USING WGS FOR SURVEILLANCE, CLUSTER DETECTION, AND EPI INVESTIGATIONS IN WASHINGTON Washington State Department of Health

USING WGS FOR SURVEILLANCE, CLUSTER DETECTION, AND EPI INVESTIGATIONS IN WASHINGTON Washington State Department of Health

Washington State Local Health Jurisdictions *Agency leader is both director and health officer (2) Clallam 74,240 Jefferson 31,360 Grays Harbor 72,970 Pacific 21,250 Wahkiakum 4,030 San Juan 16,510 Mason 63,190 Island 82,970 Kitsap 264,300 Whatcom 216,300 Skagit 124,100 Snohomish 789,400 Seattle & King County 2,153,700 Tacoma-Pierce* Thurston 859,400 276,900 Lewis 77,440 Cowlitz 105,900 Clark* 471,000 Lab & Epi DOH Main Skamania 11,690 Kittitas 44,730 Yakima 253,000 Klickitat 21,660 Chelan 76,830 Okanogan 42,110 (Chelan-Douglas) Douglas 41,420 Grant 95,630 (Benton-Franklin) Franklin 90,330 Benton 193,500 (Northeast Tri County) Ferry 7,740 Lincoln 10,700 Adams 19,870 Walla Walla 61,400 Stevens 44,510 Pend Oreille 13,370 Spokane 499,800 Whitman 48,640 Garfield 2,200 Columbia 4,100 Asotin 22,290 Washington State Total Population (estimate) April 2017: 7,310,300 Source: Office of Financial Management Departments that have combined public health with human services (16) Single County District (8) Public Health Department (8) Multi County District (3)

Washington State Department of Health 3

Volume of notifiable enteric illnesses Condition 2017 Case Count Campylobacteriosis 2215 Salmonellosis 810 Giardiasis 668 STEC 404 Shigellosis 285 Cryptosporidiosis 150 Vibriosis 96 Listeriosis 17 Cyclosporiasis 9 Washington State Department of Health 4

Current cluster detection with PFGE Laboratorians determine PFGE pattern and look for recent matches Salmonella/STEC within 60 days Generally clusters of 2+ cases reported Exceptions for very common patterns Listeria 2 cases within 120 days Communication/data sharing Email notification Shared cluster linelist (excel) Database of PFGE patterns accessible to epi Weekly lab-epi meetings Washington State Department of Health 5

Email notification Washington State Department of Health 6

Cluster linelist Organism Outbreak Code NORS ID Primary Enzyme Cluster Date EPI WA notes-cluster summary S. Okatie 1801MLOKA-1 OKAX01.0001 12/26/2017 KrisandraKratom exposure S. Enteritidis 1801MLJEG-1 JEGX01.0042 2/5/2018 Laurie Travel to Mexico assoc. S. I 4,[5],12:b:- L(+) Tartrate(+) 1712MLJKX-1 JKXX01.1478 12/1/2018 KrisandraKratom exposure Raw Milk. Does not match the 2017 cluster that E. coli O121 2018-630 EXKX01.0011 8/31/2018 Beth reported raw milk g ~10 prior to onset. g S. Infantis 1810MLJFX-1 10/8/2018 Beth Canada OB - Only AK and WA cases related by WGS. Multiple counties. Starting NHGQs Washington State Department of Health 7

PFGE Pattern Report Washington State Department of Health 8

Current WGS Status Sequencing all clinical Salmonella, Listeria, STEC WGS data not used routinely for cluster detection Special outbreak situations analysis requested at CDC Epi likes to spy in NCBI Hypothesis generation Excluding cases Including additional cases that didn t match by PFGE Washington State Department of Health 9

Epi Use 1: Answer a specific question Have we seen any recent listeriosis cases associated with an ice cream production facility? o Three known human illnesses in 2014-2015 Third case occurred a year later than the original two o Listeria can persist in the environment for many years Washington State Department of Health 10

Epi Use 1: Answer a specific question Find the SNP cluster in NCBI Search for clinical to find and highlight clinical isolates No cases on the SNP tree other than the three known cases yay! Washington State Department of Health 11

Epi Use 2: Confirm what we expect Three case-patients with STEC O26, new PFGE pattern in WA, reported eating at a common restaurant Sequencing available for two isolates says just what we suspected! Washington State Department of Health 12

