Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Kocurek, Brandon; Ramachandran, Padmini; Grim, Christopher J.; Morin, Paul; Howard, Laura; Ottesen, Andrea; Timme, Ruth; Leonard, Susan R.; Rand, Hugh; Strain, Errol; Tadesse, Daniel; Pettengill, James B.; Lacher, David W.; Mammel, Mark; Jarvis, Karen G.

doi:10.1128/spectrum.01482-23

Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

Journal Article · Mon Oct 09 00:00:00 EDT 2023 · Microbiology Spectrum

DOI:https://doi.org/10.1128/spectrum.01482-23· OSTI ID:2471364

^[1]; Ramachandran, Padmini ^[2]; Grim, Christopher J. ^[2]; Morin, Paul ^[3]; Howard, Laura ^[3]; Ottesen, Andrea ^[1]; ^[2]; Leonard, Susan R. ^[2]; Rand, Hugh ^[2]; Strain, Errol ^[2]; Tadesse, Daniel ^[1]; Pettengill, James B. ^[2]; ^[2]; Mammel, Mark ^[2]; Jarvis, Karen G. ^[2]

US Food and Drug Administration (USFDA), Laurel, MD (United States). Center for Veterinary Medicine
US Food and Drug Administration (FDA), College Park, MD (United States). Center for Food Safety and Applied Nutrition
US Food and Drug Administration (USFDA), Jamaica, NY (United States)

Microorganisms frequently colonize surfaces within food production facilities. Detection of Listeria monocytogenes in this setting relies on culture-dependent methods, but the complex dynamics of bacterial interactions within these environments and their impact on pathogen detection remain largely unexplored. To address this challenge, we applied both 16S rRNA and shotgun quasimetagenomic (enriched microbiome) sequencing of swab culture enrichments from five seafood and seven dairy production environments. Utilizing 16S rRNA amplicon sequencing, we observed variability between 355 samples taken from these 12 production facilities and a distinctive microbiome for each environment. With shotgun quasimetagenomic sequencing, we were able to assemble L. monocytogenes metagenome-assembled genomes (MAGs) from 28 of the 32 culture-positive samples. We compared these MAGs to their corresponding whole-genome sequencing assemblies, which resulted in two polyphyletic clades consisting of L. monocytogenes lineages I and II with 13,195 and 25,556 single-nucleotide polymorphism sites, respectively. The remaining four MAGs did not produce sufficient genome coverage. To understand and establish limits for pathogen detection and subtyping using shotgun quasimetagenomics, these same data sets were downsampled in slilico to produce a titration series of abundances of L. monocytogenes and analyzed. Pathogen detection was achieved for all downsampled data sets, even those with only 3× genome coverage. This study contributes to the understanding of microbial diversity within food production environments and presents insights into the level of genome coverage needed in a metagenome sequencing data set to detect, subtype, and source track a foodborne pathogen.

View Accepted Manuscript (DOE)

Research Organization:: Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: SC0014664

OSTI ID:: 2471364

Journal Information:: Microbiology Spectrum, Journal Name: Microbiology Spectrum Journal Issue: 6 Vol. 11; ISSN 2165-0497

Publisher:: American Society for MicrobiologyCopyright Statement

Country of Publication:: United States

Language:: English

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Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities

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