Purpose: Here, whole genome sequencing (WGS) was applied as a surveillance tool to track and characterize L. monocytogenes in a food processing company.
Methods: One hundred L. monocytogenes isolates from environmental and food samples were studied. These were sequenced using a MiSeq platform, de novo assembled using SPAdes, and the genomes were annotated using Prokka. The genomes were used to (i) perform core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism analysis to investigate persistence, (ii) detect the presence of antimicrobial resistance-encoding genes, and (iii) analyze the occurrence of mutations in the major virulence factors.
Results: Listeria monocytogenes isolates were classified in 18 different clonal complexes (CC), the most prevalent being CC101 (21%), CC9 (17%) and CC121 (12%). Ten cgMLST types were found to be putatively persistent, as they were identified at least three times within a 12-month period. Benzalkonium chloride tolerance genes were found in 59% of the isolates, the most prevalent gene was emrC followed by bcrABC, qacH-Tn6188 and qacC. The L. monocytogenes major virulence factor, inlA was truncated in 31% of the isolates and one environmental isolate harboured all major virulence factors, including the PTS system, which has been shown to confer hypervirulence.
Significance: This study provided a further understanding of the genetic diversity and mutations among isolates within the product and environment of one food processing company. Furthermore, WGS was an excellent tool to assess pathogenic genotypes of L. monocytogenes. This study highlighted the potential for WCS application as a prospective means of L. monocytogenes surveillance and could be used for other pathogens relevant to Public Health.