USING WGS FOR SURVEILLANCE, CLUSTER DETECTION, AND EPI ... · an ice cream production facility? ... the time lapse in receiving WGS analysis results • Spatio-temporal • Simple

Washington State Department of Health

USING WGS FOR SURVEILLANCE, CLUSTER DETECTION, AND EPI INVESTIGATIONS IN WASHINGTON

Washington State Local Health Jurisdictions

*Agency leader is both director and health officer (2)

Washington State Total Population (estimate)April 2017: 7,310,300Source: Office of Financial Management

Whatcom216,300

Skagit124,100

Snohomish789,400

Seattle & KingCounty

2,153,700

Tacoma-Pierce*859,400

Lewis77,440

Cowlitz105,900

Clark*471,000

Skamania11,690

Klickitat21,660

Island82,970

Clallam74,240

Jefferson31,360

GraysHarbor72,970

Pacific21,250

Wahkiakum4,030

Thurston276,900

Mason63,190

Yakima253,000

Kittitas44,730

Chelan76,830

Douglas41,420

(Chelan-Douglas)

Okanogan42,110

Benton193,500

Franklin90,330

(Benton-Franklin)

Grant95,630

Ferry7,740 Stevens

44,510

PendOreille13,370

Lincoln10,700

Spokane499,800

Adams19,870

Whitman48,640

Walla Walla61,400

Columbia4,100

Garfield2,200

Asotin22,290

(Northeast Tri County)San Juan16,510

Departments that have combined public health with human services (16)

Single County District (8)

Public Health Department (8)

Multi County District (3)

Kitsap264,300

Lab & Epi

DOH Main

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


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


Email notification


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

E. coli O121 2018-630 EXKX01.0011 8/31/2018 BethRaw Milk. Does not match the 2017 cluster that reported raw milk ~10 prior to onset.

S. Infantis 1810MLJFX-1 10/8/2018 Beth

g g Canada OB - Only AK and WA cases related by WGS. Multiple counties. Starting NHGQs


PFGE Pattern Report


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


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


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!


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!


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 2018o Rare PFGE patterno All clustered closely

on the treeOne unexpected

isolate in the middle!o 2017 case, from the

same countyo Different PFGE

patterno Linked to a previous

chicken outbreak

Red isolates – Same PFGE Patternisolate – Different PFGE Pattern


Epi Use 3: Find what we don’t expect

Eventually 7 case identified over a year time-frameo 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


2018 STEC WGS By the Numbers

• ~323 clinical WA STEC isolates sequenced• 39 STEC ‘clusters’ with at least two isolates in NCBI


2018 Salmonella By the Numbers

• ~779 Clinical WA isolates sequenced• Broke the NCBI search…


Epi Data Systems


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


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


Epi Data Systems - NCBI

• Bookmark links to trees in browser



• Watched isolates feature




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


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


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


Dashboards


Dashboards


Exposure data report

Event date Poultry Pork Beef Fish Raw Fish Eggs DairyLeafy Greens

Cats or kittens

Dogs or puppies Snakes

1/2/2019Unknown Unknown Unknown Unknown Unknown Unknown Unknown

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


Final Thoughts

• WGS is a powerful new tool that provides a great opportunity to learn more about outbreaks and illness sources

• But…


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

https://apps.who.int/iris/bitstream/handle/10665/272430/9789241513869-eng.pdf

Washington State Department of Health is committed to providing customers with formsand publications in appropriate alternate formats. Requests can be made by calling

800-525-0127 or by email at [email protected]. TTY users dial 711.

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USING WGS FOR SURVEILLANCE, CLUSTER DETECTION, AND EPI ... · an ice cream production facility? ... the time lapse in receiving WGS analysis results • Spatio-temporal • Simple