Outbreak Investigation using Genomic Epidemiology

Whole genome shotgun sequencing of patient isolates is used to construct a dendrogram of isolates using single nucleotide variants.

Transcript

1. Outbreak Investigation using Genomic Epidemiology Shaun Jackman 2013-03-22 1
2. Outbreak Investigation Notice an unusually high number of occurrences of a disease Culture isolates from patient samples or from environmental samples, like food and water Compare genotypes and cluster isolates 2 Original map by John Snow showing the clusters of cholera cases in the London epidemic of 1854. http:/ /en.wikipedia.org/wiki/Epidemiology
3. Methods of Genotyping PFGE — Pulse field gel electrophoresis MLST — Multilocus sequence typing CGF — Comparative genomic fingerprinting 3
4. Whole Genome Sequencing Interrogates the entire genome Yields a much finer level of detail Does not require probes of known sequences 4
5. Cluster Isolates by Genotype Identify clusters of isolates that have a similar genotype Each cluster of isolates may be an outbreak 5 Feil, Edward J., et al. "eBURST: inferring patterns of evolutionary descent among clusters of related bacterial genotypes from multilocus sequence typing data." Journal of bacteriology 186.5 (2004): 1518-1530.
7. Campylobacter 7 http:/ /en.wikipedia.org/wiki/Campylobacter
8. Causes gastroenteritis — diarrhea Found in animal poop Think twice before drinking from a stream 1,722 cases in BC 2011 That’s a lot of diarrhea Campylobacter 8 http:/ /www.equisearch.com/trail_riding/tips/be-water-wise-on-your-next-horse-camping-trip/
9. Bike race Event foodstand Lake at a summer camp Restaurant Relatives 9 Campy Investigations http:/ /forums.mtbr.com/cannondale/new-cannondale-hardtail-flash-534108-6.html
10. 0.08 Consensus 10 Campylobacter Reference
11. 0.08 Reference Consensus 11 Campylobacter
12. 0.2 2R1 H1R6 H5R6 6R6 H2R6 4R1 Consensus 8aR6 8R6 Reference 5R6 H4R6 13 Clostridium difficile
13. 0.2 561 120 8 4 563 8 2 8 3 117 8 1 559 Consensus 215 121 564 8 6 562 472 560 119 474 118 Reference 473 8 5 475 14 MRSA
14. 0.06 Consensus Reference 15 Salmonella
15. 16 William Hsiao Patrick Tang Jennifer Gardy Kim Macdonald
16. 17 The A-Z of Epidemiology: germs from Anthrax to Zoonoses. A disturbing bedtime book for kids http:/ /www.youtube.com/watch?v=P2C4U624Y6o