wgs data sharing for improved public health · •listeria monocytogenes –subtype into mlst (st6,...

WGS data sharing for improved public health

Jette Sejer Kjeldgaard, PhD, Postdoc

Research Group for Genomic Epidemiology

National Food Institute

Contact info: [email protected]

DTU Food, Technical University of Denmark

Add or change Presentation Title or Date via ”Insert”; ”Header & Footer”

WGS data sharing

• WGS

–one method -> detailed output: DNA sequence

28 September 2018 WGS data sharing for improved public health

2

– Species identification

– Sub-species identification

– Comparison

– Relatedness

– Typing

– Presence of genes

– Store and re-use!



Why share WGS data?


3

• Which isolates and how many?

• Purpose – benefits

• Examples of sharing

–Outbreak investigation

• National

• International/EU

–New resistance genes



Danish WGS surveillance by DVFA

28 September 2018 4 WGS data sharing for improved public health

Surveillance in animals, food and feed

• Control of food producers

• Control of animal flocks

• Campaigns

• Food producers self-control programmes

National and EU legislation

National surveillance programs

Projects with specific types of companies or food items with known risk of potential hazards



WGS – where and what?

• Now routine method in DVFA Lab in Ringsted (since 2016)


5

• Salmonella – WGS of all for sero typing+ AST

• Listeria monocytogenes - WGS on some - typing - MLST

• Campylobacter – WGS for projects

• E. coli – WGS on some – projects and unusual resistance profiles + AST

DTU support:

• Method development,

• WGS analysis methods and -tools

• Sequence database – storage and sharing of data



Shared surveillance and research

• Shared database

–Surveillance projects

–Source attribution

–Research projects

–Outbreak investigation


6

• Primarily Salmonella and Listeria monocytogenes

• -> high frequency or long-lasting outbreaks



Central Outbreak Management Group (DCUG)

28 September 2018 7 WGS data sharing for improved public health

Surveillance of outbreaks of foodborne bacteria

Food- and waterborne outbreak database (FUD)

One database

General analysis

-SNP trees, cgMLST




8

Central Outbreak Management Group (DCUG) collaboration

Local doctor or hospital

Clinical microbiological dept.

Veterinary samples: animals, feed and food

-Surveillance, projects and self control systems




9

DCUG purposes

• Stop outbreaks - reduce number of disease cases

–E.g. withdrawal of food from marked, sanitation of farms, import stop from specific food producer

• Learn and prevent other outbreaks

• Build knowledge about food safety

• Improve surveillance and identification of outbreaks

• Improve credibility of food producers

– Improve trust between consumer and industry



WGS-based surveillance of outbreaks of foodborne bacteria

• Salmonella enterica

–Subtyped into serotypes (Typhimurium; (4,(5),12:i:-); Enteritidis etc. and MLST (ST19, ST34…)

• Listeria monocytogenes

–Subtype into MLST (ST6, ST8, ST21)


10

WGS Whole Genome Sequencing

Example of grouping of Listeria by ST and company




11

Listeria monocytogenes coloured by MLST sequence type (ST) from companies A-Q

I

H + L

K + P

B +C + F+ P +Q




12

A16028766_R1_001.tr

im.fq

B16034907_R1_001.tr

im.fq

C16037567_R1_001.tr

im.fq

C16038591_R1_001.tr

im.fq

C16038593_R1_001.tr

im.fq

C16038598_R1_001.tr

im.fq

C16041018_R1_001.tr

im.fq

C16041019_R1_001.tr

im.fq

C16041020_R1_001.tr

im.fq

D16040900_R1_001.tr

im.fq

E16040048_R1_001.tr

im.fq

F16041072_R1_001.tr

im.fq

F16041076_R1_001.tr

im.fq

G16030093_R1_001.tr

im.fq

G16030094_R1_001.tr

im.fq

H16029814_R1_001.trim.

fq

I16034910_R1_001.tr

im.fq

I16034913_R1_001.tr

im.fq

I16034914_R1_001.tr

im.fq

I16034919_R1_001.tr

im.fq

A16028766_R1_001.trim.fq 0 12691 36464 12624 12687 12727 12689 12844 12717 36540 12755 12507 12511 37004 12506 8389 12708 12763 12794 12767

B16034907_R1_001.trim.fq 12691 0 37325 9301 122 119 127 8743 122 37289 9230 42 40 37686 9797 11984 9901 9928 9934 9932

C16037567_R1_001.trim.fq 36464 37325 0 37218 37227 37297 37280 37373 37263 3193 37353 37239 37241 3195 37192 36701 37277 37300 37319 37293

C16038591_R1_001.trim.fq 12624 9301 37218 0 9279 9299 9291 9231 9291 37268 9321 9277 9270 37656 9706 11960 10060 10084 10096 10082

