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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Poultry Microbiological Safety and Processing Research Unit » Research » Research Project #444278

Research Project: Relationship of Salmonella and Campylobacter to chicken carcass microbiome

Location: Poultry Microbiological Safety and Processing Research Unit

Project Number: 6040-32000-085-003-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Aug 1, 2023
End Date: Jul 31, 2028

1. Characterize the microbiome of commercial poultry processing facilities to understand how bacterial populations in the processing plant affects the microbial population on processed poultry meat. Special emphasis will be placed on associations between Salmonella in the processing environment microbiome and Salmonella contamination of meat processed in the facility (Sub-objective 1.1). 2. Determine Salmonella and Campylobacter prevalence and relative proportion of the pathogens in the resident microbial communities on broiler carcasses after defeathering and prior to chilling operations in commercial poultry processing facilities throughout a processing day (Sub-objective 1.2).

Collection of samples). Rinsate samples will be collected from 5 processing plants in six locations within each plant (1) after the bleed-out, (2) hot rehang, (3) pre-chill, (4) post chill, (5-6) two end-product samples. Salmonella detection and enumeration. Each sample will be cultured for Aerobic Plate Count (APC) and Enterobacteriaceae (EB) counts, cultured for presence and enumeration of Salmonella (with serotyping and confirmation), and rapid molecular test of Salmonella (LAMP assay). Environment microbiome profiling. Microbiome analysis by 16S-ribosomal RNA (rRNA) gene surveys will be performed to define microbial communities in commercial broiler processing facilities (bio-mapping). Environmental samples will be collected from processing facilities. Samples will be collected at the beginning and the end of the daily processing operation. Samples and metadata will be taken during the production shift at each of these locations using swabs, sponges, drag swabs, or rinsates. These sampling sites will include contact surfaces touched by multiple carcasses, non-contact surfaces, other locations within the facility, and broilers. Microbiome profiling. DNA will be extracted from each sample and prepared for sequencing of the V4 region of the 16S rRNA gene and sequenced. Data will be analyzed using the QIIME2 pipeline with the addition of SourceTracker2 to provide a bio-map of the facilities and to determine any correlations between the microflora of the processing facility and the microflora of the processed meat. Sampling after defeathering and prior to chilling operations throughout a processing day. Broilers from the first and last trailer load of broilers for each flock arriving at a commercial processing facility for an entire processing shift will be followed through processing operations. The total time off feed for the first and last trailer load of broilers for each flock will be recorded to correlate relationships between Salmonella and Campylobacter prevalence on defeathered and eviscerated, prechilled carcasses. Ten carcasses from each trailer (first and last) will be collected for sampling after defeathering and an additional 10 eviscerated carcasses from each trailer will be collected before immersion chilling and used for routine Salmonella and Campylobacter enumeration. Salmonella and Campylobacter detection from broiler carcasses. An aliquot will be saved for DNA extraction and the remainder used for culturing. Carcass rinsates will be plated on the appropriate selective Salmonella and Campylobacter bacteriological medium for pathogen enumeration, and samples will also be enriched to detect low numbers of the pathogens. Statistical analysis of the data will be conducted to detect significant differences in the number of Salmonella or Campylobacter recovered from different flocks of broilers. Identification will be confirmed using a Vitek MS MALDI-TOF mass-spectrophotometer. Profiling of broiler carcasses microbiome. Microbiome analysis of the microbial community will be conducted using the methods described above. The 16S rRNA profiles will show the community components that may correlate with the presence of the pathogens.