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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Poultry Microbiological Safety and Processing Research Unit » Research » Publications at this Location » Publication #281980

Title: The poultry-associated microbiome: network analysis and characterization along the farm-to-fork continuum

item Oakley, Brian
item Morales, Cesar
item Line, John
item Berrang, Mark
item Meinersmann, Richard - Rick
item TILLMAN, GLENN - Food Safety Inspection Service (FSIS)
item WISE, MARK - Biomerieux, Inc
item SIRAGUSA, GREGORY - Danisco Usa, Inc
item Hiett, Kelli
item Seal, Bruce

Submitted to: PLOS ONE
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/18/2013
Publication Date: 2/27/2013
Citation: Oakley, B., Morales, C., Line, J.E., Berrang, M.E., Meinersmann, R.J., Tillman, G.E., Wise, M.G., Siragusa, G.R., Hiett, K.L., Seal, B.S. 2013. The poultry-associated microbiome: network analysis and characterization along the farm-to-fork continuum. PLoS One. 8(2):e57190.

Interpretive Summary: The Food Safety Modernization Act emphasizes prevention of foodborne illness via monitoring of the entire food supply chain. In this study we conducted the first characterization of microbial communities associated with poultry along what is sometimes called the ‘farm-to-fork’ chain. The ultimate goal of the study is to prevent foodborne illnesses by increasing our knowledge of where beneficial bacteria and harmful bacteria might reside in the poultry supply chain. Monitoring whether disease-causing bacteria are passed through this chain is an important step to reduce or eliminate sources of foodborne illness and so we used next-generation DNA sequencing to take a census of bacterial communities along the farm-to-fork continuum. Samples were collected from the litter in poultry houses, directly from the chickens inhabiting these same houses, from these same birds after commercial processing, and finally, from consumer products purchased at retail. DNA from all samples was directly sequenced and used to measure the abundance of several important pathogens. Bacteria most similar to known human pathogens such as Campylobacter, Shigella, and Clostridium were found in all samples except the retail products. However, the actual number of Campylobacter cells associated with chicken carcasses after commercial processing was significantly lower than the numbers of cells found in chicken fecal and litter samples on farms. To specifically measure how many cells of Campylobacter jejuni (the species of Campylobacter that causes most human illnesses) were in each sample, we created a new molecular assay that uniquely measures the number of cells from this species. Because Campylobacter jejuni was significantly reduced in abundance after commercial poultry processing, we concluded that current food-safety measures targeting this species are largely effective. However, next-generation DNA sequencing of these samples also showed that there were many species closely related to C. jejuni present in these samples. Poultry products purchased at retail were dominated by Pseudomonas species which are known spoilage organisms, but also contained some Arcobacter species (a close relative of Campylobacter) which were shown to be alive. Transmission of bacteria through the food supply chain does occur but the abundance of several key pathogens was significantly reduced by commercial anti-microbial treatments.

Technical Abstract: Agriculture represents an important link between animal-associated microbes and humans as food-borne pathogens continue to be a leading cause of illness and hospitalizations. Here we combine high-throughput sequencing (HTS), network analysis, and quantitative-PCR (qPCR) assays to profile the poultry-associated microbiome and important pathogens at various stages of commercial poultry production from the farm to the consumer. Network analysis focused on the foodborne pathogen Campylobacter revealed a majority of sequence types with no significant interactions with other taxa, perhaps explaining the limited efficacy of previous attempts at competitive exclusion of Campylobacter. Analysis of longitudinal data following two flocks from the farm through processing showed a core microbiome containing multiple sequence types most closely related to genera known to be pathogenic for animals and/or humans, including Campylobacter, Clostridium, and Shigella. After the final stage of commercial poultry processing, taxonomic richness was ca. 2-4 times lower than the richness of fecal samples from the same flocks and Campylobacter abundance was significantly reduced. Interestingly, however, carcasses sampled at 48 hr after processing harboured the greatest proportion of unique taxa (those not encountered in other samples), significantly more than expected by chance. Among these were anaerobes such as Prevotella, Veillonella, Leptrotrichia, and several putative pathogens, including multiple Campylobacter sequence types. Retail products were dominated by Pseudomonas, but also contained 27 other genera, most of which were metabolically active and encountered in on-farm samples. These data represent the first HTS-based characterization of poultry-associated microbiomes along the farm-to-fork continuum and demonstrate the utility of HTS in monitoring the food supply chain and identifying sources of potential zoonoses and interactions among taxa in complex communities.