Implementation and Impact of Salmonella serotype determination using pulsed-field gel electrophoresis in New York June 14, 2017
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1 Implementation and Impact of Salmonella serotype determination using pulsed-field gel electrophoresis in New York June 14, 2017 Kimberlee Musser, PhD Chief, Bacterial Diseases Wadsworth Center, NYSDOH
2 June 14, Why determine Salmonella serotype from PFGE? We receive Salmonella a year 100% of Salmonella by PFGE since 2003 Our microbiologist with 40+ years experience was retiring Antisera had become challenging to acquire and maintain We knew that whenever PFGE and conventional serotyping disagreed that PFGE was always correct CDC Publication
3 June 14, Improving the TAT Day 2-10 Day 2-10 Day 3 Day 5-13
4 June 14, Would it be worthwhile to make this transition with NGS coming in the near future? We are already performing PFGE on all Salmonella. The transition to WGS may take longer than expected We need to find staff and resource savings now.
5 June 14, Validation and Implementation Starting point based on anecdotal experience Developed rules and algorithm Retrospective testing-2012 Discussion with Epis and Clinical Labs Adjustment, prospective testing-2013 Informed PulseNet about using Match to Server tool and changes in NY Reporting-LIMS/ Submitter and Epidemiology Electronic Reporting
6 June 14, Retrospective and Prospective Testing Conventional serotyping and PFGE PulseNet protocol performed side-by-side 4481 isolates (>150 serotypes) Poss. S. Typhi Conventional serotyping TSI PFGE
7 June 14, Rules Call PFGE determined serotype if: 100% match to one isolate with assigned pattern Match to at least 3 isolates 90%( 95% Enteritidis) with conformed serotype; and not more than 1 serotype with 90% match Exceptions are S. Typhi, S. Paratyphi
8 June 14, S. Typhi report Day 2-3
9 June 14, Retrospective Summary 2012 Number of isolates 1486 Number of serotypes 110 Similarity to serotype 100% 1267 (85.2%) >95-99% 123 (8.3%) >90-94% 38 (2.6%) <90% 25 (1.6%) >1 serotype with >90% 17 (1.1%) < 3 isolates - match against server 9 (0.6%) Able to serotype 1421 (95.6%) Unable to serotype 65 (4.4%) PFGE/serotyping discrepant 0
10 June 14, Prospective Summary Number of isolates 2995 Number of serotypes 131, 107 NYS database CDC database 100% 1723 (57.5%) 3 isolates >90% 370 (12.3%) 100% 485 (16.1%) 3 isolates >90% 144 (4.8%) Able to serotype 2722 (90.9%) Unable to serotype 273 (9.1%)
11 June 14, Steps Taken in Process SOP, algorithm changes Established reporting language Implemented reporting changes Retrospective testing Prospective testing Discontinuation date of serotyping
12 June 14,
13 June 14, Reporting ECLRS Epidemiology Report
14 June 14, Requests for serotyping? Questions about changes in submitter reports? NONE in 3 years
15 June 14, Testing to date Year Total Salmonella isolates tested by PFGE Successful PFGE serotype * * % *Conservative algorithm, increase in unusual PFGE patterns not represented in PFGE database
16 If 92% Serotyping reduced (1564) and each sample averages 45 minutes this saves 156 days of FTE time = 60% work June 14, Cost Analysis Salmonella subtyping method Cost/specimen Total Annual Cost (1700 specimens) Serotyping and PFGE on all Salmonella isolates Reagents Labor a,b Total $12.49 $ $ $195,228 PFGE as primary serotyping method with 8% reflex for serotyping $7.26 $61.81 $69.07 $117,419 Cost savings $77,809 a. Labor costs were calculated based on the average hourly rate (range $45.30-$54,790), which includes technician salary (range $37,527-$64,302), fringe benefits (48%), and indirect costs (66%). b. Labor cost per specimen was calculated by dividing the total hands on labor time per assay by the average number of runs per specimen
17 June 14, Where do we go from here? January started WGS on all Salmonella (NextSeq) Converts Nextseq files Runs through SeqSero command line (internal Galaxy Server) SeqSero results imported to LIMs LIMs import of SeqSero results and compared to PFGE serotype and conventional serotype for QA Flag if discordant 320 to date, <5 discordant
18 Acknowledgements Dianna Schoonmaker-Bopp Deborah Baker Timothy Root Nellie Dumas Lisa Thompson Amy Saylors Kara Mitchell Leeanna Armstrong Erica Lasek-Nesselquist Pascal Lapierre Lisa Mingle Samantha Wirth Bill Wolfgang Michelle Dickinson
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