Horizontal Gene Transfer Is the Main Driver of Antimicrobial Resistance in Broiler Chicks Infected with Salmonella enterica Serovar Heidelberg
Adelumola Oladeinde,
Zaid Abdo,
Maximilian O. Press,
Kimberly Cook,
Nelson A. Cox,
Benjamin Zwirzitz,
Reed Woyda,
Steven M. Lakin,
Jesse C. Thomas,
Torey Looft,
Douglas E. Cosby,
Arthur Hinton,
Jean Guard,
Eric Line,
Michael J. Rothrock,
Mark E. Berrang,
Kyler Herrington,
Gregory Zock,
Jodie Plumblee Lawrence,
Denice Cudnik,
Sandra House,
Kimberly Ingram,
Leah Lariscy,
Martin Wagner,
Samuel E. Aggrey,
Lilong Chai,
Casey Ritz
Affiliations
Adelumola Oladeinde
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Zaid Abdo
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
Maximilian O. Press
Phase Genomics Inc., Seattle, Washington, USA
Kimberly Cook
Office of National Programs, USDA-ARS, Beltsville, Maryland, USA
Nelson A. Cox
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Benjamin Zwirzitz
Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
Reed Woyda
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
Steven M. Lakin
Department of Microbiology, Immunology and Pathology, Colorado State University, Fort Collins, Colorado, USA
Jesse C. Thomas
Division of STD Prevention, National Center for HIV/AIDS, Viral Hepatitis, STD and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
Torey Looft
National Animal Disease Center, USDA-ARS, Ames, Iowa, USA
Douglas E. Cosby
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Arthur Hinton
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Jean Guard
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Eric Line
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Michael J. Rothrock
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Mark E. Berrang
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Kyler Herrington
Medical College of Georgia, Augusta, Georgia, USA
Gregory Zock
Poultry Science Department, University of Georgia, Athens, Georgia, USA
Jodie Plumblee Lawrence
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Denice Cudnik
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Sandra House
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Kimberly Ingram
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Leah Lariscy
U.S. National Poultry Research Center, USDA-ARS, Athens, Georgia, USA
Martin Wagner
Institute of Food Safety, Food Technology and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria
Samuel E. Aggrey
Poultry Science Department, University of Georgia, Athens, Georgia, USA
Lilong Chai
Poultry Science Department, University of Georgia, Athens, Georgia, USA
Casey Ritz
Poultry Science Department, University of Georgia, Athens, Georgia, USA
ABSTRACT The overuse and misuse of antibiotics in clinical settings and in food production have been linked to the increased prevalence and spread of antimicrobial resistance (AR). Consequently, public health and consumer concerns have resulted in a remarkable reduction in antibiotics used for food animal production. However, there are no data on the effectiveness of antibiotic removal in reducing AR shared through horizontal gene transfer (HGT). In this study, we used neonatal broiler chicks and Salmonella enterica serovar Heidelberg, a model food pathogen, to test if chicks raised antibiotic free harbor transferable AR. We challenged chicks with an antibiotic-susceptible S. Heidelberg strain using various routes of inoculation and determined if S. Heidelberg isolates recovered carried plasmids conferring AR. We used antimicrobial susceptibility testing and whole-genome sequencing (WGS) to show that chicks grown without antibiotics harbored an antimicrobial resistant S. Heidelberg population at 14 days after challenge and chicks challenged orally acquired AR at a higher rate than chicks inoculated via the cloaca. Using 16S rRNA gene sequencing, we found that S. Heidelberg infection perturbed the microbiota of broiler chicks, and we used metagenomics and WGS to confirm that a commensal Escherichia coli population was the main reservoir of an IncI1 plasmid acquired by S. Heidelberg. The carriage of this IncI1 plasmid posed no fitness cost to S. Heidelberg but increased its fitness when exposed to acidic pH in vitro. These results suggest that HGT of plasmids carrying AR shaped the evolution of S. Heidelberg and that antibiotic use reduction alone is insufficient to limit antibiotic resistance transfer from commensal bacteria to Salmonella enterica. IMPORTANCE The reported increase in antibiotic-resistant bacteria in humans has resulted in a major shift away from antibiotic use in food animal production. This shift has been driven by the assumption that removing antibiotics will select for antibiotic susceptible bacterial taxa, which in turn will allow the currently available antibiotic arsenal to be more effective. This change in practice has highlighted new questions that need to be answered to assess the effectiveness of antibiotic removal in reducing the spread of antibiotic resistance bacteria. This research demonstrates that antibiotic-susceptible Salmonella enterica serovar Heidelberg strains can acquire multidrug resistance from commensal bacteria present in the gut of neonatal broiler chicks, even in the absence of antibiotic selection. We demonstrate that exposure to acidic pH drove the horizontal transfer of antimicrobial resistance plasmids and suggest that simply removing antibiotics from food animal production might not be sufficient to limit the spread of antimicrobial resistance.
