Genomic analysis of azithromycin-resistant Salmonella from food animals at slaughter and processing, and retail meats, 2011–2021, United States

Abstract

ABSTRACT Azithromycin, a 15-membered ring macrolide, is among the recommended antimicrobials for treating invasive salmonellosis in humans. It is not approved for use in veterinary medicine. We analyzed the U.S. National Antimicrobial Resistance Monitoring System (NARMS) culture collections (~40,700) between 2011 and 2021 from food animals at slaughter and processing and retail meats, and identified 31 azithromycin-resistant Salmonella spp. with the first occurrence in 2015. These isolates belonged to 12 Salmonella serovars and possessed one or more macrolide resistance determinants: erm(42), mef(C), mph(A), mph(E), mph(G), and msr(E) or a point mutation (acrB_R717L), of which mph(A) was dominant (61.3%). Compared with azithromycin-susceptible controls, these determinants accounted for up to 256-fold MIC increases against azithromycin with MIC50 and MIC90 increased by 32- and 8-fold, respectively. We report the first detection of an mph(G)-mef(C)-mph(E)-msr(E)-containing Salmonella Agona isolate with very high-level azithromycin resistance (1,024 µg/mL) and the first detection of acrB_R717L accounting for azithromycin resistance in nontyphoidal Salmonella serovars in the United States. Plasmids of diverse replicon types were identified, with 86.2% carrying multidrug resistance including azithromycin and ceftriaxone, or decreased susceptibility to ciprofloxacin. This report also highlights an emerging mph(A)-containing (on an IncR plasmid) Salmonella Newport clone of cattle/beef origin with high-level azithromycin resistance (128 µg/mL) and decreased susceptibility to ciprofloxacin (0.25 µg/mL). Further work is needed to better understand the drivers of emerging azithromycin resistance in nontyphoidal Salmonella associated with food animal sources. IMPORTANCE Macrolides of different ring sizes are critically important antimicrobials for human medicine and veterinary medicine, though the widely used 15-membered ring azithromycin in humans is not approved for use in veterinary medicine. We document here the emergence of azithromycin-resistant Salmonella among the NARMS culture collections between 2011 and 2021 in food animals and retail meats, some with co-resistance to ceftriaxone or decreased susceptibility to ciprofloxacin. We also provide insights into the underlying genetic mechanisms and genomic contexts, including the first report of a novel combination of azithromycin resistance determinants and the characterization of multidrug-resistant plasmids. Further, we highlight the emergence of a multidrug-resistant Salmonella Newport clone in food animals (mainly cattle) with both azithromycin resistance and decreased susceptibility to ciprofloxacin. These findings contribute to a better understating of azithromycin resistance mechanisms in Salmonella and warrant further investigations on the drivers behind the emergence of resistant clones.

Keywords

• azithromycin
• genome
• multidrug
• mutation
• PacBio
• plasmid