Purpose: The goal of the study was to use whole genome sequencing (WGS) to determine phylogenetic relationships among L. monocytogenes strains and to determine if these relationships correspond to persistence.
Methods: In two previous longitudinal studies of L. monocytogenes in poultry processing plants, isolates were collected, separated into discreet subtypes by sequencing of actA gene, and identified as either transient or persistent. In the present study, 170 genomes were extracted, sequenced on the Illumina MiSeq platform, de novo assembled, and annotated. Genomes with acceptable assembly quality scores (160 isolates total) were analyzed to determine phylogenetic relatedness. Repeat sequences, phage sequences, and recombination regions were trimmed out. Core-genome alignment, SNP calling, and phylogenetic tree construction were performed using Harvest suite including Parsnp.
Results: Clades present on the constructed phylogenetic tree follow closely with subtypes determined via sequencing of actA gene in the original studies. No clear phylogenic relationship trends between persistent and transient subtypes analyzed could be determined. Raw sequence data and contigs will be added to the appropriate publically accessible GenBank database to be available for further analysis.
Significance: Additional analysis is needed to identify genetic factors that may be involved or interact with regulation of genes that influence ability of some strains to colonize and survive on food and non-food contact surfaces, while others are less likely to do so. In addition, this data shows WGS, along with phylogenetic analysis, is a viable option for subtyping L. monocytogenes isolates.