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
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WGS in public health microbiology - MDU/VIDRL Seminar - wed 17 jun 2015
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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
The one true assay?
Traditional workflow
Whole Genome Sequencing (WGS)
2-10 Mbp
100-300 bp30-100x depth
Simple?“Analysis” and “Results”
The promise of genomics
∷ A single assay
∷ Cheaper
∷ Faster
∷ High throughput
∷ Full single nucleotide resolution
Utility of WGS
∷ Diagnostics: strain level identification: in silico antibiogram and virulence profile
∷ Surveillance: in silico genotyping - MLST, serotyping, VNTR, MLVA: what’s lurking in our hospital/community?
Visualise and explore trees linked to genome data. Just upload .nwk and .csv! microreact.org
Sharing data
Open science
∷ Crowd-sourcing provably works: EHEC outbreak 2011: Ebola: MERS
∷ But only if people share: sequencing data: metadata: software source code for analysis
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
“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
Conclusion
Acknowledgements
∷ Slide source material: Nick Loman: Jennifer Gardy: Rob Beiko