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Medical Microbiology > Molecular and Genomic Epidemiology of Infections > Flashcards

Molecular and Genomic Epidemiology of Infections Flashcards

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USMLE® Step 1 flashcards Biology 101 flashcards
1
Q

What is molecular epidemiology?

A

A resolved measure (diversity) of differences (variables) that determines:

  • Disease distribution in time and place
  • Disease transmission
  • Disease manifestation
  • Disease progression
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2
Q

What is the purpose of molecular epidemiology?

A

Molecular epidemiology can answer many questions about outbreaks and risks

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3
Q

How can we use Molecular epidemiology to confirm outbreaks inside institutions?

A

Did patient A catch this pathogen from patient B?

Do patients A, B & C from the same hospital ward have the same strain?

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4
Q

How can molecular epidemiology confirm outbreak in the community?

A

Answers who the index case was and what the likely source is

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5
Q

How does molecular epidemiology confirm outbreaks from the past?

A

Tells us what has driven the geographical spread of important strains

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6
Q

How is molecular epidemiology used in a lab ?

A

Can confirm whether it is an outbreak or a contaminant

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7
Q

What are common disease risks?

A
  • Shifts in virulence

- Reservoirs of infection

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8
Q

How are shifts in virulence identified?

A

Has the incidence of annual infections increased from …last year?
Are drug resistant strains on the rise? From where?

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9
Q

How does molecular epidemiology identify infection reservoirs?

A

Tells us if its a new infection or recrudescence

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10
Q

How does molecular epidemiology identify disease risks?

A

We can answer these questions by looking at molecular changes or constants that occur within typical pathogens

  • Which variable is the Target
  • How many variables/targets are there
  • How much resolved diversity there is
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11
Q

What are the different targets of pathogens and their functional characteristics?

A

Classical: Biochemistry - single
Serology: O157 antigen - single
Virulence: Verotoxin - single

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12
Q

Why are functional characteristic snot enough to identify disease risks?

A

We can look at the aforementioned areas for those types of toxins, but often the pathogens are more complex and require genomic studies
For functional characteristics we tend to observe a single target

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13
Q

How do we look at genomic characteristics of disease risks?

A

For genomic characteristics it is better to look at multiple targets

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14
Q

Why do we look at multiple copies of the same gene to identify risk?

A

Multiple copies of same gene: Increases sensitivity to testing

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15
Q

What is the benefit of looking at coding sequences of pathogens?

A

Can differentiate between mutant and non-mutant

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16
Q

Outline the Genomic characteristics observed when identifying disease risks

A

DNA

  • Gene (rpo gene [rifampicin resistance] MDR TB)
  • Amino acid sequence
  • Base sequence

RNA

  • Ribosome
  • miRNA
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17
Q

What does single weighting tell us about diversity?

A

Presence or absence of toxin

  • Biochemical test
  • Presence of O157 antigen
  • Presence of Verotoxin
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18
Q

What is additive weighting?

A

Combination of single tests

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19
Q

What is the role of additive weighting?

A

To identify what the organism is, if it is advantageous, or if it’s the same as other identified organisms or if its changing

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20
Q

What are the different factors of multiple weighting?

A
  • Factoral
  • Functional
  • Temporal
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21
Q

What do factoral genomic factors tell us?

A

Presence or absence of a gene/base/s change in genome/gene relative to location in the genome

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22
Q

What are functional genomic factors?

A

Type of substitution (synonymous/non synonymous )

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23
Q

What does the temporal genomic factors tell us?

A

Mutation rate (time since the last alteration)

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24
Q

Give an example when additive weighting is used?

A

eg. Identification and typing for E.coli 0157: Verotoxin 2 +ve : Phage type 21/28

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25
Q

What are the effects of E.coli infection?

A

E.coli 0157 causes diarrhoea and vomiting due to cholera

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26
Q

How is E.coli cultured in labs?

A

E.coli produces 0157 toxin that is easily cultured on agar to produce colonies

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27
Q

How is 0157 E.coli colony identified?

A

We can sub-culture those colonies and conduct a latex test to identify which colony is the 0157 toxin producing E.coli

28
Q

How is the Stx2 gene identified using additive weighting?

A

We can also identify the stx2 gene presence by PCR

29
Q

Give an example of multiple weighting used

A

e.g. Spoligotyping of RE region of TB gene

factoral

30
Q

Why is the RE region of TB a good indicator of TB strain?

A

RE region has the possibility of containing <43 copies of the same gene

Not all 43 copies are present in all organisms and they have the ability to jump in/out as organism is transferred from one patient to another

31
Q

How is TB’s RE region used to identify TB strain?

A

As patient passes on infection to others, we can see the change in genomic copy no. and pattern which distinguishes the strain of TB

32
Q

Outline how spoligotyping of TB RE region is conducted

A
  1. PCR with RE region primers generates multiple length amplicons
  2. Hybridization of labelled PCR products onto 43 spacer specific oligonucleotides (between RE sequences)
  3. Fix on a membrane and visualise signal with RE probe
  4. Result = profile of presence / absence of specific repeats at ONE locus
33
Q

What does a spoligotyping dendogram show us?

