Genomic analysis of azithromycin-resistant
Salmonella
from food animals at slaughter and processing, and retail meats, 2011–2021, United States
Authors: Ge Beilei , Mukherjee Sampa , Li Cong , Harrison Lucas B. , Hsu Chih-Hao , Tran Thu-Thuy , Whichard Jean M. , Dessai Uday , Singh Ruby , Gilbert Jeffrey M. , Strain Errol A. , McDermott Patrick F. , Zhao Shaohua 
Published: November 2023

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 MIC
50
and MIC
90
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.