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Mol Med Final Exam > Med Micro > Flashcards

Med Micro Flashcards

0
Q

What has genomics revealed in bacteriology

A

Unexpected diversity of genome organization and content between strains

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1
Q

What differentiates pathogens from non pathogens

A

Virulence factors - either cause damage of help pathogen survive in host

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2
Q

Define host genome

A

The entire genetic complement that was obtained by vertical transmission

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3
Q

What is a microbiome

A

Interacting group of organisms that share an ecological niche

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4
Q

Define core genome

A

All the genes that each member of a species possesses

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5
Q

What are distributed genes

A

Genes in a species that are not shared by all strains of that species

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6
Q

What is a supragenome

A

All core genes plus distributed genes of a species

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7
Q

Basic tenets of damage response framework

A

Pathogenesis is outcome of host - organism interaction
Host-relevant outcome is determined by damage to host
Host damage can result from damage from microbe of by host itself

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8
Q

Limitations of AST

A 
Site of infection
Blood supply to site
IR of pt
Pharmacokinetics
Comorbidities
Demographics of pt
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9
Q

Three categories of Kirby Bauer system

A

Susceptible
Intermediate
Resistant

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10
Q

Define MIC

A

Lowest concentration of Abx that results in inhibition of visible growth

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11
Q

Define MBC

A

Minimum bacterocidal concentration

Lowest [] needed to kill 99.9% of original inoculum in a given period of time

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12
Q

Technical factors that could influence size of zone of inhibition

A 
Inoculum density 
Timing of disk application
Temp of incubation
Incubation time
Size of plate, depth of agar, spacing of disks
Potency of Abx disk
Composition of medium
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13
Q

How to determine MIC

A

Liquid/broth MIC determination

Etest

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14
Q

Types of resistance

A

Natural - wild type, all strains in species have it etc

Acquired - development of one or more resistance mechanisms to Abx that wild type is susceptible

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15
Q

Mechanisms for acquired resistance

A

Mutations

Transfer of DNA (plasmid or transposon)

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16
Q

Mode of transmission for resistant genes

A

Transformation - DNA enters cell and exchanges some DNA with host
Transduction - bacteriophage with host DNA infects cell and DNA is incorporated into new host.
Conjugation - transfer of plasmid or small DNA fragment via pilus

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17
Q

Define cross resistance

A

A single mechanism confers resistance against several members of the same Abx class

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18
Q

Define associated resistance

A

Two different mechanisms in the same bacterium confer resistance to two different families of Abx

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19
Q

Key mechanisms of Abx resistance

A

Modification of Abx (eg enzymes)
Alteration of target site
Reduced intracellular concentration
Bypass mechanisms

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20
Q

Egs of modification of Abx

A

Aminoglycaside-modifying enzymes
B-lactamases
Chloramphenicol acetylase

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21
Q

Efficacy of B-lactamases depends on what factors

A

Rapidity of drug entry
Rate of enzymatic hydrolysis
Amount of enzyme produced
Outer membrane

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22
Q

What can cause reduced intracellular concentration

A

Active efflux pumps
Porins
Impermeable membrane

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23
Q

Egs of target site modification

A

PBPs
Ribosomes
DNA gyrase

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24
Q

Three classes os B-lactamases

A

Penicillinases
Cephalosporinases
Carbapenemases

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25
Q

How does one identify high risk for carbapenem resistance

A

Recent Abx exposure
Prolonged hospital exposure
Invasive devices

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26
Q

What do carbapenems cover

A

GNB incl ESBL-producers
GPB incl MSSA
Anaerobes

27
Q

Factors limiting drug efficacy

A

Genetic drug resistance (conjugation, transformation, transduction, de novo)
Intrinsic drug resistance (efflux, permeability, enzymes)
Phenotypic drug tolerance (biphasic kill - persisters)

28
Q

Define resistance

A

Genetic, heritable, specific factors that can usually be detected at a molecular level and can be countered by combination therapy.

29
Q

Define tolerance

A

(Partially genetic) non-heritable, non-specific phenomenon with multiple redundant pathways. Tolerant persisters arise even in the presence of combination therapy

30
Q

How does one identify high risk for carbapenem resistance

A

Recent Abx exposure
Prolonged hospital exposure
Invasive devices

31
Q

What do carbapenems cover

A

GNB incl ESBL-producers
GPB incl MSSA
Anaerobes

32
Q

Gut microbiotica influenced by..

A 
Genetics 
Age
Geography
Dietary
Preterm delivery
Mode of delivery
Abx use
33
Q

Performance criteria of typing methods

A

Stability, typeability, reproducibility, discriminatory power, epidemiological concordance.
Flexible, rapid, easy.

