Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both no-antibiotics-ever (NAE) and conventional broiler complexes

Authors: ADHIKARI, YAGYA - Auburn University; BOURASSA, DIANNA - Auburn University; POUDEL, SABIN - Auburn University; BAILEY, MATTHEW - Auburn University; Buhr, Richard; MACKLIN, KENNETH - Mississippi State University

Submitted to: Poultry Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/24/2025
Publication Date: 2/4/2025
Citation: Adhikari, Y., Bourassa, D.V., Poudel, S., Bailey, M.A., Buhr, R.J., Macklin, K.S. 2025. Genotypic and phenotypic characterization of antimicrobial resistance in Salmonella strains isolated from both no-antibiotics-ever (NAE) and conventional broiler complexes. Poultry Science. 104(3):104855. https://doi.org/10.1016/j.psj.2025.104855.
DOI: https://doi.org/10.1016/j.psj.2025.104855

Interpretive Summary: Antimicrobial resistance is a serious global public health concern that could endanger the efficacy of antibiotics used for the treatment of diseases in humans, animals, and/or plants. The objective of this study was to characterize the antimicrobial resistance (AMR) genetic patterns of Salmonella strains isolated from different production stages (breeders farm, hatchery, broiler farm, processing plant) of broilers from both No-Antibiotics-Ever (NAE) and conventional commercial broiler complexes. ResFinder was used to identify AMR genes from whole genome sequences while the phenotypic resistance of 14 different antibiotics was determined using broth microdilution method. Odds ratios were calculated for different complexes and stages of broiler production (a=0.05). The major AMR genes identified were aac(6’)-Iaa, aph(6)-Id, aph(3”)-Ib, blaCARB-2, sul1, tet(A), tet(B), tet(G), floR, fosA7, gyrA, and parC. The phenotypic resistance results showed that 58% (49/85) of isolates were resistant to at least one antibiotic (AOR), 24% (20/85) of isolates were resistant to at least two or more classes of antibiotics (ATR) and 6% (5/85) of isolates were multi-drug resistant (MDR). Among 49 AOR isolates, 33%, 27%, 29%, 2% and 10% of isolates showed phenotypic resistance to the antibiotics sulfisoxazole, tetracycline, both sulfisoxazole and tetracycline, both tetracycline and ciprofloxacin, and three or more classes of antibiotics respectively. Interestingly, 80% (32/40) of Salmonella Kentucky isolates showed phenotypic resistance to either tetracycline or sulfisoxazole or both. In addition, the odds of ATR Salmonella detection were 7 times (1.37 – 43.45) more likely in the isolates from NAE complexes as compared to conventional broiler complexes. Drug-resistant Salmonella present within and surrounding production houses and facilities can potentially contaminate the raw product that could lead to complicated antimicrobial therapy during foodborne infections in consumers.

Technical Abstract: Antimicrobial resistance is a serious global public health concern that could endanger the efficacy of antibiotics used for the treatment of diseases in humans, animals, and plants. The objective of this study was to characterize the antimicrobial resistance (AMR) pattern of Salmonella strains isolated from different stages of both No-Antibiotics-Ever (NAE) and conventional integrated broiler complexes. ResFinder was used to identify AMR genes from whole genome sequences while the phenotypic resistance of 14 different antibiotics was determined using broth microdilution method. Odds ratio and 95% confidence limits were calculated for different complexes and stages of broiler production (a=0.05). The major AMR genes identified were aac(6’)-Iaa, aph(6)-Id, aph(3”)-Ib, blaCARB-2, sul1, tet(A), tet(B), tet(G), floR, fosA7, gyrA, and parC. The phenotypic results showed that 58% (49/85) of isolates were resistant to at least one antibiotic (AOR), 24% (20/85) of isolates were resistant to at least two or more classes of antibiotics (ATR) and 6% (5/85) of isolates were multi-drug resistant (MDR). Among 49 AOR isolates, 33%, 27%, 29%. 2% and 10% of isolates showed phenotypic resistance to sulfisoxazole, tetracycline, both sulfisoxazole and tetracycline, both tetracycline and ciprofloxacin, and three or more classes of antibiotics respectively. Interestingly, 80% (32/40) of Kentucky isolates showed phenotypic resistance to either tetracycline or sulfisoxazole or both. In addition, the odds of ATR Salmonella detection were 7 times (1.37 – 43.45; 95% CL) more likely in the isolates from NAE complex as compared to conventional broiler complex (p=0.0233). Drug-resistant Salmonella present within and surrounding production houses and facilities can potentially contaminate the raw product that could lead to complicated antimicrobial therapy during foodborne infections in consumers.