Using Whole Genome Sequencing for Surveillance and Outbreak Investigations Minnesota Carlota Medus PhD MPH Epidemiologist Supervisor Foodborne Diseases Unit Use of WGS for Surveillance in Minnesota ID: 766593
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Using Whole Genome Sequencing for Surveillance and Outbreak Investigations, Minnesota Carlota Medus, PhD, MPHEpidemiologist SupervisorFoodborne Diseases Unit
Use of WGS for Surveillance in Minnesota Goals of this presentation: Show Minnesota experience using WGS as part of routine surveillance Compare the utility of WGS and PFGE as part of routine surveillance, using 2017 Salmonella Enteritidis (SE) data as an example Outbreak examples, showing the role of WGS
Use of WGS for Surveillance in Minnesota Whole genome sequencing (WGS) for SE surveillance/cluster detection since 2014WGS for S. Typhimurium (STm) surveillance/cluster detection since 2017 SE and STm isolates sequenced at MDH, hqSNP analysis at Wadsworth Center, New York State Department of Health All other Salmonella and STEC are sequenced, but only analyzed on request. All Listeria isolates are also sequenced and analyzed at CDCSubtyping using pulsed-field gel electrophoresis (PFGE) continues
Laboratory-Epidemiology CommunicationLaboratoryInterpret the data and identifies clusters Communicate clusters to epidemiologistsProvide access to the data to epidemiologistsEpidemiologyShare epidemiological data with the laboratoryCommunicate with if changes neededLab and Epi jointly decided what to call a cluster
Laboratory-Epidemiology CommunicationShared drive hqSNP treesHeat maps Spreadsheet Line list of result interpretationEmail notification of new clusters
Lab IDPFGE pattern Number of SNPs Lab ID for closely related isolates Cluster ID
MDH00219 MDH00225- In-vivo, same as E2001001070 MDH00215 -Sporadic 4/19/01MDH00247 --Sporadic 8/6/12 MDH00204 - Sporadic 5/14/01 MDH00221 - Sporadic 5/14/01 MDH00203 - Sporadic 7/11/00 MDH00214 - Sporadic 3/12/01 MDH00206 - Sporadic 8/23/00 MDH00217 - Sporadic 6/10/13 MDH00237 Sporadic 6/22/11 MDH00236 - Sporadic 5/7/11 MDH00207 - Sporadic 8/31/2000 MDH00233 - Sporadic 12/7/2001 MDH00248 - Sporadic 6/10/13 MDH00205 - Sporadic 8/22/2000 MDH00216 - Sporadic 4/30/2001 MDH00224 -Sporadic 6/11/2001 MDH00254 MDH00252 MDH00253 MDH00234 MDH00226 - Sporadic 6/21/2001 MDH00231 - Sporadic 7/16/2001 MDH00202 - Sporadic 7/7/2000 MDH00208 - Sporadic- Same time, PFGE, and MLVA as Outbreak 1 MDH00209 MDH00210 MDH00211 MDH00222- In-vivo, same as E2001001070 MDH00228- In-vivo, same as E2001001070 MDH00223 MDH00220 MDH00218 MDH00213- Sporadic- Same PFGE and time as Outbreak 1 MDH00232- Sporadic 10/17/01 MDH00227 MDH00230 MDH00251 MDH00229 MDH00235- Sporadic 10/3/05 MDH00243- Sporadic, same PFGE and time as Outbreak 5 MDH00245- Sporadic 6/26/12 MDH00249 MDH00250 MDH00246-Sporadic 7/30/12 MDH00255- OH Sample 1 MDH00256- OH Sample 2 MDH00241- Sporadic, same PFGE and time as Outbreak 5 MDH00239 MDH00242 MDH00244- Environmental sample from Outbreak 5 MDH00238 MDH00240 Defined Outbreak Samples Outbreak 1- Sept 2000 Outbreak 2- May 2001 Outbreak 3- Aug 2001 Outbreak 4- Nov 2003 Outbreak 5- Aug 2008 Outbreak 6- Spring 2014 Outbreak 7- Spring 2014 0-2 SNPs 0-2 SNPs 0-2 SNPs 1SNP 0 SNPs 0-1 SNPs 0-3 SNPs Taylor et al. J Clin Micro Oct 2015
