Microbial pathogenesis studies are typically performed with reference strains, thereby overlooking microbial intra-species virulence heterogeneity. Here we integrated human epidemiological and clinical data with bacterial population genomics to harness the biodiversity of the model foodborne pathogen Listeria monocytogenes and decipher the basis of its neural and placental tropisms.Taking advantage of the clonal structure of this bacterial species, we identify clones epidemiologically associated with either food or human central nervous system (CNS) and maternal-neonatal (MN) listeriosis. The latter are also most prevalent in patients without immunosuppressive comorbidities. Strikingly, CNS and MN clones are hypervirulent in a humanized mouse model of listeriosis. By integrating epidemiological data and comparative genomics, we uncovered multiple novel putative virulence factors and demonstrated experimentally the contribution of the first gene cluster mediating Listeria monocytogenes neural and placental tropisms. This study illustrates the exceptional power of harnessing microbial biodiversity to identify clinically relevant microbial virulence attributes.
This report presents the results of the project "Closing gaps for performing a risk assessment on Listeria monocytogenes in ready-to-eat (RTE) foods: activity 3, the comparison of isolates from different compartments along the food chain, and from humans using whole genome sequencing (WGS) analysis". The main objective was to compare L. monocytogenes isolates collected in the EU from ready-to-eat (RTE) foods, compartments along the food chain and from human cases by the use of WGS. A total of 1,143 L. monocytogenes isolates were selected for the study, including 333 human clinical isolates and 810 isolates from the food chain. The isolates were whole genome sequenced. The phylogeny showed a clear delineation between L. monocytogenes lineages and between clonal complexes within lineages. A range of typing methods were applied to the sequence data, providing the framework to answer questions on genetic diversity and epidemiological relationships. Retrospective analysis of nine outbreaks showed that WGS is a powerful tool in national and international outbreak investigations as WGS can accurately rule isolates in or out of outbreaks. Source attribution models showed bovine reservoir to be the main source of human disease although other sources also contributed and generally confidence intervals were high. Numerous consistent genetic linkages between a priori unlinked strains were identified, some of which involved isolates from multiple countries. The presence of putative markers conferring the potential to survive/multiply in the food chain and/or cause disease in humans was explored by detecting the presence of putative virulence genes, AMR genes and factors conferring the ability to persist in the food processing chain. This study has demonstrated one of the major benefits of WGS, which is the ability to address a wide range of questions including those on virulence, antimicrobial resistance, source attribution, surveillance and outbreak detection and investigation, in a single experiment.
We present the LiSEQ (Listeria SEQuencing) project, funded by the European Food Safety Agency (EFSA) to compare Listeria monocytogenes isolates collected in the European Union from ready-to-eat foods, compartments along the food chain (e.g. food-producing animals, food-processing environments) and humans. In this article, we report the molecular characterization of a selection of this data set employing whole-genome sequencing analysis. We present an overview of the strain diversity observed in different sampled sources, and characterize the isolates based on their virulence and resistance profile. We integrate into our analysis the global L. monocytogenes genome collection described by Moura and colleagues in 2016 to assess the representativeness of the LiSEQ collection in the context of known L. monocytogenes strain diversity.
In order to assess antimicrobial resistance in Listeria monocytogenes, 202 food and environmental isolates from 1996 to 2006 were tested. Only four strains displayed acquired resistance. Resistance to erythromycin, tetracycline-minocycline, and trimethoprim was evidenced, and the genes erm(B), tet(M), and dfrD, already found in L. monocytogenes, were detected.
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