wgs data sharing for improved public health · •listeria monocytogenes –subtype into mlst (st6,...
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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
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WGS data sharing
• WGS
–one method -> detailed output: DNA sequence
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– Species identification
– Sub-species identification
– Comparison
– Relatedness
– Typing
– Presence of genes
– Store and re-use!
DTU Food, Technical University of Denmark
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Why share WGS data?
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• Which isolates and how many?
• Purpose – benefits
• Examples of sharing
–Outbreak investigation
• National
• International/EU
–New resistance genes
DTU Food, Technical University of Denmark
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Danish WGS surveillance by DVFA
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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
DTU Food, Technical University of Denmark
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WGS – where and what?
• Now routine method in DVFA Lab in Ringsted (since 2016)
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• 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
DTU Food, Technical University of Denmark
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Shared surveillance and research
• Shared database
–Surveillance projects
–Source attribution
–Research projects
–Outbreak investigation
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• Primarily Salmonella and Listeria monocytogenes
• -> high frequency or long-lasting outbreaks
DTU Food, Technical University of Denmark
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Central Outbreak Management Group (DCUG)
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Surveillance of outbreaks of foodborne bacteria
Food- and waterborne outbreak database (FUD)
One database
General analysis
-SNP trees, cgMLST
DTU Food, Technical University of Denmark
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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
DTU Food, Technical University of Denmark
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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
DTU Food, Technical University of Denmark
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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)
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WGS Whole Genome Sequencing
Example of grouping of Listeria by ST and company
DTU Food, Technical University of Denmark
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Listeria monocytogenes coloured by MLST sequence type (ST) from companies A-Q
I
H + L
K + P
B +C + F+ P +Q
DTU Food, Technical University of Denmark
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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
DTU Food, Technical University of Denmark
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Outbreak investigation
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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
DTU Food, Technical University of Denmark
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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
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DTU Food, Technical University of Denmark
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Human cases of monophasic variant of Typhimurium 4,(5)12:i:- linked to pork meat
DTU Food, Technical University of Denmark
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International outbreak detection
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European cross-border outbreaks with disease cases in several EU countries
• Urgent inquiry
• Share information
• Share sequences
DTU Food, Technical University of Denmark
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Enhanced international collaboration
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DTU Food, Technical University of Denmark
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Benefits of using WGS in outbreak investigation
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• 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
DTU Food, Technical University of Denmark
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Source attribution
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Links between different productions
-Transports
-Veterinarian/visitors
-Feed
-Bedding materials
-Animal host jump
DTU Food, Technical University of Denmark
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Unusual resistance phenotypes
• EURL-AR hub Bromhead
• One isolate here… one isolate there…
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• Confirmatory testing
– Azithromycin
– Daptomycin
– Ertapenem
– …
• Colistin – mcr genes
DTU Food, Technical University of Denmark
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mcr genes
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Germany
France
Italy
Spain
DTU Food, Technical University of Denmark
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Thank you for the attention!
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Jette Sejer Kjeldgaard
Research Group for Genomic Epidemiology
National Food Institute
European Union Reference Laboratory for Antimicrobial Resistance (EURL-AR)