A European-wide dataset to uncover adaptive traits of Listeria monocytogenes to diverse ecological niches

Abstract

Listeria monocytogenes (Lm) is a ubiquitous bacterium that causes listeriosis, a serious foodborne illness. In the nature-to-human transmission route, Lm can prosper in various ecological niches. Soil and decaying organic matter are its primary reservoirs. Certain clonal complexes (CCs) are over-represented in food production and represent a challenge to food safety. To gain new understanding of Lm adaptation mechanisms in food, the genetic background of strains found in animals and environment should be investigated in comparison to that of food strains. Twenty-one partners, including food, environment, veterinary and public health laboratories, constructed a dataset of 1484 genomes originating from Lm strains collected in 19 European countries. This dataset encompasses a large number of CCs occurring worldwide, covers many diverse habitats and is balanced between ecological compartments and geographic regions. The dataset presented here will contribute to improve our understanding of Lm ecology and should aid in the surveillance of Lm. This dataset provides a basis for the discovery of the genetic traits underlying Lm adaptation to different ecological niches.

Fig. 1

Distribution of the LISTADAPT collection of Listeria monocytogenes strains (n = 1484) by time, geographic region and origin of isolation. (a) and (b) show the distribution of food strains by geographic region and food type, respectively. (c) and (d) show the distribution of environmental strains by geographic region and subcompartment, respectively.

Fig. 2

Microreact screenshot representing the distribution of the whole LISTADAPT dataset (n = 1484) by geographic region (a) and time (b). The k-mer-based phylogenomic clustering of the complete dataset is shown in (c). Interactive access to strain metadata and MLST types is available through Microreact, a recently developed online tool for visualizing and sharing spacio-temporal and genetic distributions of strains (Fig. 2, accession link: https://microreact.org/project/8YtGBqEqhosJtysXTVY79M-figure-2-distribution-of-the-whole-listadapt-dataset-n1484-by-geographic-region-time-and-genetic-diversity). The dataset interactive map was generated using either the exact GPS coordinate, regional GPS coordinate or national GPS coordinate according to the level of details available for each strain. An annual timescale was used. The core genome MLST (Moura et al.) tree was generated from the draft genome assemblies using pairwise categorical difference and single linkage method in BioNumerics. The tree revealed three main clades corresponding to Lm phylogenetic lineages. Each clade included several clusters corresponding to MLST types (CC and singleton ST). Circles in shade of blue show food product isolates (clear blue: fish product, greeblue: dairy products, blue: composite dishes, deep blue: meat products). Circles in shade of orange show animal and environment isolates (beige: soil & farm environment, golden: wild animal, deep orange: farm animals). Circles size is proportional to the number of strains included.

Fig. 3

Distribution of the LISTADAPT dataset of Listeria monocytogenes genomes by multilocus sequence typing clonal complex (CC) or singleton sequence type (ST).