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dc.contributor.authorVan Walle, Ivo
dc.contributor.authorBjörkman, Jonas Torgny
dc.contributor.authorCormican, Martin
dc.contributor.authorDallman, Timothy
dc.contributor.authorMossong, Joël
dc.contributor.authorMoura, Alexandra
dc.contributor.authorPietzka, Ariane
dc.contributor.authorRuppitsch, Werner
dc.contributor.authorTakkinen, Johanna
dc.date.accessioned2018-11-19T13:27:53Z
dc.date.available2018-11-19T13:27:53Z
dc.date.issued2018
dc.identifier.citationRetrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015. 2018, 23 (33) Euro Surveill.en
dc.identifier.issn1560-7917
dc.identifier.pmid30131096
dc.identifier.doi10.2807/1560-7917.ES.2018.23.33.1700798
dc.identifier.urihttp://hdl.handle.net/10029/622253
dc.description.abstractBackground and aimThe 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/EEA-wide 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.
dc.language.isoenen
dc.rightsArchived with thanks to Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletinen
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.titleRetrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015.en
dc.typeArticleen
dc.identifier.journalEuro Surveilll 2018; 23(33):1700798; 1-11en
refterms.dateFOA2018-12-18T14:36:11Z
html.description.abstractBackground and aimThe 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/EEA-wide 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.


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Archived with thanks to Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin
Except where otherwise noted, this item's license is described as Archived with thanks to Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin