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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 #410458
Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: Biomapping of a commercial poultry hatchery in the Southeastern United States

Author
item WALID, AL HAKEEM - Oak Ridge Institute For Science And Education (ORISE)
item ZWIRZITZ, BENJAMIN - University Of Vienna
item Li, Xiang
item Oladeinde, Adelumola
item Rothrock Jr, Michael

Submitted to: International Poultry Scientific Forum
Publication Type: Abstract Only
Publication Acceptance Date: 11/25/2023
Publication Date: 1/5/2024
Citation: Walid, A., Zwirzitz, B., Li, X., Oladeinde, A.A., Rothrock Jr, M.J. 2024. Biomapping of a commercial poultry hatchery in the Southeastern United States. International Poultry Scientific Forum. p. 289.

Interpretive Summary: Pathogenic microbes can find a suitable niche within poultry hatcheries designed to nurture early chick development. Despite this concern, limited knowledge exists regarding the microbiomes within these hatcheries. For this study, a commercial hatchery was bio-mapped using sponge swabs to sample air, water, bait boxes, and eggs from prehatch (egg inventory, pre-in ovo, and post-in ovo), hatch (chick processing), and post-hatch (chick transport) areas. To determine the bacterial composition, 16S rRNA gene sequencing (using the MilSeq platform) was conducted, and the sequence data was analyzed using QIIME2(v2022.2). One-way ANOVA with a sampling area of the hatchery as the main effect, followed by Tukey’s multiple comparison method for pairwise comparison, was performed using R software. The highest bacterial richness was detected in the water samples during chick processing/transport compared to the other sample types, indicating a possible role of water in introducing microbes to the chicks. The beta diversity index (PCo) revealed that the eggshell harbors microbiomes distinct from the hatchery's environment prior to hatch; however, egg-related microbiomes (chicks fecal samples) from the transport area were more similar to the hatchery facility areas, indicating the hatchery environment’s role in shaping the early gut microbiome post-hatch. Salmonella taxa were found throughout the hatchery (they represented a core taxa microbiome of all sample types and sampling areas) but predominantly found in the chick’s feces post-hatch. SourceTracker analysis, which typically uses a reference database of microbial communities to compare against the different hatchery samples, indicated the breakroom tables as one of the main sources of Salmonella within the hatchery. In conclusion, the hatchery’s environment can be a potential reservoir for foodborne pathogens such as Salmonella; however, a more comprehensive study investigating Salmonella serotypes present in the hatchery extending through grow-out is required to determine the role of hatcheries as a source for microbial populations entering commercial poultry houses.

Technical Abstract: Pathogenic microbes can find a suitable niche within poultry hatcheries designed to nurture early chick development. Despite this concern, limited knowledge exists regarding the microbiomes within these hatcheries. For this study, a commercial hatchery was bio-mapped using sponge swabs to sample air, water, bait boxes, and eggs from prehatch (egg inventory, pre-in ovo, and post-in ovo), hatch (chick processing), and post-hatch (chick transport) areas. To determine the bacterial composition, 16S rRNA gene sequencing (using the MilSeq platform) was conducted, and the sequence data was analyzed using QIIME2(v2022.2). One-way ANOVA with a sampling area of the hatchery as the main effect, followed by Tukey’s multiple comparison method for pairwise comparison, was performed using R software. The highest bacterial richness was detected in the water samples during chick processing/transport compared to the other sample types, indicating a possible role of water in introducing microbes to the chicks. The beta diversity index (PCo) revealed that the eggshell harbors microbiomes distinct from the hatchery's environment prior to hatch; however, egg-related microbiomes (chicks fecal samples) from the transport area were more similar to the hatchery facility areas, indicating the hatchery environment’s role in shaping the early gut microbiome post-hatch. Salmonella taxa were found throughout the hatchery (they represented a core taxa microbiome of all sample types and sampling areas) but predominantly found in the chick’s feces post-hatch. SourceTracker analysis, which typically uses a reference database of microbial communities to compare against the different hatchery samples, indicated the breakroom tables as one of the main sources of Salmonella within the hatchery. In conclusion, the hatchery’s environment can be a potential reservoir for foodborne pathogens such as Salmonella; however, a more comprehensive study investigating Salmonella serotypes present in the hatchery extending through grow-out is required to determine the role of hatcheries as a source for microbial populations entering commercial poultry houses.