity to site of entry
  3. -Neural spread: infect and spread throughout the nervous system

Factors that Affect Dissemination

  • Portal of entry
  • Host immunity (innate and adaptive)
  • Cell specific virus receptors
98
Q

Outcomes of viral infection

A
  • Lysis of the infected cell (cell death).
  • No morphological or deleterious change.
  • Cell dysfunction/morphologic changes without cell death.
     Hyperplasia of cells 
    
      Excessive mucous secretion by cells 
    
        Syncytia formation
    
     Inclusion body formation    transformation of cell into immoratalized phenotype
99
Q

Latent/Chronic infections

A

-In latency: no production of infectious virus –>no replication of viral genome, no production of capisd strutural proteins

Latent viruses have the potential to undergo reactivation

Reactivation of latent viruses is in response to a stimuli (stress, injury, better cellular environment)

100
Q

Mechanisms of Viral Adaptation

A
  • point mutations: viral genomic replication is more error prone than cellular genomic replication
  • recombination of omologus nucleic acid sequences b/n related viral strains
  • reassortment of viral genes–>only with segmented RNA viruses

antigenic shift: sudden dramatic shift in viral antigen due to reassortment

antigenic drift: more subtle change in viral antigens due to point mutations

101
Q

Strategies of viral immune evasion

A

Latency. Minimal to no expression of viral antigens.

Infection of sites not readily accessible to the immune system

Antigenic variation: virus rapidly evolves and mutates antigenic sites that are critical for immune recognition

Antigenic variation: reassortment of viral genes (antigenic shift)

Viral “defense” molecules that interfere with immune function, such as antigen processing and presentation

Infection of immune cells with destruction or alteration of immune cell function

102
Q

Viral Diseases

Immediately Lethal

Self Limited

Contained-Not Eradicted

A

Rare viral diseases; cause intense vascular inflammation

eg Ebola, YF, Hanta virus

Most viral infections

Virus is eradicated by host immunity (T/B cell response)

  • Life-long immunity: Hep A
  • Short duration immunity: RSV

Chronic persistent: HIV, Hep C

Laten: Herpes

103
Q

Active Immunization Vaccine

A
  • Elicit a protective immune response: nuetralizing antibodies and cytotoxic T cells
    1) Live attenuated
  • weakened virus that can produce immunity w/o causing disease in the normal host
    eg) MMR, Flumist, OPV, Chickenpox, YF, smallpox, rotavirus
    2) Inactivated
  • viral antigens or recombinant proteins; safe in immunocompromised patients
    eg) Hep A, Hep B, Flu shot, HPV, IPV, rabies
104
Q

Passive immunization

A
  • Hyperimmune IG from human serusm: nuetralize virus and block infectivity by prohibiting viral entry into self,short half life, not widely used due to shortages and expense
  • Available: Hep A, Hep B, Chickenpox, rabies, CMV, RSV
105
Q

Virucides

A

Directly inactivate intact viruses

eg. detergents, UV lights
- limited use: muscocutaneous HSV< warts

106
Q

Immunomodulation (Viruses)

A

**stimulate the host immune response to contain or eradicate an infection **

1) inducing host factors w/ antiviral properties:

interferon-degrade viral RNA, inhibit viral protein synthesis and enchance CTL, NK activity and cytokine relsease

2) Decreasing immuno suppression:

treat HIV in AIDS patient w/ Kaposi sarcome

decrease dose of immunosuppressive agents in a kidney strandplant patient w/ EBC related lymphoma

107
Q

Antivirals

A
  • Target virus specific proteins: low affinity for host encoded proteins
  • act only on replicating viruses: viruses in latent/quiescent phase are not susceptible
  • effective in early phase of infection: often used to late to make an impact
  • development of drug resistance
108
Q

Mechanism of Action of Antivirals

A

**Polymerase inhibitors **

  • nucleoside/nucleotide analogues
  • pyrophosphate analogues

used for herpes viruses

Ion channel blockers

used for influenza

Neuraminidase inhibitors

used for influenza

+antivirals for Hep B and C

109
Q

Retrovirus Replication

A

Retrovirus Replication

  1. +RNA is converted to dsDNA using reverse transcriptase (RT) brought into the cell as part of the virus particle
  2. Integration of the viral dsDNA genome into host cell DNA to generate the provirus - integrase brought into the cell as part of the virus particle carries out this step.
  3. Viral mRNAs are made from the provirus genome using the host cell machinery.
  4. Viral mRNAs are translated by the host cell machinery
    - make capsid, envelope, RT, protease and integrase plus other viral proteins.
  5. Some of the viral RNA made in step 3 is packaged into new virus particles along with RT, integrase and protease to generate new infectious virus.
110
Q

