Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015
| Autor(a) principal: | |
|---|---|
| Data de Publicação: | 2018 |
| Outros Autores: | , , , , , , , , |
| Tipo de documento: | Artigo |
| Idioma: | eng |
| Título da fonte: | Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
| Texto Completo: | http://hdl.handle.net/10400.18/6280 |
Resumo: | European Listeria WGS typing group - Vítor Borges (Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal) |
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Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015Listeria monocytogenesWGSSurveillance SystemWhole Genome SequencingListeriosisEuropeInfecções GastrointestinaisEuropean Listeria WGS typing group - Vítor Borges (Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal)Free PMC Article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6205253/Background and aim: The trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/ EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEAwide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/ EEA countries from 2010–15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58–68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.Timothy Dallman (Public Health England (PHE), United Kingdom): The research in the United Kingdom was funded by the National Institute for Health Research Health Protection Research Unit (NIHR HPRU) in Gastrointestinal Infections at University of Liverpool in partnership with Public Health England, in collaboration with University of East Anglia, University of Oxford and the Institute of Food Research. Alexandra Moura, Alexandre Leclercq and Marc Lecuit: The research in France was supported by Institut Pasteur, Inserm and Santé Publique France.European Centre for Disease Prevention and ControlRepositório Científico do Instituto Nacional de SaúdeVan Walle, IvoBjörkman, Jonas TorgnyCormican, MartinDallman, TimothyMossong, JoëlMoura, AlexandraPietzka, ArianeRuppitsch, WernerTakkinen, JohannaEuropean Listeria Wgs Typing Group2019-03-22T15:59:40Z2018-082018-08-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10400.18/6280engEuro Surveill. 2018 Aug;23(33):pii=1700798. doi: 10.2807/1560-7917.ES.2018.23.33.17007981560-79110.2807/1560-7917.ES.2018.23.33.1700798info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-07-20T15:41:20Zoai:repositorio.insa.pt:10400.18/6280Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T18:40:56.798649Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse |
| dc.title.none.fl_str_mv |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| title |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| spellingShingle |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 Van Walle, Ivo Listeria monocytogenes WGS Surveillance System Whole Genome Sequencing Listeriosis Europe Infecções Gastrointestinais |
| title_short |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| title_full |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| title_fullStr |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| title_full_unstemmed |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| title_sort |
Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015 |
| author |
Van Walle, Ivo |
| author_facet |
Van Walle, Ivo Björkman, Jonas Torgny Cormican, Martin Dallman, Timothy Mossong, Joël Moura, Alexandra Pietzka, Ariane Ruppitsch, Werner Takkinen, Johanna European Listeria Wgs Typing Group |
| author_role |
author |
| author2 |
Björkman, Jonas Torgny Cormican, Martin Dallman, Timothy Mossong, Joël Moura, Alexandra Pietzka, Ariane Ruppitsch, Werner Takkinen, Johanna European Listeria Wgs Typing Group |
| author2_role |
author author author author author author author author author |
| dc.contributor.none.fl_str_mv |
Repositório Científico do Instituto Nacional de Saúde |
| dc.contributor.author.fl_str_mv |
Van Walle, Ivo Björkman, Jonas Torgny Cormican, Martin Dallman, Timothy Mossong, Joël Moura, Alexandra Pietzka, Ariane Ruppitsch, Werner Takkinen, Johanna European Listeria Wgs Typing Group |
| dc.subject.por.fl_str_mv |
Listeria monocytogenes WGS Surveillance System Whole Genome Sequencing Listeriosis Europe Infecções Gastrointestinais |
| topic |
Listeria monocytogenes WGS Surveillance System Whole Genome Sequencing Listeriosis Europe Infecções Gastrointestinais |
| description |
European Listeria WGS typing group - Vítor Borges (Instituto Nacional de Saúde Doutor Ricardo Jorge, Lisbon, Portugal) |
| publishDate |
2018 |
| dc.date.none.fl_str_mv |
2018-08 2018-08-01T00:00:00Z 2019-03-22T15:59:40Z |
| dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
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info:eu-repo/semantics/article |
| format |
article |
| status_str |
publishedVersion |
| dc.identifier.uri.fl_str_mv |
http://hdl.handle.net/10400.18/6280 |
| url |
http://hdl.handle.net/10400.18/6280 |
| dc.language.iso.fl_str_mv |
eng |
| language |
eng |
| dc.relation.none.fl_str_mv |
Euro Surveill. 2018 Aug;23(33):pii=1700798. doi: 10.2807/1560-7917.ES.2018.23.33.1700798 1560-791 10.2807/1560-7917.ES.2018.23.33.1700798 |
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info:eu-repo/semantics/openAccess |
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openAccess |
| dc.format.none.fl_str_mv |
application/pdf |
| dc.publisher.none.fl_str_mv |
European Centre for Disease Prevention and Control |
| publisher.none.fl_str_mv |
European Centre for Disease Prevention and Control |
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reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação instacron:RCAAP |
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Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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RCAAP |
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RCAAP |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação |
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