Purpose: The study was conducted in order to analyze 41 Listeria monocytogenes factory isolates by WGS.
Methods: DNA was extracted and sequenced on an Illumina MiSeq platform. In parallel, selected isolates were sequenced with PacBio to create reference genomes. Single Nucleotide Polymorphism (SNP) calling, based on raw read mapping on a closely related reference, using the CFSAN-FDA pipeline, was performed to obtain the pairwise SNP distance matrix. The closest public available sequence data was included in the analysis to understand the biological context.
Results: From the 41 isolates, 30 isolates were grouped in 4 clusters (< 20 SNPs within one cluster) and 11 isolates could not be grouped to any of the defined clusters. One cluster consisted of 22 isolates where the other 3 clusters consisted of 2 to 3 isolates. The largest cluster consisted of isolates from and around a drain in one area of the factory. The drain was suspected of being the source of contamination by the factory quality team. The WGS results confirmed the suspicion of a drain as a source of contamination. Within this cluster, three isolates were found in other places in the factory, identifying a cross-contamination from the drain. The results showed that no raw material was linked to the drain contamination.
Significance: WGS was able to confirm the cause of contamination in the factory, which was suspected to be due to a "resident" strain with no links to recent raw materials. The application of WGS for source tracking showed to be promising; although, today, it is still a research tool, since bioinformatics pipelines evolve very quickly and the knowledge of the biological interpretation from SNP differences, in function of time and place, between isolates is scarce.