From Traditional Typing to Genomic Precision: Whole-Genome Sequencing of Listeria monocytogenes Isolated from Refrigerated Foods in Chile

Ready-to-eat (RTE) foods are the most common sources of <i>Listeria monocytogenes</i> transmission. Whole-genome sequencing (WGS) enhances the investigation of foodborne outbreaks by enabling the tracking of pathogen sources and the prediction of genetic traits related to virulence, stress, and antimicrobial resistance, which benefit food safety management. The aim of this study was to evaluate the efficacy of WGS in the typing of 16 <i>L. monocytogenes</i> strains isolated from refrigerated foods in Chile, highlighting its advantages in pathogen identification and the improvement of epidemiological surveillance and food safety. Using cgMLST, a cluster was identified comprising 2 strains with zero allele differences among the 16 strains evaluated. Ninety-four percent of the isolates (15/16) were serotype 1/2b, and 88% of them (14/16) were ST5. All strains shared identical virulence genes related to adhesion (<i>ami</i>, <i>iap</i>, <i>lapB</i>), stress resistance (<i>clpCEP</i>), invasion (<i>aut</i>, <i>iapcwhA</i>, <i>inlAB</i>, <i>lpeA</i>), toxin production (<i>hly</i>), and intracellular regulation (<i>prfA</i>), with only 13 strains exhibiting the <i>bcrBC</i> and <i>qacJ</i> gene, which confer resistance to quaternary ammonium. The pCFSAN010068_01 plasmids were prevalent, and insertion sequences (ISLs) and composite transposons (cns) were detected in 87.5% of the strains. The presence of various antibiotic resistance genes, along with resistance to thermal shocks and disinfectants, may provide <i>L. monocytogenes</i> ST5 strains with enhanced environmental resistance to the hygiene treatments used in the studied food production plant.