Lecture 3: Molecular Epidemiology and Next Generation Sequencing

Question 1

What did John Snow do?

Answer 1

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.

Question 2

What is epidemiology?

Answer 2

The pattern of disease within a population

Question 3

What is MLST?

Answer 3

Multilocus sequence typing

Question 4

How does MLST work?

Answer 4

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.

Question 5

What GC content does SA have?

Answer 5

33%

Question 6

What type of bacteria is SA?

Answer 6

gram positive (fermicute)

Question 7

What does MRSA stand for?

Answer 7

Methicillin resistant SA

Question 8

When is SA difficult to treat?

Answer 8

If gets into blood and when forms films on pace makers etc

Question 9

What is one of the most important hospital strains?

Answer 9

ST239

Question 10

What is globally the most common strain?

Answer 10

ST239

Question 11

What is unusual about ST239 and what does having a large SCCmec element mean?

Answer 11

Only found in hospitals as gets outcompeted elsewhere and means it is multiply resistant

Question 12

What is the full genome sequence of this strain called?

Answer 12

TW20

Question 13

What will the reference genome not have?

Answer 13

SNPs

Question 14

How can you use SNPs to build a phylogeny tree?

Answer 14

More closely related strains will have more similar SNPs

Question 15

Why are European strains more diverse?

Answer 15

Had more time to diversify

Question 16

what has diversification in SA come from?

Answer 16

A single bottleneck

Question 17

What happened in northern Thailand with SA?

Answer 17

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.

Question 18

What happened in a maternity ward?

Answer 18

200 day outbreak of MRSA, deep cleaned removed it for 2 months. Was found to be carried on a health worker.

Question 19

What does whole genome sequencing allow us to do?

Answer 19

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

Question 20

What does inference of transmission need?

Answer 20

Combination of genetic and epidemiological data

Question 21

What two things could diversity within a host mean?

Answer 21

reflect time since original colonisation or multiple infection

Question 22

What was the increase of MRSA death rates in 2007 caused by? How was the increase stopped?

Answer 22

ST22. Used more barrier nursing in hospitals and better hygiene

Question 23

What percent of hospitals in the UK acquired MRSA from ST22 from 2000-2005?

Answer 23

75%

Question 24

Isolates from individual hospitals are as diverse as those from different countries, true or false

Answer 24

True

Question 25

How can the accessory genome inform us?

Answer 25

On antibiotic resistance, host switching, can predict which antibiotics a genome will be resistant to.

Question 26

WGS revealed host switching, what is this?

Answer 26

SA can switch from humans to monkeys but not vice versa and when in monkeys loses accessory genes associated with human infection.

Question 27

What is Lactococcus Garviae?

Answer 27

Gram positive. causes gastroenteritis in humans, mastitis in cows and affects some fish

Question 28

What happened in the rainbow trout outbreak of L. Garviae?

Answer 28

2 independent outbreaks. GWAS identified SNPs associated with the trout host. 25kb genomic island arisen independently twice in both major outbreak clades

Question 29

What was the Haiti cholera outbreak?

Answer 29

WGS of the cholera showed it was from Nepalese aid workers. 6% of Haitians effected as human waste from the UN camps entered rivers.