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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 #430070
Research Project: Reduction of Foodborne Pathogens and Antimicrobial Resistance in Poultry Production Environments

Location: Egg and Poultry Production Safety Research Unit

Title: The fitness of salmonella enteritidis in poultry is strongly shaped by interactions between bacteriophages, plasmids, and the microbial community

Author
item Oladeinde, Adelumola
item CHUNG, TAEJUNG - Oak Ridge Institute For Science And Education (ORISE)
item BRADSHAW, DAVID - Oak Ridge Institute For Science And Education (ORISE)
item DIARRA, MOUSSA - Agriculture And Agri-Food Canada
item REHMAN, ATTIQ - Agriculture And Agri-Food Canada
item COOK, KIMBERLY - US Department Of Agriculture (USDA)
item CARILLO, CATHERINE - Canadian Food Inspection Agency
item ABDO, ZAID - Colorado State University
item Bearson, Shawn
item Rothrock Jr, Michael
item Plumblee Lawrence, Jodie
item Satterlee, Timothy

Submitted to: American Society for Microbiology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/19/2026
Publication Date: 5/19/2026
Citation: Oladeinde, A.A., Chung, T., Bradshaw, D., Diarra, M., Rehman, A., Cook, K., Carillo, C., Abdo, Z., Bearson, S., Rothrock Jr, M.J., Plumblee Lawrence, J.R., Satterlee, T.R. 2026. The fitness of salmonella enteritidis in poultry is strongly shaped by interactions between bacteriophages, plasmids, and the microbial community. American Society for Microbiology. https://doi.org/10.1128/asmam.00008-26.
DOI: https://doi.org/10.1128/asmam.00008-26

Interpretive Summary: Foodborne illnesses linked to Salmonella Enteritidis strains with decreased susceptibility to quinolones including ciprofloxacin are on the rise in the United States, Canada, and Europe. In this study, we report for the first time that the gyrA mutation responsible for this phenotype is associated with a bacteriophage and a particular plasmid group. We showed that when either of the two mobile genetic elements are carried by a S. Enteritidis strain, the likelihood of having gyrA mutation was negligible. Using broiler chicken litter microcosms, we provided insights into how the microbiome could be harnessed to limit the continued spread of these fitter lineages of S. Enteritidis strains. Our study shows that the survival and evolution of S. Enteritidis in poultry environments are strongly shaped by interactions between bacteriophages, plasmids, and the microbial community.

Technical Abstract: Salmonella enterica serovar Enteritidis is a major cause of foodborne illness linked to poultry across the globe, and its decreased susceptibility to quinolone antibiotics such as ciprofloxacin poses a significant threat to public health. Yet, the ecological and genetic pressures that drive the fitness of this pathogen in poultry environments remain poorly defined. In this study, we combined broiler chicken litter microcosm experiments, whole genome sequencing, and machine learning to investigate factors that shape the fitness and antimicrobial resistance development of S. Enteritidis. We analyzed more than 10,000 genomes to assess the role bacteriophages, plasmids, and chromosomal mutations play in driving S. Enteritidis fitness. Our findings reveal that an underreported bacteriophage named ESSI-2 and IncX1 plasmids strongly influenced whether strains carried the gyrA mutations associated with decreased ciprofloxacin susceptibility. Strains of S. Enteritidis lacking both ESSI-2 phage and IncX1 plasmid developed parallel mutations in genes linked to DNA topology, antimicrobial peptide resistance, and virulence. We found that reused litter reduced S. Enteritidis survival compared to fresh litter wood shavings and suggest that microbiome interventions could be used to reduce the spread of antibiotic resistant Enteritidis strains.