Lecture 3: Molecular Epidemiology and Next Generation Sequencing Flashcards
What did John Snow do?
First to suggest infectious agent was water born not air (myazma). He mapped cases of cholera and found they were all near one water pump infected by sewage.
What is epidemiology?
The pattern of disease within a population
What is MLST?
Multilocus sequence typing
How does MLST work?
Take fragments of 7 core genes and sequence both strands. Compare these to known alleles on database. Assign alleles at the 7 loci to give the sequence type.
What GC content does SA have?
33%
What type of bacteria is SA?
gram positive (fermicute)
What does MRSA stand for?
Methicillin resistant SA
When is SA difficult to treat?
If gets into blood and when forms films on pace makers etc
What is one of the most important hospital strains?
ST239
What is globally the most common strain?
ST239
What is unusual about ST239 and what does having a large SCCmec element mean?
Only found in hospitals as gets outcompeted elsewhere and means it is multiply resistant
What is the full genome sequence of this strain called?
TW20
What will the reference genome not have?
SNPs
How can you use SNPs to build a phylogeny tree?
More closely related strains will have more similar SNPs
Why are European strains more diverse?
Had more time to diversify
what has diversification in SA come from?
A single bottleneck
What happened in northern Thailand with SA?
One variant was restricted to a ward which was brought in by a patient and before genome sequencing they would all have been the same strain.
What happened in a maternity ward?
200 day outbreak of MRSA, deep cleaned removed it for 2 months. Was found to be carried on a health worker.
What does whole genome sequencing allow us to do?
identify the source of the outbreak, identify when an outbreak is occurring at an early stage and reconstruct individual transmission events that have occurred over the course of the outbreak
What does inference of transmission need?
Combination of genetic and epidemiological data
What two things could diversity within a host mean?
reflect time since original colonisation or multiple infection
What was the increase of MRSA death rates in 2007 caused by? How was the increase stopped?
ST22. Used more barrier nursing in hospitals and better hygiene
What percent of hospitals in the UK acquired MRSA from ST22 from 2000-2005?
75%
Isolates from individual hospitals are as diverse as those from different countries, true or false
True
How can the accessory genome inform us?
On antibiotic resistance, host switching, can predict which antibiotics a genome will be resistant to.
WGS revealed host switching, what is this?
SA can switch from humans to monkeys but not vice versa and when in monkeys loses accessory genes associated with human infection.
What is Lactococcus Garviae?
Gram positive. causes gastroenteritis in humans, mastitis in cows and affects some fish
What happened in the rainbow trout outbreak of L. Garviae?
2 independent outbreaks. GWAS identified SNPs associated with the trout host. 25kb genomic island arisen independently twice in both major outbreak clades
What was the Haiti cholera outbreak?
WGS of the cholera showed it was from Nepalese aid workers. 6% of Haitians effected as human waste from the UN camps entered rivers.
