Abstract
Background 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.
Highlights
Invasive infection by Listeria monocytogenes (Lm) leads to relatively rare but serious food-borne disease mainly affecting elderly people, immunocompromised individuals and pregnant women
The contamination (CNTM) quality control (QC) detected three L. ivanovii isolates (0.1%; CNTM result set to FAIL) and 31 isolates that contained bacterial DNA from genera other than Listeria spp. (1.1%; CNTM set to WARN)
For multi-country clusters, this increased to 34, 84 and 181 weeks, respectively. In this large multi-country study, we examined both the analytical and general epidemiological aspects of surveillance for human Lm infections using whole genome sequencing (WGS)
Summary
Invasive infection by Listeria monocytogenes (Lm) leads to relatively rare but serious food-borne disease mainly affecting elderly people, immunocompromised individuals and pregnant women. In the European Union and European Economic Area (EU/EEA), 2,224 human cases of invasive listeriosis were reported in 2015, with an overall case fatality rate of 18.8% [4]. Reported numbers of cases of listeriosis suggest that the incidence of disease slightly increased over the period of 2010–15. Most cases are considered sporadic and detected outbreaks usually involve small numbers of patients, which limits statistical power in analytical epidemiological studies. 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). 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. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies
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