Replication of - strand RNA viruses

A
  1. Negative Strand Viruses Require a packaged RNA polymerase.
    (-)RNA is converted to (+)RNA using RNA polymerase brought into the cell as part of the virus particle.
  2. Viral (+)RNA are translated by the host cell machinery
    - make capsid, envelope, RNA polymerase plus other viral proteins.
  3. RNA polymerase makes (-) RNA which is packaged into virus particles along RNA polymerase to generate new infectious virus.
111
Q

Replication of + Strand RNA viruses

A
  1. Viral RNA genome brought in with the virus can function as mRNA to encode viral proteins using host cell translation machinery.
  2. Viral RNA polymerase made in step 1 used to make complementary copies of the viral genome
112
Q

Incubation period

A

time from exposure to development of disease

113
Q

Infectious period

A

length of time a person can transmit disease

114
Q

Latent period

A

period of infection without being infectious

–this may occur right after exposure or late in the disease

115
Q

Epidemic

Endemic

Pandemic

A

occurence of cases of illness in excess of expectancy

epidemic whose incidence remains stable for a long time

global outbreak

116
Q

Incidence

Incidence rate

A

number of NEW CASES in a given time period within a given population

number of NEW CASES PER POPULATION at risk for the disease over time

Comparing incidence and incidence rates can help determine if an epidemic is occuring

117
Q

Prevalence

A

total number of cases of a disease/# of individuals in population

**Important if an infection is of long duration

**can be broken down by groups of interest (race, gender, etc)

118
Q

Attack Rate (infectivity)

A

proportion of exposed individuals who become ill

119
Q

Primary / secondary cases

A

primary: the person who infects a poplation
secondary: those who subsequently contract the infection

120
Q

Case fatality rate

A

proportion of infected individuals who die of the infection. this is a function of the severity of the infection and is heavily influenced by how many mild cases are not diagnosed

121
Q

Reservoir

A

ecological niche of pathogen: where it normally lives and replicates

122
Q

Vector

A

any organism, usually an arthropod, which transmits pathogen to susceptible individuals

i.e. tick, skeetos

123
Q

Zoonosis

A

infection that can spread from vertebrate animals to man

124
Q

basic reproductive rate (Ro) the number of secondary cases following a single introduction into a fully susceptible population

A

the number of secondary cases following a single introduction into a fully susceptible population

If Ro < 1, then every new generation of infection will affect fewer individuals and the disease will die out. Population that is vaccinated or became immune affects disease spread
If Ro = 1 then approximately the same number of individuals are infected with every new generation causing endemicity
If Ro > 1 then there is an ever increasing number of infected individuals causing epidemic or pandemic

125
Q

Herd Immunity Threshold

A

the fraction of a population that must be immune to a given microorganism to prevent an outbreak beyond one index case

–>the higher the Ro of infection, the higher the herd immunity threshold

126
Q

Modes of Disease Transmission

A

Airborne: long distance respiratory transmission

Droplet: medium to short distance respiratory transmission

Contact: transmission via environment

Sexual: body fluids are exchanged

Fecal/Oral: food supply or direct contact

127
Q

Steps to evaluate/control an outbreak

A

Verify index cases & diagnosis.
Draw an epidemic curve (chronological histogram)
Develop a case definition.
Perform additional case finding.
Create a line listing of cases, exposures, other features than can point to an etiology
Develop a hypothesis.
Test the hypothesis.
Refine and repeat #6-7
Implement control measures.
Communicate findings.

128
Q

Intoxication

A

ingestion of preformed toxinis sufficient to obtain disease

Food born intoxications often involve heat and pH stable toxins

Symptoms develop quickly since toxin is already present in body

Symptoms often include GI tract: vomitting, diarrhea, cramps

Exception: food borne botulism

129
Q

Ingestions acquired infection

A

Typically cause inflammation–>increase in fecal leukocytes

GI symptoms–>cramps, diarrhea, fever

May remain in GI tract or disseminate

Symptoms tend to develop slowly

130
Q

Important Factors in emerging infections

A
  1. Interspecies crossing
    Close human proximity to birds, pigs (Influenza) and bats Encroachment to new reservoirs (humans handling jungle meat-Ebola)
  2. Adaptation of a virus to the human host
    Change (human) as incidental host to reservoir (SARS) Improved human-human transmission (HIV)
    Tissue tropism can determine pathogenicity (diarrhea in SARS)
  3. Susceptible hosts
    International travel increases the size of population at risk (SARS) Antigenic shift exposes non immune humans to a “new” disease (H5N1) Decreased childhood vaccination rates due to concerned parents (measles)
  4. Global warming
    Expansion of mosquito habitats (Dengue, chikungunya)
  5. Improved diagnostic tests
    Reveal new pathogens of existing syndromes (Metapneumovirus)
131
Q

Category A Biological Weapons

A

can be easily disseminated or transmitted from person to person
result in high mortality rates and have the potential for major public health impact
might cause public panic and social disruption
require special action for public health preparedness.

anthrax

plague

botulism

smallpox

tularemia

viral hmorrhagic fevers

132
Q

Category B Biological Weapons

A

are moderately easy to disseminate
result in moderate morbidity rates and low mortality rates
require specific enhancements of CDC’s diagnostic capacity and enhanced disease surveillance.

