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ARS Home » Southeast Area » Athens, Georgia » U.S. National Poultry Research Center » Egg and Poultry Production Safety Research Unit » Research » Research Project #438928

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

Location: Egg and Poultry Production Safety Research Unit

2021 Annual Report

1. Identify factors within the hatchery and brooder phase that induce serotype diversity and homologous recombination within Salmonella enterica subspecies I for the purpose of facilitating reduction of colonization of chicks through environmental remediation. 1.A. Investigate Salmonella ecology within commercial hatchery environments through the use of bio-mapping. 1.B. Identify conditions that facilitate either Homologous Recombination (HR) and/or Clonal Expansion (CX) by Salmonella enterica within the hatchery environment. 1.C. Develop intervention strategies for impeding emergence of new serotypes of Salmonella enterica in the hatchery and brooder environments. 2. Identification, characterization, and application of probiotic commensal microbes as an alternative to antibiotics to reduce Salmonella prevalence within commercial poultry houses. 2.A. Identification of non-pathogenic bacterial species that are modulated upon Salmonella Heidelberg infection. 2.B. Evaluate and characterize potential non-pathogenic strains to be included in the proLitterbiotic (pLb) culture collection. 2.C. Evaluate efficacy of proLitterbiotic (pLb) under live production scenarios. 3. Identify environmental and management drivers of foodborne pathogen ecology under pastured poultry rearing systems. 3.A. Environmental and microbiological characterization of pastured poultry farms to identify drivers of foodborne pathogen ecology. 3.B. Predict Salmonella prevalence during live production within pastured poultry flocks. 3.C. Evaluate the effectiveness of implementing probiotic/all-natural products within the diet of very young chicks (<1 week of age) on poultry gut health and product safety.

Our goal is to reduce pathogenic and antibiotic resistant Salmonella in eggs and poultry products entering the processing/post-harvest environment by generating research that identifies the drivers of Salmonella ecology in pre-harvest environments. This investigation will begin at the nexus of commercial poultry management (hatchery) and extend onto the farms where the birds are reared to processing weight, and we will investigate the variables that genotypically and phenotypically affect the presence of Salmonella pre-harvest. A better understanding of Salmonella ecology and diversity through the pre-harvest phase of poultry production will reduce Salmonella loads entering the processing environment and result in a safer product for the consumer. We will test alternative hypotheses about which pre-harvest environmental factors and management practices influence genomic (clonality, diversity) and phenomic (growth potential, antibiotic resistance) attributes of Salmonella. We will develop and test a “proLitterbiotic” culture to evaluate its efficiency to reduce the development of multidrug resistant Salmonella in live broiler chickens. Live production studies will use pastured poultry farms as a model for poultry management as we have access to working and experimental pastured poultry farms for more controlled research experiments. Expected outcomes for regulatory agencies, the conventional and pastured poultry industries and the consumer include: i) data-supported approaches for identifying risks associated with contamination of poultry entering the processing/post-harvest environments; ii) tools that facilitate characterization of Salmonella serovars and how mixtures correlate to epidemiological trends; iii) new approaches to interventions intended to disrupt the ability of Salmonella to maintain an optimized genome; iv) correlation of genomic markers to antimicrobial resistances present between and within Salmonella serovars within pre-harvest environments; and v) identification of best pre-harvest practices and alternatives to antibiotics that will help producers reduce foodborne pathogens in consumer products.

Progress Report
This project continues research from expired project 6040-32000-011-000D, "Reduction of Invasive Salmonella enterica in Poultry through Genomics, Phenomics and Field Investigations of Small Multi-Species Farm Environments." Selection of non-pathogenic litter bacterial strains for the development of a proLitterbiotic to reduce pathogenic Salmonella serotypes. ARS researchers in Athens, Georgia, began the characterization of twenty-nine Bacillus species isolated from reused litter previously inoculated with either Salmonella Heidelberg or Enteritidis. These isolates are being evaluated for their potentials as direct-fed microbials and for proLitterbiotic development. We used whole genome sequencing to confirm the species of Bacillus to be subtilis (n=17) and velezensis (n =12). Five B. subtilis strains and one B. velezensis strain carried plasmids. The carriage of plasmid by these strains indicate that they do not meet our criteria for proLitterbiotic inclusion i.e., no plasmid carriage, and the six strains will not be considered further. We will further characterize the strains that passed this inclusion test (n =23) for the mobility of the chromosomal region encoding virulence and antibiotic resistance genes. Determination of bacterial pathogen diversity in acidified re-used poultry litter during commercial live production. ARS researchers investigated the diversity and changes in abundances of several bacterial foodborne pathogens (Salmonella, Campylobacter, Staphylococcus), commensal bacteria (Escherichia, Enterococcus) and fungi from commercial poultry house acidified litter. Not only are these changes in abundance and diversity observed through a single flock within a house, but are also being followed over multiple flocks for an entire production year. Preliminary findings from the first flock show that litter acidification does not allow for Campylobacter growth throughout grow-out, but appears to only reduce Salmonella, E. coli, Staphylococcus, and Enterococcus populations during the first few weeks of grow-out, with those populations either returning to pre-acidification levels or exceeding them by the end of the grow-out period I6 weeks).