LiSEQ – whole-genome sequencing of a cross-sectional survey of Listeria monocytogenes in ready-to-eat foods and human clinical cases in Europe

Abstract

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.

Dynamics of mobile genetic elements of Listeria monocytogenes persisting in ready-to-eat seafood processing plants in France

“…Strains from L. monocytogenes lineage II and serotype 1/2a have been more frequently collected in foods and food processing environments than strains from lineage I [12]. Accordingly, L. monocytogenes clonal complexes (CCs), defined as clusters of multilocus sequence typing (MLST) that share at least six alleles, have been epidemiologically associated with human listeriosis and with foods, based on the relative frequency among clinical and food-related sources [12][13][14]. These observations suggest that some L. monocytogenes clonal groups might harbour unique genotypic and phenotypic features facilitating their survival and growth in food and FPEs, as well as their potential transmission to humans.…”

Exploring Listeria monocytogenes Transcriptomes in Correlation with Divergence of Lineages and Virulence as Measured in Galleria mellonella

“…Overrepresentation of serotypes 1/2a, 1/2b, 1/2c, and 4b is observed in food and clinical isolates, and serotype 4b accounts for the majority of cases of listeriosis in humans (8,9). Additionally, multilocus sequence typing (MLST) unravelled clonal structure (10) as well as the uneven distribution of clonal complexes (CCs) in clinical and food isolates in which hyper-and hypovirulent clones were further identified (11,12).…”

First Report on the Finding of Listeria mnocytogenes ST121 Strain in a Dolphin Brain

“…The IT-OTH-CP-36 genome was compared to all the CC121 genomes available from the ANSES Laboratory for Food Safety database, including 107 genomes described by Félix et al [ 27 ], 54 genomes described by Henri et al [ 18 ], 6 by Fritsch et al [ 61 ], 29 by Palma et al [ 25 ], 143 genomes from the Liseq collection [ 17 ] and 21 new genomes specifically sequenced in the framework of this study. These genomes included 11 genomes of strains from Ireland, four from Republic of North Macedonia, four from France and two from Czech Republic.…”

“…ST is defined as the unique association of alleles from the seven housekeeping genes and CC as a cluster of STs sharing at least six alleles out of 7. In lineage II, clonal complex (CC121) is a frequently reported genotype belonging to the few clones known to be epidemiologically important in Europe and worldwide [ 15 , 17 ]. CC121 strains pose a serious challenge to the food industry, as they are overrepresented in all food sectors [ 18 , 19 ], and can persist in different food processing plants for years [ 20 , 21 , 22 , 23 , 24 , 25 ].…”

“…A low incidence of human CC121 strains has been described during recent years [ 16 , 17 , 31 , 32 , 33 ]. Compared to CC1, CC4 and CC6 strains, CC121 strains have been shown to be hypovirulent in humanized mouse models and have been less often isolated in highly immuno-compromised patients [ 33 ].…”