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MICR3310 > 10 - Molecular Epidemiology > Flashcards

10 - Molecular Epidemiology Flashcards

1
Q

Bacterial species

A

Collection of strains with a conserved core of genes and phenotypes

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2
Q

Bacterial strain

A
  • Subvariant of bacterial species
  • Can be defined by genetic content and sometimes phenotype
  • Isolates of a strain may share 99% of gene sequence identity
  • Strains of same species may have completely different phenotype
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3
Q

What do genotypes and phenotypes of strains change based upon

A
  • Mutation of the core genome
  • Acquisition of foreign DNA from other sources
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4
Q

Bacterial cell division

A
  • If replication is faithful, both bacterial cells are identical = same isolate
  • But if replication has errors, the bacterial cells are not identical = different strains
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5
Q

DNA damage

A

Permanent, heritable change to base sequence of DNA

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6
Q

Rate of DNA polymerase error

A

1 in 10^8 to 10^11 nucleotides

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7
Q

Alkylation

A
  • Electrophiles add alkyl groups to phosphates, stalls replication
  • eg. carcinogens, ethylmethane sulphonate (EMS)
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8
Q

UV induced thymine dimers

A
  • DNA absorbs UV at 260nm
  • Forms intra-strand pyrimidine dimers, mainly T-T
  • Distortion of double helix prevents DNA replication, thus is lethal
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9
Q

Oxygen radicals

A
  • Cause single and ds breaks
  • e.g. gamma and X rays
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10
Q

Epidemiology

A

Study of distribution & determinants of disease and health related events and its
application in control and prevention.

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11
Q

Difference between infectious disease epidemiology and epidemiology

A
  • Two or more populations (E deals with 1)
  • A case is a risk factor (E risk –> case)
  • Cause often known (E identifies cause)
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12
Q

Sporadic disease

A
  • Occasional cases occurring at irregular intervals
  • Caused by unrelated strains of same infectious agent
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13
Q

Endemic disease

A
  • Persistent occurrence with a
    low to moderate level
  • Caused by unrelated strains of the same infectious agent
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14
Q

Hyper endemic disease

A
  • Persistently high levels of occurence
  • Appearance of small clusters of disease in the population caused by highly related strains
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15
Q

Epidemic outbreak

A
  • Occurrence clearly in excess
    of the expected level for a given time period
  • Appearance of large clusters of disease in the population caused by highly related strains
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16
Q

Pandemic

A
  • Epidemic spread over
    several countries or
    continents, affecting a large
    number of people
  • Appearance of large clusters of disease in the population caused by highly related strains
17
Q

Basic reproductive number (R)

A

The mean number of
individuals directly infected by an infectious case through the total infectious period, when introduced to a susceptible population

18
Q

Endemic R number

A
  • R = 1
  • Transmission occur, but the number of cases remains constant
19
Q

Epidemic / pandemic R number

A
  • R > 1
  • Number of cases increases
20
Q

What is the identification of causative agent of an outbreak confounded by

A
  • Presence of other strains in the environment that do
    not cause disease
  • Presence of hosts which carry virulent organisms but do not show signs of disease
21
Q

Use of molecular typing methods in outbreak investigations

A
  • Outbreak (Rise in cases beyond expected in defined period)
  • Typing (identify outbreak strain)
  • Hypothesis generation (common exposure –> possible source)
  • Environmental sampling (identify common strain)
  • Typing (Link environmental isolate to outbreak strain)
  • Intervention
22
Q

Molecular typing strengths

A
  • Do not need a live culture to make an identification
  • Therefore, more time efficient
  • Also very sensitive as amplification technology will detect very low numbers of organisms in a sample
23
Q

Weaknesses of molecular typing

A
  • Antibiotyping is very important and requires culture
  • Need to be aware that detection of an organism does not always equate with causation of disease
  • Change in staff training and education
  • Initial cost of set up (Specialist machines)
24
Q

Suitable methods for outbreak investigations,
Short term/local surveillance,
Control of hygiene measures

A
  • PCR based methods
  • Mostly on bacteria and fungi
  • Medium discriminatory power
25
Q

Suitable methods for long term/global epidemiological studies, Population genetics, Analysis of population-based
interventions (eg.Vaccination)

A
  • WGS bacteria or virus with small genome
  • High discriminatory power
26
Q

Discriminatory power

A

A method’s ability to
assign a different type to two unrelated strains sampled
randomly from the population of a given
species

27
Q

Most accurate method for assessing divergence and relatedness

A

Sequencing

28
Q

Multi locus sequence typing (MLST)

A
  • Involves the PCR amplification and sequencing
    of 7 housekeeping genes which are highly conserved relative to other genes
  • Convenient as can be efficiently sequenced using a
    single primer extension reaction in each direction
  • Each sequence is assigned an allele number based
    on SNPs
29
Q

MLST analysis

A
  • Alleles are given a unique integer as a label
  • A combination of 7 alleles is given a unique integer = sequence type (ST)
  • STs can be clustered and analysed to create phylogenetic trees showing relatedness
  • An average of 30 alleles per locus allows about 20 billion genotypes to be resolved
30
Q

Advantages of MLST

A
  • Data is unambiguous
  • Reproducible between labs
  • Easily transferred and compared between labs
  • Scalable and automated using high throughput sequencing
31
Q

Disadvantages of MLST

A
  • Expensive
  • Data bases only available for some pathogens
32
Q

Phylogeny

A

A model of the relationships between organisms, genes, proteins or other structures based on common ancestry

33
Q

Common uses of phylogenetic trees

A
  • Classification (taxonomy)
  • Grouping of genes, proteins, and other molecular sequences including non-coding sequences
  • Epidemiological investigations
  • Analysis of parallel evolution between host and parasite
34
Q

Whole genomic multilocus sequence typing (WGMLST)

A
  • Uses more than 7 housekeeping genes
  • As databases become larger and algorithms faster, larger sets of genes can be used for typing
35
Q

WGMLST uses

A
  • Most useful for recombining populations
  • N. gonorrhoeae which is naturally transformable which leads to a population structure that is non-clonal (panmictic)
  • This means that the rate of recombination is higher than mutation resulting in an index of association (IA = 0) (random)
36
Q

What are the primary drivers in the evolution of microbial populations?

A
  • Induced DNA damage (alkylation, thymine dimers, oxygen radicals)
  • Spontaneous

MICR3310 (28 decks)

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