Molecular and Genomic Epidemiology of Infections Flashcards
- What is molecular Epidemiology?
A resolved measure (diversity) of differences (variables)
that determines:
a) Disease distribution in time and place
b) Disease transmission
c) Disease manifestation
d) Disease progression
- What kinds of questions can molecular epidemiology answer?
- -> Confirming Outbreaks ( eg source of pathogen, geographical spread, is it actually an outbreak or is it a contamination)
- > Identifying Disease risks (virulence changed? resistant strains ? new infection or recrudescence of old one?)
- How much difference is enough to tell if a pathogen is present?
We need to look at molecular changes , and see why is there changes (resolving diversity).
- What are the three functional characteristics to determine what pathogen you’re looking for?
- Classical = Biochemistry
- Serology = how is the host affected
- Virulence = Verotoxins
- What genomic characteristics might we look at?
look at DNA – how many genes do we look at?
—Resistant genes
Look for changes that caused by genes – phenotypes. Or look at amino acids->protein -> see how protein is affected . look at base sequence eg SNPs – maybe make it more virulent or less virulent. Look at Ribosome or miRNA.,
-Changes in translocations/re-arrangements – happens during transmissions –
Looks of targets to look at
- What is the resistant gene in rifampicin , ans what does this treat?
rpo gene is the resistant gene in rifampicin that we treat with MDR TB.
- What is the difference between single weighting and additive weighting?
single weighting = Just looking at whether the pathogen is there or not through one test eg for test for antigen or verotoxin
Additive = Do many tests - know exactly what the organism is and how virulent it is
8. What do you know about the 0157 e.coli? ie symptoms toxin produced how we test for it what type of weighting?
0157- Diarrhoea Vomiting. Produces toxin – O157 Toxin ( 2+ve) – grow it on media – grows colonies- can sub culture colonies – do a latex test with antibodies on blue latex beads –> show gene (stx2) is there using PCR ,do phage testing – to give us a phage number 21/288
additive weighting of single tests (multiple single tests)
- How did scientists investigate an epidemic outbreak of E.Coli in Godstone farm 2009?
-kids were getting ill
-we need to know if cases are the same organism , which organism, same phage type, same toxin
-To close down zoo- hazard
-Which animals are infected
Tests are done ,
Tells us where its from- sheep(poo-straw-positive samples found using VTEC)
Wasn’t in sand pit or water – we know it wasn’t coming through water
- What do you look at when you do multiple weighting for factoral genomic factors?
Presence or absence of a gene/base/s change
in genome/gene relative to location in the genome
- How we can test using multiple weighting for TB?
We can use Spoligotyping (rapid PCR , tells us strains of TB) 1. PCR with RE region primers generates multiple length amplicons
2.Hybridization of labelled PCR products onto
43 spacer specific oligonucleotides (between RE sequences)
fixed on a membrane then visualise signal with RE probe
Result is a profile of the presence/absence of specific repeats at ONE locus
- What can we do with the results from a spoligotyping?
Make a dendrogram that shows relatedness of patterns
- One other system for detecting factoral multiple copy number systems is VNTR, what is this?
Variable Number of Tandem Repeats (VNTR)
The result of this is a profile of the number of specific repeats at multiple genomic loci
- How can you use multiple weighting of functional genomic factors to detect pathogens?
You can look at the types of substitutions that occur in the genome (eg synonymous or not)
ie important to note that a small amount of changes to bases can result in lots of different types of aa->proteins->organism
- What are silent mutations?
Mutations that are Intragenic (between genes) or Synonymous (not altering coding)
- What are non-synonymous mutations?
Substitutions causing coding to be altered
- What are some examples of 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 the sequence AAA?
STOP codon
- What is DRIFT?
- > Gradual alteration in sequence
- > These drifts mean that maybe a mutation could not allow present antibodies made to bind to their pathogens antigen
- Why cant vaccines completely wipe out a pathogen?
Herd immunity (after large vaccination program) kills most but also selects for escape mutants that maintain the drift --> people who were once immune wont be immune anymore
- What is antigenic drift?
Its when an antigen keeps getting its sequenced changed by drift and eventually wont bind to antibodies
*SAME ANTIGEN–> CHANGED. NOT NEW ANTIGEN**
- What does multiple weighting of temporal genomic factors tell us?
Tells us the mutation rate ( the time since the last alteration)
- Bases are changing but maybe a different time between changes
- You would imagine that change likelihood is constant
- What is this idea of a “ Constant Molecular Clock” ??
Accurate predictions in molecular epidemiology thus requires
an assumption that evolution is driven by a
constant molecular clock
24.How does mutation contribute to evolution?
Diversity progresses because random mutations occurring at a regular rate
- What are 5 factors affecting the speed of the ‘molecular clock’?
- Replication Rate
- Proof Reading Enzyme
- Pressure from the host
- Redundancy
- Transmission Rate
- How does replication rate affect the molecular clock?
A high division rate provides a higher mutation rate
- How does polymerase
proof reading fidelity affect the molecular clock?
Some species (eg HIV) have low fidelity promoting high mutation rate
- How does Selection pressure from the host or environment affect the molecular clock?
High selection pressure removes ‘weak’ mutants and emphasises clusters
Loss of selection pressure allows deletions
- How does the Degree of redundancy in the genome affect the molecular clock?
multiple copies of a single gene in the genome allow for mutations in one copy without compromising overall functionality
Movement or recombination within genome may not effect phenotype
- How does transmission rate affect the molecular clock?
High transmission rates relative to the mutation rate
results in dissemination and single strain outbreaks
- Which virus has a high transmission rate and why?
Influenza virus
eg Flu A , because there are 2-3 bases changing per year there is a 1.5 transmission per infection
- What caused the bird flu outbreak in 1990s?
-> Antigenic Drift of Haemagglutinin and Neuraminidase antigens
- Which types of genes are most likely to change?
Hyper-variable genes change more rapidly than conserved genes
but
Conserved genes are more likely to be associated with phenotype and virulence
- Do all changes result in a new organism?
Not all changes are new
Some may revert BACK to an older profile (convergent evolution)
- Large and rapid changes are rare in genes but why would this be particularly useful to a pathogen?
Large and rapid changes are rare
but often lead to escape from existing herd protection
- What is antigenic shift?
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). New types will not be protected against by previous infection or
vaccination - leading to new epidemics.
- Difference between antigenic drift and antigen shift?
antigenic drift - same antigen , some genomic changes, immunity might still work
Antigenic shift - new antigen with combination of another viral protein. No immunity
- How can we test transmission effectively for eg in hospital acquired infections
- Look at molecular restriction digest typing = monitor effectiveness of control measures (DNA extracted and cut with the same restriction enzymes then pieces
separated on a gel then visualised)
- How can we see where reservoirs of infection are?
* 2 ways*
Through contact tracing eg one person with HIV spreading it to another two- who did they spread it too
Determining the introduction events - pinpointing the first case and where it all began from eg ebola first case in Guinea
- What can we look foe when we’re trying to find the spread or emergence of resistance?
-Drug resistance polymorphisms
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41.Molecular epidemiology offers a variety of methods to test questions
Involving disease transmission, strain virulence, pathogen evolution
Choosing the most appropriate system requires…?
- Knowing the most appropriate variable/s
- Quantitating variations and deriving diversity
- Generating identities or clusters
- Applying related data geographic location
time of isolation
incidence
prevalence
transmission rate
severity of disease