Epi Use 3: Find what we don t expect Four Salmonella I 4,[5],12:i:- cases from a single county, 2 Fall 2017, 2 May 2018 o Rare PFGE pattern o All clustered closely on the tree One unexpected isolate in the middle! o 2017 case, from the same county o Different PFGE pattern o Linked to a previous chicken outbreak Red isolates Same PFGE Pattern isolate Different PFGE Pattern Washington State Department of Health 13

Epi Use 3: Find what we don t expect Eventually 7 case identified over a year time-frame o All reported shopping at the same location of a warehouse store Investigated and reported as an outbreak Jump start on hypothesis generation by the presence of the isolate from a previous outbreak was critical Washington State Department of Health 14

2018 STEC WGS By the Numbers ~323 clinical WA STEC isolates sequenced 39 STEC clusters with at least two isolates in NCBI Washington State Department of Health 15

2018 Salmonella By the Numbers ~779 Clinical WA isolates sequenced Broke the NCBI search Washington State Department of Health 16

Epi Data Systems Washington State Department of Health 17

Epi Data Systems - WDRS New MAVEN-based surveillance implemented summer 2018 Allows for the electronic capture of much more complete exposure data Working through growing pains of system transition Washington State Department of Health 18

Salmonellosis exposure data in WDRS ORCA student team Public Health/Epidemiology graduate students Hired as temporary DOH employees Attempt NHGQ interviews on all eligible cases of salmonellosis Data is entered into WDRS Washington State Department of Health 19

Epi Data Systems - NCBI Bookmark links to trees in browser Washington State Department of Health 20

Epi Data Systems - NCBI Watched isolates feature Washington State Department of Health 21

Epi Data Systems - NCBI Washington State Department of Health 22

Epi Data Systems - SEDRIC SEDRIC provides an easy way to exchange information between states and CDC SEDRIC allows state partners to work backwards from PNUSA numbers in NCBI to find state isolate numbers Washington State Department of Health 23

Plans for the post-pfge world WGS cluster communications plans will closely mirror existing PFGE protocols Laboratorians will use Bionumerics to look for clusters and communicate via email/cluster list Usefulness of allele codes will be assessed once they are released. Exploring ways to better access allele codes on the Epi side. Epi will use NCBI as a secondary tool to provide context for clusters Washington State Department of Health 24

Plans for the post-pfge world Exploring alternate cluster detection methods to address the time lapse in receiving WGS analysis results Spatio-temporal Simple case counts Serotype-specific case counts Better automation of analyzing exposure data Washington State Department of Health 25

Dashboards Washington State Department of Health 26

Dashboards Washington State Department of Health 27

Exposure data report Event date Poultry Pork Beef Fish Raw Fish Eggs Dairy Leafy Greens 1/2/2019Unknown Unknown Unknown Unknown Unknown Unknown Unknown Cats or kittens Washington State Department of Health 28 Dogs or puppies 1/3/2019Yes Yes No No No No No Yes Yes Yes No 1/4/2019No Maybe Yes No Yes No No Yes No No 1/3/2019Yes Yes Yes No No Yes No Yes 1/11/2019No No No No No No No No No No Yes 1/12/2019Yes Yes Yes No No Unknown Yes Yes No Yes No 1/14/2019Yes No Yes Yes No No No Yes Yes 1/13/2019No No No Yes No Yes Yes Yes 1/15/2019No No Yes No Yes 1/21/2019Yes Yes No No Yes No No 1/17/2019Yes No No No No Yes Yes No No No No 1/1/2019Yes Yes Yes Yes Yes Yes Maybe No Yes Yes No 1/24/2019Yes 1/21/2019Yes Yes Yes No No Yes Yes No No Yes No 1/6/2019No No No No No No No No No Yes No Snakes

Final Thoughts WGS is a powerful new tool that provides a great opportunity to learn more about outbreaks and illness sources But Washington State Department of Health 29

Final Thoughts Lastly, the added value of WGS surveillance is maximized by breaking down the silos of epidemiology and microbiology and engaging informatics specialists in data analysis and visualization. At the same time, the increasingly recognized value of datasharing creates new challenges of interdisciplinary communication and the communication of WGS results to the public. Whole genome sequencing for foodborne disease surveillance Landscape paper, World Health Organization. https://apps.who.int/iris/bitstream/handle/10665/272430/9789241513869-eng.pdf Washington State Department of Health 30

Washington State Department of Health is committed to providing customers with forms and publications in appropriate alternate formats. Requests can be made by calling 800-525-0127 or by email at civil.rights@doh.wa.gov. TTY users dial 711.