A

Spoligotyping dendogram showing relatedness of pattern

Allows us to identify taxonomic changes in strains of toxins around the world

34
Q

How is PCR to identify VNTRs used to identify factoral diversity in pathogens?

A

Result is a profile of the number of specific repeats at multiple genomic loci

Can produce a VNTR dendogram from PCR results showing relatedness of pattern

35
Q

Why are base changes causing diversity more complex?

A

Base changes are more complex due to redundancy in the way mutations produce different types of amino acids

No. of base triplet combinations for each a.a. is 3

36
Q

What are silent mutations?

A

Mutations that are Intragenic (between genes) or Synonymous (not altering coding)

37
Q

What are non-synonymous substitutions?

A

Substitutions causing coding to be altered

38
Q

What are corruptive mutations?

A

Deletions or Insertions (disrupting coding frame) ` Creation of STOP codons (truncation) Corruption of STOP codons
(elongation) Corruption of CONTROL sequences (eg. promoters)

39
Q

What is genetic drift?

A

Gradual alteration in sequence

40
Q

How does genetic drift occur in Influenza?

A

Flu virus mutations occur randomly in the haemagglutinin and neuraminidase genes causing losses in certain genes and products

41
Q

Why are some strains of influenza more lethal than others?

A

Some mutations have more influence on Ab binding affinity than others

42
Q

How does herd immunity effect flu genetic drift?

A

Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift

43
Q

What is the fate of an escape mutant of a virus?

A

Each escape produces a new strain that either dies out or also becomes an escape

44
Q

What is antigenic drift?

A

Antigenic drift is the same antigen changing its sequence base by base

45
Q

What is the significance of the molecular clock in pathogenic epidemiology?

A

Accurate predictions in molecular epidemiology thus requires an assumption that evolution is driven by a ‘Constant Molecular Clock’

46
Q

How does the molecular clock affect bacterial replication rate?

A

A high division rate provides a higher mutation rate

47
Q

What factors affect the ‘molecular clock’ speed?

A
  • Bacterial replication rate
  • DNA/RNA polymerase proofreading fidelity
  • Host/Environment selection pressure
  • Degree of genome redundancy
  • Transmission rate
48
Q

What is the significance of DNA/RNA pol. proofreading fidelity?

A

Some species (eg HIV) have low fidelity promoting high mutation rate

49
Q

What is the effect of high selection pressure?

A

High selection pressure removes ‘weak’ mutants and emphasises clusters

50
Q

What does a low selection pressure favour?

A

Loss of selection pressure allows deletions

51
Q

How does copy no. affect mutation rate?

A

Multiple copies of a single gene in the genome allow for mutations in one copy without compromising overall functionality

52
Q

How does genomic redundancy effect the phenotype?

A

Movement or recombination within genome may not affect phenotype

53
Q

What are the effects of high transmission rates?

A

High transmission rates relative to the mutation rate results in dissemination and single strain outbreaks
(Flu A = 2-3 bases per year and 1.5 transmissions per infection)

54
Q

Explain how 2 genes can drift at the same time (flu)?

A

Both genes are having same drift at the same speed due to the same host pressure on the different types of escape

55
Q

Which genes are more susceptible to mutations?

A

Hyper-variable genes change more rapidly than conserved genes

56
Q

Which genes are highly associated with virulence?

A

Conserved genes are more likely to be associated with phenotype and virulence

57
Q

What is convergent evolution?

A

Not all changes are new Some may revert BACK to an older profile

58
Q

What is the effect of large and rapid changes in genes?

A

Large and rapid changes are rare but often lead to escape from existing herd protection

59
Q

Outline in detail how antigenic shift occurs

A

Antigenic shift is a sudden replacement of an antigen by recombination with another viral type that has evolved separately
(either in another animal or another human population)

60
Q

How do new epidemics arise?

A

Antigenic shift => New types will not be protected against by previous infection or vaccination

61
Q

What are the common epidemiological associations of disease?

A

Transmission: Hospital acquired infection

Reservoirs of infection : Contact tracing, Determining Introduction Events

Spread or emergence of resistance

62
Q

What is the use of a molecular restriction digest?

A

Molecular Restriction Digest typing can monitor effectiveness of control measures

63
Q

What is the purpose of contact sourcing?

A

Molecular typing can aide in outbreak sourcing

64
Q

How can we predict resistance in antibiotics?

A

Can predict resistance of antibiotics by looking at certain SNPs via PCR

65
Q

What is the purpose of molecular epidemiology?

A

Molecular epidemiology offers a variety of methods to test questions Involving disease transmission, strain virulence, pathogen evolution

66
Q

What is required to choose the most appropriate system against pathogens?

A
  1. Knowing the most appropriate variable/s
  2. Quantitating variations and deriving diversity
  3. Generating identities or clusters
  4. Applying related data:
67
Q

What related data is used to determine the correct course of action?

A
  • geographic location
  • time of isolation
  • incidence
  • prevalence
  • transmission rate
  • severity of disease

Medical Microbiology (15 decks)

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