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Outbreak Investigation using Genomic Epidemiology

Outbreak Investigation using Genomic Epidemiology

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

Shaun Jackman

March 22, 2013

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  1. 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
  2. Methods of Genotyping PFGE — Pulse field gel electrophoresis MLST

    — Multilocus sequence typing CGF — Comparative genomic fingerprinting 3
  3. Whole Genome Sequencing Interrogates the entire genome Yields a much

    finer level of detail Does not require probes of known sequences 4
  4. 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.
  5. 6

  6. 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/
  7. 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
  8. 0.2 2R1 H1R6 H5R6 6R6 H2R6 4R1 Consensus 8aR6 8R6

    Reference 5R6 H4R6 13 Clostridium difficile
  9. 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
  10. 17 The A-Z of Epidemiology: germs from Anthrax to Zoonoses.

    A disturbing bedtime book for kids http:/ /www.youtube.com/watch?v=P2C4U624Y6o