Cargando…
Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain
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...
Autores principales: | , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
American Society for Microbiology
2016
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959480/ https://www.ncbi.nlm.nih.gov/pubmed/26873315 http://dx.doi.org/10.1128/AEM.00078-16 |
_version_ | 1782444406944563200 |
---|---|
author | Yang, Xiang Noyes, Noelle R. Doster, Enrique Martin, Jennifer N. Linke, Lyndsey M. Magnuson, Roberta J. Yang, Hua Geornaras, Ifigenia Woerner, Dale R. Jones, Kenneth L. Ruiz, Jaime Boucher, Christina Morley, Paul S. Belk, Keith E. |
author_facet | Yang, Xiang Noyes, Noelle R. Doster, Enrique Martin, Jennifer N. Linke, Lyndsey M. Magnuson, Roberta J. Yang, Hua Geornaras, Ifigenia Woerner, Dale R. Jones, Kenneth L. Ruiz, Jaime Boucher, Christina Morley, Paul S. Belk, Keith E. |
author_sort | Yang, Xiang |
collection | PubMed |
description | 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. botulinum were 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. |
format | Online Article Text |
id | pubmed-4959480 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | American Society for Microbiology |
record_format | MEDLINE/PubMed |
spelling | pubmed-49594802016-07-26 Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain Yang, Xiang Noyes, Noelle R. Doster, Enrique Martin, Jennifer N. Linke, Lyndsey M. Magnuson, Roberta J. Yang, Hua Geornaras, Ifigenia Woerner, Dale R. Jones, Kenneth L. Ruiz, Jaime Boucher, Christina Morley, Paul S. Belk, Keith E. Appl Environ Microbiol Public and Environmental Health Microbiology 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. botulinum were 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. American Society for Microbiology 2016-04-04 /pmc/articles/PMC4959480/ /pubmed/26873315 http://dx.doi.org/10.1128/AEM.00078-16 Text en Copyright © 2016 Yang et al. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Public and Environmental Health Microbiology Yang, Xiang Noyes, Noelle R. Doster, Enrique Martin, Jennifer N. Linke, Lyndsey M. Magnuson, Roberta J. Yang, Hua Geornaras, Ifigenia Woerner, Dale R. Jones, Kenneth L. Ruiz, Jaime Boucher, Christina Morley, Paul S. Belk, Keith E. Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title | Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title_full | Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title_fullStr | Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title_full_unstemmed | Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title_short | Use of Metagenomic Shotgun Sequencing Technology To Detect Foodborne Pathogens within the Microbiome of the Beef Production Chain |
title_sort | use of metagenomic shotgun sequencing technology to detect foodborne pathogens within the microbiome of the beef production chain |
topic | Public and Environmental Health Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4959480/ https://www.ncbi.nlm.nih.gov/pubmed/26873315 http://dx.doi.org/10.1128/AEM.00078-16 |
work_keys_str_mv | AT yangxiang useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT noyesnoeller useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT dosterenrique useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT martinjennifern useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT linkelyndseym useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT magnusonrobertaj useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT yanghua useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT geornarasifigenia useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT woernerdaler useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT joneskennethl useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT ruizjaime useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT boucherchristina useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT morleypauls useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain AT belkkeithe useofmetagenomicshotgunsequencingtechnologytodetectfoodbornepathogenswithinthemicrobiomeofthebeefproductionchain |