This Is AuburnElectronic Theses and Dissertations

Longitudinal Studies of Escherichia coli, Campylobacter jejuni, and Salmonella Ssp. in Broiler Chickens Using Automated Ribotyping




McCrea, Brigid

Type of Degree



Poultry Science


The prevalence, distribution and characteristics of Escherichia coli, Campylobacter jejuni, and Salmonella spp. through an integrated broiler chicken operation from the day of hatch through processing were examined. Two farms were sampled during four consecutive flocks to determine the prevalence and persistence of bacteria of food safety concern in the poultry house environment. Bird movement from the farms through the processing plant was monitored using transport crate drag swabs and carcass rinses. An alternative method of litter sampling was employed using surgical shoe covers. In lieu of drag swabs, surgical shoe covers were a practical method of litter sampling to determine the level of flock colonization, were more effective at recovering Salmonella isolates, and yielded three times as many Salmonella serotypes as drag swabs. Litter samples are a method of assessing flock health prior to processing. The depth at which the litter is sampled was tested to determine if isolates recovered from surface sampling methods accurately reflected the E. coli population in the house. Deep litter, shallow litter, and surgical shoe cover samples were compared using automated ribotyping to elucidate trends in recovery. E. coli isolates were recovered from all three sample types and examined to determine the genetic diversity of the isolates. There was no significant correlation among strains between flock age, house, flock number, or farm and ribogroups. Based upon the patterns of E. coli recovery between the different sample types, our results indicate that any of the methods are capable of recovering the common isolates although surgical shoe covers were simplest to use. C. jejuni and Salmonella spp. isolates were recovered from multiple chicken house environmental samples taken on chick delivery day, mid-growout, and processing day. Birds were traced through the processing plant to determine if isolates from the farm, at any age, persisted on carcasses to the final product. The majority of Salmonella isolates were ribotyped as S. Kentucky, all of which were of same strain. All environmental samples taken on chick placement day in the first flocks were S. Kentucky-free but eggshells and chick mortality were positive. This indicated that the source may have been the hatchery or breeder flocks. All Campylobacter isolates were ribotyped as C. jejuni although no isolates were recovered on chick placement day. Three core isolates were identified and persisted from the farm to the processing plant. All in all, this study was able to create a library of ribotypes for multiple bacterial organisms and track the subtypes over the course of multiple flocks. Surgical shoe covers were found to be a suitable replacement for drag swabs and litter samples for the assessment of Salmonella colonization. Additionally, the E. coli results indicated that surface sampling methods, i.e., such as surgical shoe covers, do adequately gather a representative sample of isolates from the litter as a whole. A clonal population of Salmonella Kentucky indicated that the breeder flocks or hatchery was the source of the organism. Campylobacter samples provided information on the most effective samples for gathering multiple isolates as well as persistent core isolates that remained in the environment during multiple flocks. This database may be used in the future for longitudinal studies and comparisons.