10 - Molecular Epidemiology Flashcards
1
Q
Bacterial species
A
Collection of strains with a conserved core of genes and phenotypes
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
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
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
5
Q
DNA damage
A
Permanent, heritable change to base sequence of DNA
6
Q
Rate of DNA polymerase error
A
1 in 10^8 to 10^11 nucleotides
7
Q
Alkylation
A
- Electrophiles add alkyl groups to phosphates, stalls replication
- eg. carcinogens, ethylmethane sulphonate (EMS)
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
9
Q
Oxygen radicals
A
- Cause single and ds breaks
- e.g. gamma and X rays
10
Q
Epidemiology
A
Study of distribution & determinants of disease and health related events and its
application in control and prevention.
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)
12
Q
Sporadic disease
A
- Occasional cases occurring at irregular intervals
- Caused by unrelated strains of same infectious agent
13
Q
Endemic disease
A
- Persistent occurrence with a
low to moderate level - Caused by unrelated strains of the same infectious agent
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
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
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
Suitable methods for long term/global epidemiological studies, Population genetics, Analysis of population-based
interventions (eg.Vaccination)
- WGS bacteria or virus with small genome
- High discriminatory power
26
Discriminatory power
A method’s ability to
assign a different type to two unrelated strains sampled
randomly from the population of a given
species
27
Most accurate method for assessing divergence and relatedness
Sequencing
28
Multi locus sequence typing (MLST)
- 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
MLST analysis
- 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
Advantages of MLST
- Data is unambiguous
- Reproducible between labs
- Easily transferred and compared between labs
- Scalable and automated using high throughput sequencing
31
Disadvantages of MLST
- Expensive
- Data bases only available for some pathogens
32
Phylogeny
A model of the relationships between organisms, genes, proteins or other structures based on common ancestry
33
Common uses of phylogenetic trees
- 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
Whole genomic multilocus sequence typing (WGMLST)
- Uses more than 7 housekeeping genes
- As databases become larger and algorithms faster, larger sets of genes can be used for typing
35
WGMLST uses
- 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
What are the primary drivers in the evolution of microbial populations?
- Induced DNA damage (alkylation, thymine dimers, oxygen radicals)
- Spontaneous
