This study aimed to gain a better understanding of how resistance determinants in Salmonella and Campylobacter contribute to 14-, 15- and 16-membered ring macrolide resistance phenotypes. A total of 126 azithromycin-resistant (AziR) and -susceptible (AziS) [Salmonella (n = 45) and Campylobacter (n = 81)] isolates were selected for antimicrobial susceptibility testing (AST) and WGS. Seven functional macrolide resistance determinants, including erm(42), mef(C), mph(A), mph(E), mph(G), msr(E) and one point mutation (acrB_R717L) were previously identified in AziR Salmonella. These determinants resulted in an 8- and 16-fold 15-membered ring gamithromycin and azithromycin MIC50 increase, respectively, compared with AziS isolates, with a maximum MIC increase of up to 256. The same isolates also exhibited up to a 32-fold 14-membered ring erythromycin MIC50 increase. Salmonella with erm(42) or acrB_R717L showed up to 128-fold 16-membered ring macrolide tildipirosin MIC increase, compared with isolates that were susceptible or carrying other macrolide resistance genes. In Campylobacter, all AziR isolates had an MIC50 ranging from 32 to 4096 mg/L of the various membered ring macrolides, whereases all susceptible Campylobacter isolates had significantly lower MIC50 values, ranging from 0.25 to 4 mg/L. The MIC50 of the various ring macrolides for AziR Campylobacter isolates was 16- to 4096-fold higher when compared with AziS Campylobacter. Our study has revealed that the function of macrolide resistance genes in Salmonella can be associated with specific macrolide ring structures, whereas the single 23S rRNA mutation in Campylobacter results in significantly elevated MICs of all macrolides. for the various ring macrolides.

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.

Salmonella enterica is one of the most common bacterial foodborne pathogens in the United States, causing illnesses that range from self-limiting gastroenteritis to more severe, life threatening invasive disease. Many Salmonella strains contain plasmids that carry virulence, antimicrobial resistance, and/or transfer genes which allow them to adapt to diverse environments, and these can include incompatibility group (Inc) FIB plasmids. This study was undertaken to evaluate the genomic and phenotypic characteristics of IncFIB-positive Salmonella enterica serovar Typhimurium isolates from food animal sources, to identify their plasmid content, assess antimicrobial resistance and virulence properties, and compare their genotypic isolates with more recently isolated S. Typhimurium isolates from food animal sources. Methods: We identified 71 S. Typhimurium isolates that carried IncFIB plasmids. These isolates were subjected to whole genome sequencing and evaluated for bacteriocin production, antimicrobial susceptibility, the ability to transfer resistance plasmids, and a subset was evaluated for their ability to invade and persist in intestinal human epithelial cells. Results: Approximately 30% of isolates (n = 21) displayed bacteriocin inhibition of Escherichia coli strain J53. Bioinformatic analyses using PlasmidFinder software confirmed that all isolates contained IncFIB plasmids along with multiple other plasmid replicon types. Comparative analyses showed that all strains carried multiple antimicrobial resistance genes and virulence factors including iron acquisition genes, such as iucABCD (75%), iutA (94%), sitABCD (76%) and sitAB (100%). In 17 cases (71%), IncFIB plasmids, along with other plasmid replicon types, were able to conjugally transfer antimicrobial resistance and virulence genes to the susceptible recipient strain. For ten strains, persistence cell counts (27%) were noted to be significantly higher than invasion bacterial cell counts. When the genome sequences of the study isolates collected from 1998–2003 were compared to those published from subsequent years (2005–2018), overlapping genotypes were found, indicating the perseverance of IncFIB positive strains in food animal populations. This study confirms that IncFIB plasmids can play a potential role in disseminating antimicrobial resistance and virulence genes amongst bacteria from several food animal species.

BACKGROUND:Antimicrobial resistance in Salmonella enterica is often plasmid encoded. A key resistance plasmid group is the incompatibility group (Inc) A/C plasmids that often carry multiple resistance determinants. Previous studies showed that IncA/C plasmids were often co-located with other plasmids. The current study was undertaken to evaluate the impact of plasmid co-carriage on antimicrobial resistance and plasmid transfer.METHODS:A total of 1267 Salmonella isolates, representing multiple serotypes and sources were previously subjected to susceptibility testing and 251 isolates with resistance to at least 5 antimicrobial agents were identified for further study. Each isolate was subjected to PCR-based replicon typing, and those with IncA/C plasmids were selected for plasmid isolation, PCR-based mapping of IncA/C plasmid backbone genes, and conjugation assays to evaluate resistance plasmid transferability.RESULTS:Of the 87 identified IncA/C positive isolates, approximately 75% carried a plasmid with another identified replicon type, with the most common being I1 (39%), FIA, FIIA, FIB and HI2 (each 15%). PCR-based mapping indicated significant diversity in IncA/C backbone content, especially in regions encoding transfer-associated and hypothetical proteins. Conjugation experiments showed that nearly 68% of the isolates transferred resistance plasmids, with 90% containing additional identified plasmids or larger (>50 kb) non-typeable plasmids.CONCLUSIONS:The majority of IncA/C-positive strains were able to conjugally transfer antimicrobial resistance to the recipient, encoded by IncA/C and/or co-carried plasmids. These findings highlight the importance of co-located plasmids for resistance dissemination either by directly transferring resistance genes or by potentially providing the needed conjugation machinery for IncA/C plasmid transfer.