title: Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain.
abstract: Foodborne illnesses associated with pathogenic bacteria are a global public health and economic challenge. The diversity of microorganisms (pathogenic and nonpathogenic) that exists within the food and meat industries complicates efforts to understand pathogen ecology. Further, little is known about the interaction of pathogens within the microbiome throughout the meat production chain. Here, a metagenomic approach and shotgun sequencing technology were used as tools to detect pathogenic bacteria in environmental samples collected from the same groups of cattle at different longitudinal processing steps of the beef production chain: cattle entry to feedlot, exit from feedlot, cattle transport trucks, abattoir holding pens, and the end of the fabrication system. The log read counts classified as pathogens per million reads for Salmonella enterica,Listeria monocytogenes,Escherichia coli,Staphylococcus aureus, Clostridium spp. (C. botulinum and C. perfringens), and Campylobacter spp. (C. jejuni,C. coli, and C. fetus) decreased over subsequential processing steps. Furthermore, the normalized read counts for S. enterica,E. coli, and C. botulinumwere greater in the final product than at the feedlots, indicating that the proportion of these bacteria increased (the effect on absolute numbers was unknown) within the remaining microbiome. From an ecological perspective, data indicated that shotgun metagenomics can be used to evaluate not only the microbiome but also shifts in pathogen populations during beef production. Nonetheless, there were several challenges in this analysis approach, one of the main ones being the identification of the specific pathogen from which the sequence reads originated, which makes this approach impractical for use in pathogen identification for regulatory and confirmation purposes.
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Xiang
authors.initials: X
authors.lastname: Yang
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Noelle R
authors.initials: NR
authors.lastname: Noyes
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Enrique
authors.initials: E
authors.lastname: Doster
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Jennifer N
authors.initials: JN
authors.lastname: Martin
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Lyndsey M
authors.initials: LM
authors.lastname: Linke
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Roberta J
authors.initials: RJ
authors.lastname: Magnuson
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Hua
authors.initials: H
authors.lastname: Yang
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Ifigenia
authors.initials: I
authors.lastname: Geornaras
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Dale R
authors.initials: DR
authors.lastname: Woerner
authors.affiliation: Department of Biochemistry and Molecular Genetics, University of Colorado Denver School of Medicine, Aurora, Colorado, USA.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: Jones
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Jaime
authors.initials: J
authors.lastname: Ruiz
authors.affiliation: Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Christina
authors.initials: C
authors.lastname: Boucher
authors.affiliation: Department of Clinical Sciences, Colorado State University, Fort Collins, Colorado, USA.
authors.forename: Paul S
authors.initials: PS
authors.lastname: Morley
authors.affiliation: Department of Animal Sciences, Colorado State University, Fort Collins, Colorado, USA keith.belk@colostate.edu.
authors.forename: Keith E
authors.initials: KE
authors.lastname: Belk
mesh_terms: D000818:Animals; D001419:Bacteria / Q000145:classification* / Q000235:genetics*; D002417:Cattle; D004783:Environmental Microbiology; D005511:Food Handling; D056186:Metagenomics; D064307:Microbiota; D000069466:Red Meat / Q000382:microbiology*; D017422:Sequence Analysis, DNA