Whole-Genome Shotgun Sequencing of Three Listeria monocytogenes Strains Isolated from a Ready-to-Eat Salad-Producing Facility in Switzerland.

Ready-to-eat (RTE) raw foods harbor the risk of transmitting Listeria monocytogenes from the environment to the consumer. We isolated three strains from a facility producing RTE salad. These strains were used to perform challenge tests on different RTE salad products. Here, we present the shotgun genome sequences of all three of these strains.

GENOME ANNOUNCEMENT

Genomic DNA from Listeria monocytogenes strains N16-0716, N16-0855, and N16-1125 was extracted from a brain heart infusion culture using a DNA blood and tissue kit (Qiagen) and subjected to whole-genome sequencing using the MiSeq platform (Illumina) and a Nextera XT library kit utilizing either 500 or 600 cycles of paired-end reads (Illumina). The paired-end libraries were generated and sequenced in conjunction with the Nextera XT DNA sample preparation guide on the Illumina MiSeq instrument (1). The reads were de novo assembled with SPAdes version 3.11 (2) into genomes of 2,968,449 bp with 37.9% GC content (N16-0716), 3,138,349 bp with 38.8% GC content (N16-0855), and 3,124,080 bp with 38.6% GC content (N16-1125). The genomes were annotated using the Rapid Annotations using Subsystems Technology (RAST) annotation server (3), and 2,931 (N16-0716), 3,072 (N16-0855), and 3,078 (N16-1125) coding sequences were identified.

Multilocus sequence type (MLST) analysis using the BIGSdb database (http://bigsdb.pasteur.fr/listeria) confirmed our earlier PCR-based analysis, which found that N16-0716 was sequence type 517 (ST517) clonal complex 517 (CC517), N16-0855 was ST6 CC6, and N16-1125 was ST91 CC14. An analysis of known virulence genes in comparison to the laboratory strain 10403S revealed that all genes associated with the LIPI-1 island were present in all three strains. In all three strains, full-length plcB was present with several amino acid (aa) substitutions between the strains. The alternative start codon GTG was used in plcB of all three strains (as well as in 10403S). All other full-length genes on LIPI-1 were present, and none of the known prfA* mutations were detected. Two different alleles of hly were present between the strains, separated by four aa substitutions. In plcA, mpl, and actA, several aa substitutions were detected between the strains, and ilsA coding for listeriolysin S on LIPI-3 was found only in N16-0855. Full-length InlA was present in all sequences, with several aa substitutions between the strains.

Screening of the genomes against the ARG-ANNOT (4) and MEGARes (5) databases of antimicrobial resistance genes using the method described by Carroll et al. (6) and implemented in BTyper version 2.2.0 (7) revealed the presence of the multidrug efflux pumps norB, msrA, and mepA in all three strains.

PHASTER (8) identified two intact phages in N16-0716, two intact and one incomplete phage in N16-0855, and four intact phages in N16-1125.

Accession number(s).

This whole-genome shotgun project has been deposited in GenBank under the accession no. QELV00000000 (N16-0716), QELU00000000 (N16-0855), and QELT00000000 (N16-1125).