Application of Quasimetagenomics Methods to Define Microbial Diversity and SubtypeListeria monocytogenesin Dairy and Seafood Production Facilities

Abstract

Microorganisms frequently colonize surfaces and equipment within food production facilities.Listeria monocytogenesis a ubiquitous foodborne pathogen widely distributed in food production environments and is the target of numerous control and prevention procedures. Detection ofL. monocytogenesin a food production setting requires culture dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remains largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from seafood and dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between samples taken from different production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assembleL. monocytogenesmetagenome assembled genomes (MAGs) and compare these MAGSs to their previously sequenced whole genome sequencing (WGS) assemblies, which resulted in two polyphyletic clades (lineages I and II). Using these same datasets together with in silico downsampling to produce a titration series of proportional abundances ofL. monocytogenes, we were able to begin to establish limits forListeriadetection and subtyping using shotgun quasimetagenomics. This study contributes to the understanding of microbial diversity within food production environments and presents insights into how many reads or relative abundance is needed in a metagenome sequencing dataset to detect, subtype, and source track at a SNP level, as well as providing an important foundation for utilizing metagenomics to mitigate unfavorable occurrences along the farm to fork continuum.

Microbial composition and dynamics in environmental samples from a ready-to-eat food production facility with a long-term colonisation of Listeria monocytogenes

“…Previous studies have described the microbiome of FPE's such as abattoirs and meat processing plants [54][55][56][57][58][59], fermented-products production facilities [13,54,[59][60][61][62][63] and fruit and vegetables processing plants [14,64,65], and identified distinctive microbiomes depending on the type of commodities [59,66]. However, very few studies describe the FPE of RTE meals [67], despite the importance of this type of food in the contamination with foodborne pathogens during processing [15].…”