10 - Molecular Epidemiology Flashcards
Bacterial species
Collection of strains with a conserved core of genes and phenotypes
Bacterial strain
- 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
What do genotypes and phenotypes of strains change based upon
- Mutation of the core genome
- Acquisition of foreign DNA from other sources
Bacterial cell division
- If replication is faithful, both bacterial cells are identical = same isolate
- But if replication has errors, the bacterial cells are not identical = different strains
DNA damage
Permanent, heritable change to base sequence of DNA
Rate of DNA polymerase error
1 in 10^8 to 10^11 nucleotides
Alkylation
- Electrophiles add alkyl groups to phosphates, stalls replication
- eg. carcinogens, ethylmethane sulphonate (EMS)
UV induced thymine dimers
- DNA absorbs UV at 260nm
- Forms intra-strand pyrimidine dimers, mainly T-T
- Distortion of double helix prevents DNA replication, thus is lethal
Oxygen radicals
- Cause single and ds breaks
- e.g. gamma and X rays
Epidemiology
Study of distribution & determinants of disease and health related events and its
application in control and prevention.
Difference between infectious disease epidemiology and epidemiology
- Two or more populations (E deals with 1)
- A case is a risk factor (E risk –> case)
- Cause often known (E identifies cause)
Sporadic disease
- Occasional cases occurring at irregular intervals
- Caused by unrelated strains of same infectious agent
Endemic disease
- Persistent occurrence with a
low to moderate level - Caused by unrelated strains of the same infectious agent
Hyper endemic disease
- Persistently high levels of occurence
- Appearance of small clusters of disease in the population caused by highly related strains
Epidemic outbreak
- 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
Pandemic
- 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
Basic reproductive number (R)
The mean number of
individuals directly infected by an infectious case through the total infectious period, when introduced to a susceptible population
Endemic R number
- R = 1
- Transmission occur, but the number of cases remains constant
Epidemic / pandemic R number
- R > 1
- Number of cases increases
What is the identification of causative agent of an outbreak confounded by
- 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
Use of molecular typing methods in outbreak investigations
- 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
Molecular typing strengths
- 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
Weaknesses of molecular typing
- 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)
Suitable methods for outbreak investigations,
Short term/local surveillance,
Control of hygiene measures
- PCR based methods
- Mostly on bacteria and fungi
- Medium discriminatory power
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
Discriminatory power
A method’s ability to
assign a different type to two unrelated strains sampled
randomly from the population of a given
species
Most accurate method for assessing divergence and relatedness
Sequencing
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
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
Advantages of MLST
- Data is unambiguous
- Reproducible between labs
- Easily transferred and compared between labs
- Scalable and automated using high throughput sequencing
Disadvantages of MLST
- Expensive
- Data bases only available for some pathogens
Phylogeny
A model of the relationships between organisms, genes, proteins or other structures based on common ancestry
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
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
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)
What are the primary drivers in the evolution of microbial populations?
- Induced DNA damage (alkylation, thymine dimers, oxygen radicals)
- Spontaneous
