Medical Microbiology: Molecular and Genomic Epidemiology of Infections Flashcards
What is molecular epidemiology?
- It’s a resolved measure (diversity) of differences (variables) that determines:
- Disease distribution in time and place
- Disease transmission
- Disease manifestation
- Disease progression
What are some of the questions that molecular epidemiology can answer?
- Questions to do with confirming outbreaks:
- Inside institutions - Did patient A catch pathogen from patient B?
- In the community - Who was the first case and what’s the likely source?
- In the past - What’s driven geographical spread of important strains in the past
- In the lab - Is this an outbreak or a contaminant?
- Questions to do with identifying disease risk:
- Shifts in virulence - Are drug resistant strains on the rise? From where?
- Reservois of infection - New infection or recurrent?
What targets for molecular epidemiology can be looked at?
- Functional characteristics
- Classical (Biochemistry)
- Serology (O157 antigen)
- Virulence (Verotoxin)
- Genomic charcteristics
- DNA (gene, amino acid sequence, base sequence)
- RNA (Ribosome, miRNA)
For each of the diffferent types of molecular targets for molecular epidemiology how many targets should you look at?
- Functional charcteristics - you would look at single targets
- Genomic characteristics
- Genes - look at multiple number of genes or multiple copies of the same gene
- For the coding sequence, base sequence and genome locus position you’d also look at multiple targets
How could you determine how diverse each of the targets used for molecule epidemiology are?
- Give target single weighting - target is either present or absence
- Give target additive weighting - combination of single tests
Give an example of a combination of tests you could do, as part of additive weighting, to identify and type the E.coli 0157: Verotoxin
- Grow E.Coli 0157 on selective media - to see conditions it grows best in
- Latex agglutination test - Can show that particular colony grown on selective media is E.Coli 0157 and produces verotoxin
- PCR - Can show which strains of E.coli contain the stx2 gene and therefore produce verotoxin
- Phage typing - Used to give E.coli 0157 a phage number
When determining the diversity of the targets used for molecular epidemiology you can also use multiple weighting. Explain the concept of multiple weighting
- When using multiple weighting instead of using a combination of tests looking at one target like in additive weighting, you look at multiple genomic factors
What are the different types of genomic factors you can look at when using multiple weighting?
- Factoral - Presence or absence of a gene/base/s change in a genome/gene relative to location in the genome
- Functional - Type of substitution (synonymous/non synonymous)
- Temporal - Mutation rate (time since the last alteration)
Explain how spoligotyping of M. Tuberculosis is an example of looking at factoral genomic factors as part of multiple weighting
- DR region of M. tuberculosis genome has possibility of having up to 43 copies of same gene
- Copies “jump in and out” as strain is transferred from one person to another
- This results in copy number for this gene being different as well as copies of gene being in different positions within DR region for each strain
- Ultimately this decides which strain of M.tuberculosis it is
- Spoligotyping results in a profile of the presence/absence of specific repeats of this gene at each of the 43 positions within the DR region
How does spligotyping of M.tuberculosis work?
- PCR with DR region primers generates multiple length amplicons
- Hybridise labelled PCR products onto 43 spacer specific oligonucleotides fixed on a membrane then visualise signal with probe
Give an example of how you can look at functional genomic factors when using multiple weighting
- For any particular organism you can look at a particular DNA sequence (e.g. GATTTGA)
- For that particular sequence you can identify how many different sequences are produced based on a no. of different single base substitution mutations
- You can also group the DNA sequences formed from the mutations based on how similar they are to each other
Explain why the effects mutations can have on the amino acid sequence, and therefore the protien produced, makes looking at functional genomic factors more difficult
- There’s redundancy in the genetic code - you can change a base without changing amino acid produced, for example:
- Silent mutations - Mutations that are intragenic or synonymous (doesn’t change AA sequence)
- Non-synonymous mutations - mutations that change AA sequence and therefore change protein produced
- Corruptive mutations - Have a variety of affects including addition/corruption of stop codons; corruption of promoter regions and deletions/insertions which disrupt reading frame
- All of this means that predicting changes that mutations will cause by looking at functional genomic factors isn’t simple
What is antigenic drift?
- The same antigen changing its sequence base by base - E.g. Haemaglutinin and Neuraminidase genes in Influenza virus
How does herd immunity affect antigenic drift?
- Mutations to base sequence of antigens occurs 3/4 times per year resulting in production of new strains
- Herd immunity (after large vaccination program) kills most of these strains
- Also selects for escape mutants that maintain the drift - Herd immunity means virus will detect antibodies for antigens it posseses and so it’ll change its antigens allowing it escape immunity
Explain the concept of looking at temporal genomic factors for multiple weighting
- Idea that you look and record the amout of time it takes for a mutation to occur within a particular DNA sequence
- You can compare the times it takes for different mutations to occur and cluster types of mutations together that take similar times to occur within same DNA sequence
What is antigenic shift?
- Antigenic shift is a sudden replacement of an antigen with a new antigen due to recombination with another viral type that has evolved separately (either in another animal or another human population)
