Antimicrobial resistance and genomic characterization of Salmonella Dublin isolates in cattle from the United States

Abstract

Salmonella enterica subspecies enterica serotype Dublin is a host-adapted serotype in cattle, associated with enteritis and systemic disease. The primary clinical manifestation of Salmonella Dublin infection in cattle, especially calves, is respiratory disease. While rare in humans, it can cause severe illness, including bacteremia, with hospitalization and death. In the United States, S. Dublin has become one of the most multidrug-resistant serotypes. The objective of this study was to characterize S. Dublin isolates from sick cattle by analyzing phenotypic and genotypic antimicrobial resistance (AMR) profiles, the presence of plasmids, and phylogenetic relationships. S. Dublin isolates (n = 140) were selected from submissions to the NVSL for Salmonella serotyping (2014–2017) from 21 states. Isolates were tested for susceptibility against 14 class-representative antimicrobial drugs. Resistance profiles were determined using the ABRicate with Resfinder and NCBI databases, AMRFinder and PointFinder. Plasmids were detected using ABRicate with PlasmidFinder. Phylogeny was determined using vSNP. We found 98% of the isolates were resistant to more than 4 antimicrobials. Only 1 isolate was pan-susceptible and had no predicted AMR genes. All S. Dublin isolates were susceptible to azithromycin and meropenem. They showed 96% resistance to sulfonamides, 97% to tetracyclines, 95% to aminoglycosides and 85% to beta-lactams. The most common AMR genes were: sulf2 and tetA (98.6%), aph(6)-Id (97.9%), aph(3’’)-Ib, (97.1%), floR (94.3%), and blaCMY-2 (85.7%). All quinolone resistant isolates presented mutations in gyrA. Ten plasmid types were identified among all isolates with IncA/C2, IncX1, and IncFII(S) being the most frequent. The S. Dublin isolates show low genomic genetic diversity. This study provided antimicrobial susceptibility and genomic insight into S. Dublin clinical isolates from cattle in the U.S. Further sequence analysis integrating food and human origin S. Dublin isolates may provide valuable insight on increased virulence observed in humans.

A retrospective and regional approach assessing the genomic diversity ofSalmonellaDublin

“…Dublin in France, which was not previously demonstrated. As previously shown ( 54 , 58 ), S . Dublin is a highly clonal serotype and harbours a highly conserved genome ( 13 , 53 , 54 , 59 ), which is found here with a low number of intra and inter-cluster SNPs, and from the few numbers of SNPs excluded from recombination events.…”

Whole-Genome Investigation of Salmonella Dublin Considering Mountain Pastures as Reservoirs in Southern Bavaria, Germany

“…Furthermore, recent data revealed that the proportion of resistance in S . Dublin isolates in the United States is higher than in other Salmonella serotypes [ 18 , 19 , 46 ]. Furthermore, S. Dublin is one of the serotypes showing the highest multidrug resistance [ 19 ].…”

Epidemiological Analysis on the Occurrence of Salmonella enterica Subspecies enterica Serovar Dublin in the German Federal State Schleswig-Holstein Using Whole-Genome Sequencing

“…In contrast, S. Dublin strains from both cattle and human beings coming from non-European countries such as the United States, Canada or China revealed a comprehensive antimicrobial resistance pattern [ 2 , 30 , 31 , 32 , 33 ]. The acquisition of plasmids that carry resistance genes such as IncA/C2, ColRNAI, or incompatibility (Inc) groups of plasmids have been identified in S. Dublin MDR isolates from cattle in the United States [ 34 ]. It is suggested that the difference between the European and American isolates is the carriage of the IncA/C2 plasmid [ 31 ].…”

“…It is suggested that the difference between the European and American isolates is the carriage of the IncA/C2 plasmid [ 31 ]. Other genetic mechanisms identified include point mutations in resistance genes encoded in the chromosome ( gyr A for fluoroquinolones and quinolones) and multidrug efflux pumps as the ones encoded by the mdfA gene [ 34 ]. Plasmid replicons associated with virulence such as IncFII(S) and IncX1 were the most predominant detected among the strains.…”