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© Therese Couderc, Marc Lecuit
Publication : Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin

Retrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin - 01 Aug 2018

Van Walle I, Björkman JT, Cormican M, Dallman T, Mossong J, Moura A, Pietzka A, Ruppitsch W, Takkinen J,

Link to Pubmed [PMID] – 30131096

Euro Surveill. 2018 08;23(33)

Background and aimThe 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.

https://www.ncbi.nlm.nih.gov/pubmed/30131096