How genomics is changing the practice of public health microbiology. The role of whole genome sequencing as the "one true assay". Another powerful tool for the epidemiologist.
WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015
1. Whole genome sequencing in
public health microbiology
A/Prof Torsten Seemann
Victorian Life Sciences Computation Initiative (VLSCI)
Microbiological Diagnostic Unit Public Health Laboratory (MDU PHL)
Doherty Centre for Applied Microbial Genomics (DCAMG)
The University of Melbourne
MDU/VIDRL Mini Seminar - Melbourne, AU - Wed 17 June 2015
11. Reference based analysis
∷ Implies you have a “close” reference
: need to be careful with draft genomes
∷ Very sensitive
: single mutation precision
∷ Core genome only
: ignores novel DNA in your isolate
13. De novo analyses
∷ Does not require a reference
∷ Access to whole pan-genome
: new plasmids
: unexpected antibiotic resistance elements
: virulence factors
∷ Limited by short reads
: misleading results in repeated regions
: not suitable for high-res SNP analysis
14. Best practice
∷ Use both approaches
: reference-based + de novo
∷ Best of both worlds
: and worst of both worlds - interpretation is non-trivial
∷ Still need
: good epidemiology, metadata and domain knowledge!
28. Open science
∷ Crowd-sourcing provably works
: EHEC outbreak 2011
: Ebola
: MERS
∷ But only if people share
: sequencing data
: metadata
: software source code for analysis
29. GenomeTrakr
∷ International cooperation
: Led by FDA + NCBI
: >20 collaborating institutes inc. UK PHE, DK DTU, MX
: Salmonella and Listeria
∷ Public SRA BioProject #183844
: Real-time submission of WGS genome reads
: Nightly updates of phylogenomic trees
: Contains ~8000 strains of Salmonella
30. “GenomeTrakka”
∷ A shared online system for all Australian labs
: upload samples
: automated standard/specific analyses
: simple reports and visualization
: easy to submit to international archives (SRA)
∷ Access control
: each lab controls their own data
: jurisdictions can share data in national outbreaks