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Title: Associations of GI microflora with campylobacter status in commercial broiler chickens

item OAKLEY, BRIAN - Former ARS Employee
item Cox Jr, Nelson
item Meinersmann, Richard - Rick
item Berrang, Mark

Submitted to: International Association for Food Protection Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 3/15/2016
Publication Date: 7/31/2016
Citation: Oakley, B., Cox Jr, N.A., Meinersmann, R.J., Berrang, M.E. 2016. Associations of GI microflora with campylobacter status in commercial broiler chickens. International Association for Food Protection Proceedings. 50:T4-08.

Interpretive Summary: none

Technical Abstract: Introduction: Nextgeneration DNA sequencing is a powerful tool for food safety. One potential use for this technology is to compare the microflora of food animals hosting foodborne pathogens to pathogen-free animals to better understand the ecology of foodborne pathogens to design possible intervention strategies. Purpose: The purposes of this study were to: 1) characterize the cecal microflora of commercial broilers (N=96) collected at harvest over the course of approximately one year (April 2013May 2014), 2) determine the incidence of Campylobacter in these same samples, and 3) identify any taxa differentially represented in Campylobacter positive versus negative birds. Methods: Intact ceca were collected from whole GI tracts removed from commercial broilers at processing. Cecal contents were used for selective cultivation of Campylobacter and for characterization of the microflora using barcoded sequencing of 16S rRNA genes on the Illumina MiSeq platform. Results: The composition of the cecal microflora was stable across seasons. The most abundant genera included Bacteroides, Janthinobacterium (phylum Proteobacteria), and Clostridiales such as Butyricicoccus and Flavonifractor. Campylobacter was detected in all sampling months with an average of 53% of samples positive. Comparisons of the microflora between Campylobacter positive and negative samples showed two genera were significantly overrepresented in Campylobacter positive samples. These two genera, Alistipes and Rikenella, have been previously shown to be associated with intestinal inflammation. Significance: To our knowledge, this study represents the first comparison of the microflora associated with Campylobacter status using next-generation DNA sequencing methods. As illustrated by the several genera identified here, this approach may be useful in identifying potential indicator taxa and may provide insights into the pathogenesis and ecological niche of Campylobacter as a foodborne pathogen.