Transitioning from PFGE to WGS in Wyoming...Eric Brown FDA using WGS for SE & Eija Trees using WGS...
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Transitioning from PFGE to WGS in Wyoming Wanda Manley, MS February 2019
Transcript of Transitioning from PFGE to WGS in Wyoming...Eric Brown FDA using WGS for SE & Eija Trees using WGS...
Transitioning from PFGE to WGS in Wyoming
Wanda Manley, MSFebruary 2019
The timeline:
2011 2012 2013
2014 2015 2016…InFORM in Atlanta: Eric Brown FDA using WGS for SE & EijaTrees using WGS for STEC
InFORM in San Antonio: Heather Carleton on WGS and Peter Gerner-Smidt and Eija Trees on Listeria Initiative
WY PHL includes a MiSeq in ELC – under Laboratory Capacity (denied)
WY PHL includes a MiSeq in ELC : training in Oct, instrument installed in Dec
WY PHL WGS certified, a second scientist trained and certified in 2017, and a third scientist trained and certified in 2018
Wyoming demographics:
• One of the smallest PHLs
• ~ 80,000 samples/year
• 10 FTEs in Microbiology• Most on some type of
federal $$
• 10th largest state
• Smallest population - ~550,000
• 2 towns over 50,000
• ~ 175 recognized communities
• ~ 270 heath care facilities
2016: The transition year• Changed the workflow in the PFGE/WGS lab
• Batching PFGE when possible• PFGE plugs and DNA extracts done simultaneously in the same work area• 1 person PulseNet certified for PFGE previously• 2nd person certified for PFGE E. coli O157, Salmonella by end of 2015• 3rd person trained for plug making, subbing plates, etc. in October 2016
• PFGE certified for 4 PulseNet organisms by end of 2017• Dropped all PFGE “special projects”
• Flexible – (1) FTE, and (2) ¼ FTE• Everyone had to learn to do everything
• Low to moderate sample load (we started with 16 and moved to 24/WGS run) Campylobacter
• Worked out of the freezer to fill runs as needed
• Partners – we brought them along with us (WSVL, WY Ag Lab, and UW)
• Cost cutting measures in some areas to fund WGS reagents
Since 2016:• Purchased a QiaCube in July 2017 for automated DNA
extraction
• Purchased a second thermocycler to reduce a potential bottleneck in the molecular section
• Purchased a TapeStation in July 2018 – in implementation
• Now looking at more automation for the MiSeq
• Purchased a MinIon – working with several partners to develop a workflow for ONT
Sequencing every week:• Sequence ~1000 isolates a year
• Working out of the enteric freezer• Somewhat targeted
• Clusters and outbreaks of interest• Specific serotypes• Specific types (puppies and puppy exposures)
• Sequencing non PulseNet organisms• NTMs for another PHL validation• Klebsiella for MCR• Bacterial ID instead of 16s
• Sequencing for partners within the state• Starting to offset some of our sequencing reagent costs
On the horizon:• Equipment redundancy
• iSeq or MinIon?
• More automation for the Illumina platform
• Training other sections of the lab
• GHOST training for Hepatitis C
• 16s as the ABI 3130 is phased out in 2019
• Outreach to other potential partners
• Bioinformatics
• BioNumerics
• Other pipelines
Sharing information between WY PHL and WY ID Epi:
• WY PHL builds an epi report for every new isolate that receives PFGE analysis• It is unlikely we will be able to continue this with WGS
• Google Team Drive with shared information about every sequencing run (run number and date, PNUSA, and StarLIMS number for all PulseNet organisms)
• Updated with every WGS run, SeqSero/Serotype Finder• We store BaseSpace files on Google Team Drive also – easy to share with epi or anyone else
• VM pipeline courtesy of CO DPHE
• WY PHL Microbiology Manager• Hoping to recruit a bioinformatics fellow in the next year or two
• NCBI Pathogen Detection Pipeline
• BioNumerics 7.6 for epi ??
