Prevalence and antimicrobial resistance of Salmonella in conventional and no antibiotics ever broiler farms in the United States

Abstract

Non-typhoidal Salmonella is the second most common bacterial cause of foodborne illness in the United States. More than 50% of the poultry meat sold in the U.S. is categorized as no antibiotics ever (NAE), yet it is unclear how these practices affect the prevalence and antimicrobial resistance (AMR) of Salmonella . The aim of this study was to evaluate and compare the prevalence of Salmonella and the incidence of AMR in conventional (n=2) and NAE (n = 2) broiler farms in the Southeast US. Broiler cecal (n = 420) and ileal contents (n = 420), along with litter (n = 24), feed (n = 24) and water (n = 24) samples were collected from four broiler farms. Sample collection was carried out during a full production cycle and following the birds to the processing facilities. The BAX® Real-Time PCR system was used to detect Salmonella positive samples. Phenotypic antimicrobial susceptibility was evaluated following the National Antimicrobial Resistance Monitoring System (NARMS) method, and whole genome sequencing (WGS) was carried out for screening of AMR genes. The software tool SeqSero2 and the McOutbryk SNP calling pipeline were used for serotype identification and phylogenetic analysis, respectively. Conventional broilers had the highest Salmonella prevalence (80% and 73%; P ≤ 0.05) at day 21. The Salmonella prevalence declined as the birds aged. Antimicrobial resistance among Salmonella isolates from all sample types was high in all four farms (76%), exhibiting frequent resistance to tetracycline (76%) and streptomycin (70%). Salmonella isolates recovered from NAE broilers carried higher (P ≤ 0.05) rates of AMR than isolates from conventionally raised chicken. Salmonella enterica serotype Kentucky was the predominant serotype, harboring genes tet(B), aph(3″)-Ib and aph(6)-Id (which encode resistance to tetracycline and streptomycin, respectively). Farm-related strains of the serotype were identified, exhibiting persistence in the litter environment. • Broilers from NAE farms had lower Salmonella prevalence in the Southeast US. • Resistance to tetracycline and streptomycin among Salmonella was widespread. • Salmonella Kentucky was the predominant serotype on farms in the Southeast US. • Phylogeny of S. Kentucky strains exhibited farm-specific association. • Antimicrobial resistant genes tet(B), aph(3″)‐Ib , aph(6)‐Id and fosA7 were found.