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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Publications at this Location » Publication #421114
Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: Foodborne pathogens prevalence, load and ecology on pasture-raised broilers processed on-farm or at a small USDA-inspected facility

Author
item AL HAKEEM, WALID - Department Of Energy
item CHUNG, TAEJUNG - Department Of Energy
item KIM, MINHO - Department Of Energy
item Oladeinde, Adelumola
item Rothrock Jr, Michael

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: 11/25/2024
Publication Date: 1/5/2025
Citation: Al Hakeem, W.G., Chung, T., Kim, M., Oladeinde, A.A., Rothrock Jr, M.J. 2025. Foodborne pathogens prevalence, load and ecology on pasture-raised broilers processed on-farm or at a small USDA-inspected facility. International Poultry Scientific Forum. p. 324.

Interpretive Summary:

Technical Abstract: Gaining access to the US retail market poses a significant challenge for small pasture-raised farms as a USDA-inspected status is required, for which a lot of these producers are ineligible. Therefore, many farmers process their birds on-site (on the farm), in mobile units, or transport them to small-scale USDA-inspected slaughter facilities that can handle a small number of birds. There is a scare of information regarding the food safety of these methods. Therefore, the aim of this experiment is to investigate the association between microbial communities and foodborne pathogen in pasture raised birds that are proceed with two different methods. Between 2016 and 2017, preharvest samples (feces, pasture soil), processing (ceca, whole carcass rinses) and final product (whole carcass rinses on farm or USDA-inspected facility) samples were collected from 4 flocks from the same pastured poultry farms from 2014 – 2017. Genomic DNA was extracted, 16S rDNA microbiome sequencing was conducted (Illumina MiSeq), and microbiomes were analyzed and compared using QIIME 1.9.1 to determine how microbiomes shifted throughout production continuum. E. coli, Campylobacter, Salmonella, and Listeria were identified using cultural methods. One-way ANOVA with farm location or sample type as the main effect, followed by Tukey’s multiple comparison method for pairwise comparison, was performed using R software. Bacterial differential abundance was analyzed using ANCOM-BC2 using R software. The feces showed the highest (p<0.05) E. coli and Campylobacter loads (6.54 and 3.90 log10 CFU/mL, respectively) and prevalence (100% and 93.3%, respectively), while the final product whole carcass rinses had the lowest (p<0.05) E. coli and Campylobacter loads (1.63 and 0 log10 CFU/mL, respectively) and prevalence (85.21% and 0%, respectively), showing a downward trend observed from preharvest to postprocessing samples. Salmonella prevalence was low (3%) across all samples. Among the 4 tested pathogens, Listeria was significantly more prevalent in final product processed at sampling plant. Overall, microbiomes in soil and ceca samples harbored a higher taxonomic richness than farm. Beta-diversity analysis demonstrated significant differences between the microbiomes of feces and ceca, but not for on-farm and USDA-facility final product. The final product on farm and in a USDA-inspected facility showed no significant differences in their bacterial communities; however, the high Listeria prevalence on the USDA-inspected facility indicates that chicken slaughterhouses can be a source of foodborne pathogens detected in the final product.