Whole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity

Abstract

Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.

The Relationship between Biofilm Phenotypes and Biofilm-Associated Genes in Food-Related Listeria monocytogenes Strains

“…CC121, as the most prevalent L. monocytogenes CC, followed by CC7, CC8, and CC9, were found in the Norwegian food system and were associated with an increased prevalence of stress survival and resistance determinants [60]. The analysis of fish production chains resulted in the predominant assignment of ST121 isolates from salmon [61]. A persistent ST451 strain was identified in a rabbit meat processing plant in the Czech Republic [62] and was found as the most prevalent CC, particularly in food and animal isolates during the 11-year study in Slovakia [63].…”