Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective
Abstract Background Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being repl...
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| Format: | Article |
| Language: | English |
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BMC
2018-12-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-018-5243-3 |
| _version_ | 1818853982273011712 |
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| author | Jillian Rumore Lorelee Tschetter Ashley Kearney Rima Kandar Rachel McCormick Matthew Walker Christy-Lynn Peterson Aleisha Reimer Celine Nadon |
| author_facet | Jillian Rumore Lorelee Tschetter Ashley Kearney Rima Kandar Rachel McCormick Matthew Walker Christy-Lynn Peterson Aleisha Reimer Celine Nadon |
| author_sort | Jillian Rumore |
| collection | DOAJ |
| description | Abstract Background Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being replaced with whole-genome sequencing (WGS) in public health laboratories. The capacity of WGS to revolutionize global foodborne disease surveillance has positioned this tool to become the new gold standard; however, to ensure evidence standards for public health decision making can still be achieved, the performance of WGS must be thoroughly validated against current gold standard methods prior to implementation. Here we aim to verify the performance of WGS in comparison to pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) for eight retrospective outbreaks of VTEC O157:H7 from the Canadian perspective. Since real-time implementation and routine use of WGS in public health laboratories is highly reliant on standardized data analysis tools, we also provide a comparative analysis of two popular methodologies for WGS analyses; an in-house developed single nucleotide variant phylogenomics (SNVPhyl) pipeline and the BioNumerics whole genome multilocus sequence typing (wgMLST) tool. To provide a useful and consistent starting point for examining laboratory-based surveillance data for VTEC O157:H7 in Canada, we also aim to describe the number of genetic differences observed among outbreak-associated isolates. Results WGS provided enhanced resolution over traditional subtyping methods, and accurately distinguished outbreak-related isolates from non-outbreak related isolates with high epidemiological concordance. WGS also illuminated potential linkages between sporadic cases of illness and contaminated food, and isolates spanning multiple years. The topologies generated by SNVPhyl and wgMLST were highly congruent with strong statistical support. Few genetic differences were observed among outbreak-related isolates (≤5 SNVs/ < 10 wgMLST alleles) unless the outbreak was suspected to be multi-strain. Conclusions This study validates the superiority of WGS and indicates the BioNumerics wgMLST schema is suitable for surveillance and cluster detection of VTEC O157:H7. These findings will provide a useful and consistent starting point for examining WGS data for prospective laboratory-based surveillance of VTEC O157:H7, but however, the data will continue to be interpreted according to context and in combination with epidemiological and food safety evidence to inform public-health decision making in Canada. |
| first_indexed | 2024-12-19T07:45:28Z |
| format | Article |
| id | doaj.art-6f19a11836474b78a8369fe1aa79d16c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-19T07:45:28Z |
| publishDate | 2018-12-01 |
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| spelling | doaj.art-6f19a11836474b78a8369fe1aa79d16c2022-12-21T20:30:19ZengBMCBMC Genomics1471-21642018-12-0119111310.1186/s12864-018-5243-3Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspectiveJillian Rumore0Lorelee Tschetter1Ashley Kearney2Rima Kandar3Rachel McCormick4Matthew Walker5Christy-Lynn Peterson6Aleisha Reimer7Celine Nadon8Division of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaOutbreak Management Division, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of CanadaOutbreak Management Division, Centre for Foodborne, Environmental and Zoonotic Infectious Diseases, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaDivision of Enteric Diseases, National Microbiology Laboratory, Public Health Agency of CanadaAbstract Background Rapid and accurate identification of Verotoxigenic Escherichia coli (VTEC) O157:H7 is dependent on well-established, standardized and highly discriminatory typing methods. Currently, conventional subtyping tests for foodborne bacterial pathogen surveillance are rapidly being replaced with whole-genome sequencing (WGS) in public health laboratories. The capacity of WGS to revolutionize global foodborne disease surveillance has positioned this tool to become the new gold standard; however, to ensure evidence standards for public health decision making can still be achieved, the performance of WGS must be thoroughly validated against current gold standard methods prior to implementation. Here we aim to verify the performance of WGS in comparison to pulsed-field gel electrophoresis (PFGE) and multiple-locus variable-number tandem repeat analysis (MLVA) for eight retrospective outbreaks of VTEC O157:H7 from the Canadian perspective. Since real-time implementation and routine use of WGS in public health laboratories is highly reliant on standardized data analysis tools, we also provide a comparative analysis of two popular methodologies for WGS analyses; an in-house developed single nucleotide variant phylogenomics (SNVPhyl) pipeline and the BioNumerics whole genome multilocus sequence typing (wgMLST) tool. To provide a useful and consistent starting point for examining laboratory-based surveillance data for VTEC O157:H7 in Canada, we also aim to describe the number of genetic differences observed among outbreak-associated isolates. Results WGS provided enhanced resolution over traditional subtyping methods, and accurately distinguished outbreak-related isolates from non-outbreak related isolates with high epidemiological concordance. WGS also illuminated potential linkages between sporadic cases of illness and contaminated food, and isolates spanning multiple years. The topologies generated by SNVPhyl and wgMLST were highly congruent with strong statistical support. Few genetic differences were observed among outbreak-related isolates (≤5 SNVs/ < 10 wgMLST alleles) unless the outbreak was suspected to be multi-strain. Conclusions This study validates the superiority of WGS and indicates the BioNumerics wgMLST schema is suitable for surveillance and cluster detection of VTEC O157:H7. These findings will provide a useful and consistent starting point for examining WGS data for prospective laboratory-based surveillance of VTEC O157:H7, but however, the data will continue to be interpreted according to context and in combination with epidemiological and food safety evidence to inform public-health decision making in Canada.http://link.springer.com/article/10.1186/s12864-018-5243-3VTECEscherichia coliO157:H7Whole genome sequencingOutbreakwgMLST |
| spellingShingle | Jillian Rumore Lorelee Tschetter Ashley Kearney Rima Kandar Rachel McCormick Matthew Walker Christy-Lynn Peterson Aleisha Reimer Celine Nadon Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective BMC Genomics VTEC Escherichia coli O157:H7 Whole genome sequencing Outbreak wgMLST |
| title | Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective |
| title_full | Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective |
| title_fullStr | Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective |
| title_full_unstemmed | Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective |
| title_short | Evaluation of whole-genome sequencing for outbreak detection of Verotoxigenic Escherichia coli O157:H7 from the Canadian perspective |
| title_sort | evaluation of whole genome sequencing for outbreak detection of verotoxigenic escherichia coli o157 h7 from the canadian perspective |
| topic | VTEC Escherichia coli O157:H7 Whole genome sequencing Outbreak wgMLST |
| url | http://link.springer.com/article/10.1186/s12864-018-5243-3 |
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