34
Q

Phases of bacterial growth

A 
Lag
Log
Declining
Stationary 
Death
35
Q

What contributes to pathogenicity

A

Transmissibility
Survival
Infectivity

36
Q

Virulence factors

A

Cell wall
Toxins (endo, exo)
Enzymes (coagulases, kinases, hyaluronidase, collagenase)

37
Q

Bacterial mechanisms of host evasion

A 
Adherence
Capsule (impairs phagocytosis)
Biofilms
Ag variation
Resistance to phagocyte lysosomes killing
IgA proteases
38
Q

Abx that inhibit cell wall synthesis

A

B lactams
Glycopeptides
Fosphomycin

39
Q

Abx that act on protein synthesis

A 
Aminoglycasides
Tetracyclines
MLS (macrolides, lincosamides, streptogramins)
Quinolones 
Sulphinamides and trimethoprim
40
Q

Lab detection methods of cabapenemases

A

Modified hodge test
Effects of inhibitors result in synergy
Nordmann-poirel test

PCR
rtPCR
Molecular beacons

41
Q

Clinical management of patient w carbapenemase infection

A

Abx (colistin, tigecycline)
Remove source
Infection control
Isolate

42
Q

Mi biome analysis methods

A

16S RNA sequencing

Total micro biome DNA sequencing

43
Q

Rx strategies for diseases caused by change in micro biome

A 
Nutrition change
Fecal transplantation
Microbial supplementation (probiotics)
44
Q

Diseases associated w change in microbiome

A 
Resp disease
Obesity
Cirrhosis 
Autoimmunity
Kwashiorkor 
IBD
Chron's
Clon cancer
45
Q

Phenotypic methods for microbial typing

A

Serotyping
Mass spectrometry
Multi locus enzyme electrophoresis

46
Q

Genotypic methods for microbial typing

A 
Fragment based (PFGE, PCR fingerprint, VNTR)
Sequence based (multi locus sequence typing, single locus ST, SNP genotyping, WGS)
Hybridization methods (oligo typing, microarray)
47
Q

Performance criteria of a typing method

A
  • stability
  • typeability
  • reproducibility
  • discriminatory power
  • epidemiological concordance
48
Q

Examples of phenotypic typing methods

A
  • bio typing
  • antibiogram-based typing
  • serotyping
  • phage typing
  • bacteriocin typing
  • multilocus enzyme electrophoresis
  • MS
49
Q

Drawbacks of phenotypic typing methods

A
  • typeability
  • reproducibility
  • discriminatory power
50
Q

Examples of genotyping methods

A
  • fragment- based methods
  • sequence based methods
  • hybridization methods
51
Q

Examples of fragment based methods

A
  • restriction endo nuclease based methods
  • PCR fingerprinting
  • multilocus variable number of tandem repeat analysis
52
Q

Describe ribotyping

A
  • couples genome digestion by a frequent cutting restriction endo nuclease with a 4-bpr ecognition sequence
  • hybridization with a probe complementary to rDNA
53
Q

Define a plasmid

A

Autonomous self-replicating extra chromosomal DNA elements that frequently encode bacterial virulence factors or contain antimicrobial resistance genes

54
Q

Process of pulse field gel electrophoresis

A
  • bacterial cells are lysis and large fragments of the bacterial chromosome are generated by macro restriction analysis
  • DNA fragments are separated during electrophoresis using an electric field of periodically alternating polarity
55
Q

Process of multilocus variable number of tandem repeat analysis

A
  • amplifying ghee fragments of DNA that differ in size by the number of repeat segments contained within the amplicon
  • length of an allele is directly correlated to the number of repeats
56
Q

Process of repPCR

A

Amplification of short genomic fragments lying between repetitive elements by using low-stringency PCR with outward primers

57
Q

Examples if sequence based methods

A
  • multi-locus typing
  • single locus sequence typing
  • single nucleotide polymorphism genotyping
  • while genome sequencing
58
Q

Process of multi locus sequence typing (MLST)

A
  • analyses 400-500 bp internal fragments of five to seven housekeeping genes common to many bacteria
  • each gene sequence considered as an allele type
  • allele type of each gene sequence is combined into allelic profile
59
Q

Advantages of MLST

A
  • explore evolutionary relationships and population structure
  • useful for clonal type identification
  • gold standard for defining subspecies genetic population structure of micro organisms
  • proposed method for legionella pneumophila infections
60
Q

Disadvantages of MLST

A
  • less discriminating for hospital outbreaks
  • labour and time consuming
  • expensive
61
Q

What is used to type s aureus

A

Spa typing

Analysis of hyper variable region of staph protein a

62
Q

What is used for s pyogenes typing

A

Emm typing

Analyses variation in the surface-associated strep virulence protein m

63
Q

Define SNP

A

A change in a single nucleotide in one sequence relative to wild type due to random nucleotide mutation, horizontal gene transfer or iatrogenic recombination

64
Q

Theories of the origin of viruses

A
  • regressive
  • cellular origin
  • co-evolution
65
Q

Types of mobile viral elements

A
  • pseudo genes
  • retroposons
  • transposons
  • group 2 introns
66
Q

Mechanisms of endogenous viruses causing cancer

A
  • oncogene transfer
  • insertional mutagenesis
  • activating oncogene with promoter
  • inhibiting a promoter suppressing an oncogene

Mol Med Final Exam (6 decks)

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