Molecular and Genomic Epidemiology of Infections Flashcards
What is molecular epidemiology?
A resolved measure (diversity) of differences (variables) that determines:
- Disease distribution in time and place
- Disease transmission
- Disease manifestation
- Disease progression
What is the purpose of molecular epidemiology?
Molecular epidemiology can answer many questions about outbreaks and risks
How can we use Molecular epidemiology to confirm outbreaks inside institutions?
Did patient A catch this pathogen from patient B?
Do patients A, B & C from the same hospital ward have the same strain?
How can molecular epidemiology confirm outbreak in the community?
Answers who the index case was and what the likely source is
How does molecular epidemiology confirm outbreaks from the past?
Tells us what has driven the geographical spread of important strains
How is molecular epidemiology used in a lab ?
Can confirm whether it is an outbreak or a contaminant
What are common disease risks?
- Shifts in virulence
- Reservoirs of infection
How are shifts in virulence identified?
Has the incidence of annual infections increased from …last year?
Are drug resistant strains on the rise? From where?
How does molecular epidemiology identify infection reservoirs?
Tells us if its a new infection or recrudescence
How does molecular epidemiology identify disease risks?
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
What are the different targets of pathogens and their functional characteristics?
Classical: Biochemistry - single
Serology: O157 antigen - single
Virulence: Verotoxin - single
Why are functional characteristic snot enough to identify disease risks?
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
How do we look at genomic characteristics of disease risks?
For genomic characteristics it is better to look at multiple targets
Why do we look at multiple copies of the same gene to identify risk?
Multiple copies of same gene: Increases sensitivity to testing
What is the benefit of looking at coding sequences of pathogens?
Can differentiate between mutant and non-mutant
Outline the Genomic characteristics observed when identifying disease risks
DNA
- Gene (rpo gene [rifampicin resistance] MDR TB)
- Amino acid sequence
- Base sequence
RNA
- Ribosome
- miRNA
What does single weighting tell us about diversity?
Presence or absence of toxin
- Biochemical test
- Presence of O157 antigen
- Presence of Verotoxin
What is additive weighting?
Combination of single tests
What is the role of additive weighting?
To identify what the organism is, if it is advantageous, or if it’s the same as other identified organisms or if its changing
What are the different factors of multiple weighting?
- Factoral
- Functional
- Temporal
What do factoral genomic factors tell us?
Presence or absence of a gene/base/s change in genome/gene relative to location in the genome
What are functional genomic factors?
Type of substitution (synonymous/non synonymous )
What does the temporal genomic factors tell us?
Mutation rate (time since the last alteration)
Give an example when additive weighting is used?
eg. Identification and typing for E.coli 0157: Verotoxin 2 +ve : Phage type 21/28
What are the effects of E.coli infection?
E.coli 0157 causes diarrhoea and vomiting due to cholera
How is E.coli cultured in labs?
E.coli produces 0157 toxin that is easily cultured on agar to produce colonies
How is 0157 E.coli colony identified?
We can sub-culture those colonies and conduct a latex test to identify which colony is the 0157 toxin producing E.coli
How is the Stx2 gene identified using additive weighting?
We can also identify the stx2 gene presence by PCR
Give an example of multiple weighting used
e.g. Spoligotyping of RE region of TB gene
factoral
Why is the RE region of TB a good indicator of TB strain?
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
How is TB’s RE region used to identify TB strain?
As patient passes on infection to others, we can see the change in genomic copy no. and pattern which distinguishes the strain of TB
Outline how spoligotyping of TB RE region is conducted
- PCR with RE region primers generates multiple length amplicons
- Hybridization of labelled PCR products onto 43 spacer specific oligonucleotides (between RE sequences)
- Fix on a membrane and visualise signal with RE probe
- Result = profile of presence / absence of specific repeats at ONE locus
What does a spoligotyping dendogram show us?
Spoligotyping dendogram showing relatedness of pattern
Allows us to identify taxonomic changes in strains of toxins around the world
How is PCR to identify VNTRs used to identify factoral diversity in pathogens?
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
Why are base changes causing diversity more complex?
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
What are silent mutations?
Mutations that are Intragenic (between genes) or Synonymous (not altering coding)
What are non-synonymous substitutions?
Substitutions causing coding to be altered
What are corruptive mutations?
Deletions or Insertions (disrupting coding frame) ` Creation of STOP codons (truncation) Corruption of STOP codons
(elongation) Corruption of CONTROL sequences (eg. promoters)
What is genetic drift?
Gradual alteration in sequence
How does genetic drift occur in Influenza?
Flu virus mutations occur randomly in the haemagglutinin and neuraminidase genes causing losses in certain genes and products
Why are some strains of influenza more lethal than others?
Some mutations have more influence on Ab binding affinity than others
How does herd immunity effect flu genetic drift?
Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift
What is the fate of an escape mutant of a virus?
Each escape produces a new strain that either dies out or also becomes an escape
What is antigenic drift?
Antigenic drift is the same antigen changing its sequence base by base
What is the significance of the molecular clock in pathogenic epidemiology?
Accurate predictions in molecular epidemiology thus requires an assumption that evolution is driven by a ‘Constant Molecular Clock’
How does the molecular clock affect bacterial replication rate?
A high division rate provides a higher mutation rate
What factors affect the ‘molecular clock’ speed?
- Bacterial replication rate
- DNA/RNA polymerase proofreading fidelity
- Host/Environment selection pressure
- Degree of genome redundancy
- Transmission rate
What is the significance of DNA/RNA pol. proofreading fidelity?
Some species (eg HIV) have low fidelity promoting high mutation rate
What is the effect of high selection pressure?
High selection pressure removes ‘weak’ mutants and emphasises clusters
What does a low selection pressure favour?
Loss of selection pressure allows deletions
How does copy no. affect mutation rate?
Multiple copies of a single gene in the genome allow for mutations in one copy without compromising overall functionality
How does genomic redundancy effect the phenotype?
Movement or recombination within genome may not affect phenotype
What are the effects of high transmission rates?
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)
Explain how 2 genes can drift at the same time (flu)?
Both genes are having same drift at the same speed due to the same host pressure on the different types of escape
Which genes are more susceptible to mutations?
Hyper-variable genes change more rapidly than conserved genes
Which genes are highly associated with virulence?
Conserved genes are more likely to be associated with phenotype and virulence
What is convergent evolution?
Not all changes are new Some may revert BACK to an older profile
What is the effect of large and rapid changes in genes?
Large and rapid changes are rare but often lead to escape from existing herd protection
Outline in detail how antigenic shift occurs
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)
How do new epidemics arise?
Antigenic shift => New types will not be protected against by previous infection or vaccination
What are the common epidemiological associations of disease?
Transmission: Hospital acquired infection
Reservoirs of infection : Contact tracing, Determining Introduction Events
Spread or emergence of resistance
What is the use of a molecular restriction digest?
Molecular Restriction Digest typing can monitor effectiveness of control measures
What is the purpose of contact sourcing?
Molecular typing can aide in outbreak sourcing
How can we predict resistance in antibiotics?
Can predict resistance of antibiotics by looking at certain SNPs via PCR
What is the purpose of molecular epidemiology?
Molecular epidemiology offers a variety of methods to test questions Involving disease transmission, strain virulence, pathogen evolution
What is required to choose the most appropriate system against pathogens?
- Knowing the most appropriate variable/s
- Quantitating variations and deriving diversity
- Generating identities or clusters
- Applying related data:
What related data is used to determine the correct course of action?
- geographic location
- time of isolation
- incidence
- prevalence
- transmission rate
- severity of disease
