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Abstract

Background and aim

The trend in reported case counts of invasive (), 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). WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010–15. Quality controls for contamination, mixed 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. : 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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2018-08-16
2024-12-22
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Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Ivo+Van+Walle&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Van Walle Ivo</a>, <a href="/search?value1=Jonas+Torgny+Bj%C3%B6rkman&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Björkman Jonas Torgny</a>, <a href="/search?value1=Martin+Cormican&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Cormican Martin</a>, <a href="/search?value1=Timothy+Dallman&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Dallman Timothy</a>, <a href="/search?value1=Jo%C3%ABl+Mossong&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Mossong Joël</a>, <a href="/search?value1=Alexandra+Moura&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Moura Alexandra</a>, <a href="/search?value1=Ariane+Pietzka&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pietzka Ariane</a>, <a href="/search?value1=Werner+Ruppitsch&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Ruppitsch Werner</a>, <a href="/search?value1=Johanna+Takkinen&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Takkinen Johanna</a>, <a href="/search?value1=European+Listeria+WGS+typing+group&option1=author&noRedirect=true" class="nonDisambigAuthorLink">European Listeria WGS typing group</a></span>. Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015. <a href="/content/ecdc">Euro Surveill.</a> 2018;23(33):pii=1700798. <a href="https://doi.org/10.2807/1560-7917.ES.2018.23.33.1700798" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2018.23.33.1700798</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 01 Dec 2017;&nbsp;&nbsp; <span class="generated">Accepted</span>: 13 Mar 2018 </span> </p>
/content/10.2807/1560-7917.ES.2018.23.33.1700798
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