133
Q

Category C Biological Weapons

A

Third highest priority agents include emerging pathogens that could be engineered for mass dissemination in the future because of
availability
Ease of production and dissemination
Potential for high morbidity and mortality rates and major health impact

134
Q

Antigenic variation

A

systematic changes or variations in surface molecules to avoid elimination by the immune response

avoidance of antibodies usually

usually seen in extracellular pathogens or those that are extracellular part of the time

T cell epitopes change as well, but this is not usually in a pattern. –>“immune escape” such as HIV

135
Q

Types of Antigenic variation

A

1) Phase variation: switching on/off genes that produce a phenotpe

–>must be able to go in both directions

eg. E.coli fimbraie
2) Antigenic drift: accumulation of mutations that alters antigen composition and changes recogniton by the immune system; often the result of error prone replication

eg influenza, HIV

3) Antigenic shift: abrupt and major change in surface antigen due to gene conversion, rearrangement, reassortment

eg influenza, gonorrhea, t. brucei

136
Q

Why does antigenic variation occur?

A

Evolution of the population of microbes in response to the immune response of the host

Selective pressure by (usually) antibodies to change surface molecules to avoid being killed

Need successive changes to avoid being eliminated by pre-existing antibodies

137
Q

Invasins:

A

Invasins:
bacterial surface proteins

  • provoke phagocytic ingestion of bacterium by host cell
  • some act as adhesins (binding), or work with adhesins to bind
  • cause cytoskeletal rearrangements that lead to engulfment
  • actin rearrangements and formation of pseudopod-like structures
  • can involve Type III secretion systems on bacteriabacterial surface proteins
  • provoke phagocytic ingestion of bacterium by host cell
  • some act as adhesins (binding), or work with adhesins to bind
  • cause cytoskeletal rearrangements that lead to engulfment
  • actin rearrangements and formation of pseudopod-like structures
  • can involve Type III secretion systems on bacteria
138
Q

Enterotoxin Actions

A

Alter intestinal cyclic nucleotide levels–>cholera toxin, LT of ETEC (cAMP), ST of ETEC (cGMP)

Kill cells (shiga toxin)

Act as superantigen to induce an inflammatory response (S.aureus enterotoxins)

Affect tight junction permeability by inducing signal tranduction changes (C diff)

139
Q

Characteristics of extotoxins

A

Most are proteins
b. Active in smaller amounts than endotoxin
c. One bacterial cell can make >1 toxin
d. Gram-positive bacteria are generally better toxin producers, but there are
some good toxin-producing Gram-negatives

140
Q

Tetanus toxin

A

works on CNS in spinral cord (travels up motor nueron into the CNS)

blocks release of inhibitory neurotransmitters like glycine

results in constant stimulation of the motor neuron

motor neuron constantly exceites muscle

141
Q

Botulinum toxin

A

acts at neuromuscular junction

blocks release of acetylcholine (excitatory neurotransmitters)

w/o acetylcholine, muscles don’t contract

results in flaccid paralysis

142
Q

coordinate regulation

A

all virulence genes necessary for one step in the pathogenic cycle are expressed at the same time

143
Q

global regulator

A

coordinate regulation is achieved with just the single regulatory element

144
Q

Mechanisms to sense environemental changes used by bacteria

A

1) two component regulatory systems
- one bacteria can have multiple two component regulatory systems
- one two component regulatory system can regulate another
2) quorum sensing systems

145
Q

two component regulatory systems

A
  • These systems regulate many bacterial functions, including virulence factor expression.
  • These systems are found in both Gram+ and Gram- bacteria

.•Components include:

–Sensor protein: transmembrane protein that, when stimulated, undergoes a conformational change that activates a histidine kinase domain.

–Transcriptional regulator: cytoplasmic protein that is phosphorylated by the activated sensor protein. When phosphorylated, it causes increased expression of some genes but decreased expression of others.

146
Q

quorum sensing

A

•Bacterial pathogens often must reach a critical density in the human body before causing disease.•Some pathogens sense their population density, and then adjust their virulence factor expression, using quorum sensing.•Quorum sensing involves secretion of a small molecule (a peptide or homoserine lactone) called an autoinducer.

147
Q

Persistence

A

ability of a pathogen to remain long term within the host

–result of failure of host defense to clear the pathogen

148
Q

Latency

A

form of persistence infection in which the pathogen is quiesant

–causes no overt disease

149
Q

Reactivation

A

persistent/latent pathogen reenters productive replication

usually causes overt disease

150
Q

carrier state

A

infected individual that displays no overt disease

-serves as a reservoir for spread of disease

151
Q

Toxoid

A

bacterial toxin rendered non toxic; used to induce anti-toxin antibodies