C16038593_R1_001.trim.fq 12687 122 37227 9279 0 9 17 8704 10 37198 9198 37 36 37596 9767 11922 9872 9899 9905 9906

C16038598_R1_001.trim.fq 12727 119 37297 9299 9 0 16 8731 9 37269 9229 34 32 37665 9786 11980 9889 9915 9922 9921

C16041018_R1_001.trim.fq 12689 127 37280 9291 17 16 0 8730 16 37255 9228 42 40 37646 9788 11956 9888 9913 9921 9920

C16041019_R1_001.trim.fq 12844 8743 37373 9231 8704 8731 8730 0 8726 37420 7323 8666 8660 37824 8350 11858 9972 10002 10000 10009

C16041020_R1_001.trim.fq 12717 122 37263 9291 10 9 16 8726 0 37240 9211 37 35 37631 9796 11957 9895 9922 9929 9929

D16040900_R1_001.trim.fq 36540 37289 3193 37268 37198 37269 37255 37420 37240 0 37389 37198 37197 23 37207 36768 37309 37326 37351 37327

E16040048_R1_001.trim.fq 12755 9230 37353 9321 9198 9229 9228 7323 9211 37389 0 9196 9207 37795 8061 12150 10074 10105 10102 10108

F16041072_R1_001.trim.fq 12507 42 37239 9277 37 34 42 8666 37 37198 9196 0 3 37595 9775 11935 9871 9898 9905 9906

F16041076_R1_001.trim.fq 12511 40 37241 9270 36 32 40 8660 35 37197 9207 3 0 37586 9776 11933 9881 9909 9915 9916

G16030093_R1_001.trim.fq 37004 37686 3195 37656 37596 37665 37646 37824 37631 23 37795 37595 37586 0 37610 37220 37696 37715 37741 37711

G16030094_R1_001.trim.fq 12506 9797 37192 9706 9767 9786 9788 8350 9796 37207 8061 9775 9776 37610 0 11971 9953 9977 9985 9987

H16029814_R1_001.trim.fq 8389 11984 36701 11960 11922 11980 11956 11858 11957 36768 12150 11935 11933 37220 11971 0 12227 12263 12300 12278

I16034910_R1_001.trim.fq 12708 9901 37277 10060 9872 9889 9888 9972 9895 37309 10074 9871 9881 37696 9953 12227 0 4 2 8

I16034913_R1_001.trim.fq 12763 9928 37300 10084 9899 9915 9913 10002 9922 37326 10105 9898 9909 37715 9977 12263 4 0 4 10

I16034914_R1_001.trim.fq 12794 9934 37319 10096 9905 9922 9921 10000 9929 37351 10102 9905 9915 37741 9985 12300 2 4 0 5

I16034919_R1_001.trim.fq 12767 9932 37293 10082 9906 9921 9920 10009 9929 37327 10108 9906 9916 37711 9987 12278 8 10 5 0

WGS-based surveillance of outbreaks – SNP analysis



Outbreak investigation


13

Identifier: Serotype and/or MLST

Collect and share sequences with the serotype and/or MLST identifier

Compare sequences by genomic tools:

SNP analysis or cgMLST



Outbreak investigation II

• Outbreak of a common type of pathogen

-e.g. S. Typhimurium

Suspect the source is pork meat

• Compare few human isolates with many veterinary and food isolates


14




15

Human cases of monophasic variant of Typhimurium 4,(5)12:i:- linked to pork meat



International outbreak detection


16

European cross-border outbreaks with disease cases in several EU countries

• Urgent inquiry

• Share information

• Share sequences



Enhanced international collaboration


17



Benefits of using WGS in outbreak investigation


18

• Build a database of DNA sequences

– for analysis, storage and sharing

• Outbreaks are identified faster by clustering

– long term outbreaks are identified

• Easy comparison between disease cases and food items

– old isolates and outbreaks (especially important for Listeria)

– human and veterinary isolates

• Genomic tools are highly discriminatory

– compared to e.g.

• MLVA

• PFGE

• Phage type



Source attribution


19

Links between different productions

-Transports

-Veterinarian/visitors

-Feed

-Bedding materials

-Animal host jump



Unusual resistance phenotypes

• EURL-AR hub Bromhead

• One isolate here… one isolate there…


20

• Confirmatory testing

– Azithromycin

– Daptomycin

– Ertapenem

– …

• Colistin – mcr genes



mcr genes


21

Germany

France

Italy

Spain



Thank you for the attention!


22

Jette Sejer Kjeldgaard

[email protected]

Research Group for Genomic Epidemiology

National Food Institute

European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR)

wgs data sharing for improved public health · •listeria monocytogenes –subtype into mlst (st6,...

Documents