Cluster PFGE Pattern (MN pattern name) No. Cases.0004 (SE1)27.0002 (SE11)30.0005 (SE43) 4 .0021 (SE77) 17 .0049 (SE16) 7 WGS Cluster Number Corresponding PFGE pattern No. Cases Cluster 1 .0002 7 Cluster 2 .0004 6 Cluster 3 .0008 2 Cluster 4 .0021 12 Cluster 5 .0004 3 Clusters 6 .0002 6 Cluster 7 .0004 7 Cluster 9 .0049 6 Cluster 10 .0002 3 Cluster 11 .0116 &.1076 2 Cluster 12 .0002 2 Cluster 13 .0054 2 Cluster 14 .0042 2 v s. PFGE Clusters and WGS Clusters, January-April, 2017
2017 SE hqSNP TreeIsolates in a 90-day time periodIncludes closely related (within 10 SNPs) 2014-2017 isolates 0.02
Cluster 9 Cluster 7 Cluster 5 Cluster 2 Cluster 4 Travel to Jamaica Restaurant-associated outbreak
0.02 2017 SE hqSNP Tree Isolates in a 90-day time periodIncludes closely related (within 10 SNPs) 2014-2017 isolates
Cluster 3 Cluster 6 Cluster 11 Cluster 13 Cluster 10 Cluster 12 Cluster 1 Travel to Dominican Republic Travel to Mexico 0.02
No. of CasesWeek of Specimen Collection Cases by week of specimen collection, PFGE alone(n=27) Week of Specimen CollectionNo. of Cases WGS cluster cases by week of specimen collection
hqSNP Tree for SE Pattern .0004 IsolatesTravel to JamaicaEthiopian FoodUnsolved
Cluster 9 Cluster 7 Cluster 5 Cluster 2 Cluster 4 Travel to Jamaica
No. of CasesWeek of Specimen Collection Cases by week of specimen collection, PFGE alone(n=7) Week of Specimen CollectionNo. of Cases WGS cluster 9 cases by week of specimen collection
Outbreak ExamplesOf the 13 WGS clusters, 4 were not travel-associated, 3 were solvedThe examples from 2017 surveillance described here showed WGS Refined the case definition: excluded cases that were not part of the outbreakA common PFGE pattern (pattern 4) was “split” into multiple outbreaksTravelers likely represented real outbreaks
Outbreak ExamplesStuffed chicken example, 2015
JEGX01.0005/JEGA26.0037WGS 0-1 SNPs Number of Cases May 2 3 4 5 6 7 1 June 8 Week of Specimen Collection 4 18 25 1 29 22 15 8 11 27 20 13 6 July Ate Brand A chicken Salmonella Enteritidis Cases, Brand A Stuffed Chicken Investigation by Date of Specimen Collection, May-July 2015 JEGX01.0004/JEGA26.0002 WGS 0 SNPs
JEGX01.0005/JEGA26.0037Different sequences Number of Cases May 2 3 4 5 6 7 1 June 8 Week of Specimen Collection 4 18 25 1 29 22 15 8 11 27 20 13 6 July JEGX01.0004/JEGA26.0002 Different sequences Salmonella Enteritidis Cases, Brand A Stuffed Chicken Investigation by Date of Specimen Collection, May-July 2015 Ate Brand A chicken products JEGX01.0005/JEGA26.0037 WGS 0-1 SNPs JEGX01.0004/JEGA26.0002 WGS 0 SNPs
Outbreak ExamplesStuffed chicken example, 2015Product testing helped identify additional cases that did not match the initial outbreak cases by PFGE or WGS WGS identified this really small polyclonal outbreak even though there were a lot of PFGE-matching cases at the same time
Acknowledgements Minnesota Dept. of Health, Foodborne Diseases Unit Kirk Smith Dana Eikmeier Josh Rounds Stephanie Meyer Amy Saupe Marijke Decuir Team Diarrhea Minnesota Dept. of Health, Public Health Laboratory Angie Jones Taylor Dave Boxrud Xiong (Sean) Wang & Sequencing Core Victoria Lappi Megan Nichols Enterics lab PFGE lab New York Dept. of Health, Wadsworth Center Bill Wolfgang Pascal Lapierre Samantha Wirth Bioinformatics Core