Molecular epidemiology and antibiotic resistance phenotypes and genotypes of salmonellae from food supply chains in China

•Antibiotic abuse in animals is the major origin of MDR and super-MDR isolates.•Resistance phenotypes and genotypes of Salmonella had ST- and serovar features.•ST17 (S. Indiana) is an emerging super-MDR clone carried by chickens.•ST17 harbors a new cluster of blaCTX-M and/or blaOXA-1-like with blaTEM-1-like.

Salmonella is an important zoonotic agent and a vehicle for antibiotic resistance genes. Here, 294 isolates from humans and food-producing animals were subjected to serotyping, multilocus sequence typing, and assessment of phenotypic (15 antibiotics) and genotypic (32 resistance genes) antimicrobial resistance. Twenty-two serotypes and 35 sequence types (STs) were identified, the most common STs being ST11, including S. Enteritidis from chickens and humans; ST17, including S. Indiana from chickens; and ST40, including S. Derby from pigs and humans. Antimicrobial resistance phenotypes and genotypes exhibited ST- and serovar-specific features. ST11, clonal complex (CC) 19, ST40, and ST155 were moderately multidrug-resistant (MDR) clones, most of the isolates of which were resistant to between 3 and 6 antibiotics. Isolates of a super-MDR clone, ST17, demonstrated resistance against 9 to 14 antimicrobials, in particular, ampicillin, amoxicillin-clavulanic acid, cefotaxime, cefepime, cefoperazone, ceftriaxone, and ciprofloxacin. Consistent with this, ST17 (S. Indiana) was associated with a gene cluster comprising blaCTX-M (and/or blaOXA-1-like together with blaTEM-1-like), sul1, aacC4, aac(6)-1b, floR, and dfrA17, while the moderately-MDR clones (ST11, S. Enteritidis) were more closely linked to the blaTEM-1-like gene. The similar genetic clones isolated from animals and humans indicate a common ancestor, and implicate animals as a major salmonellae source. Antibiotic abuse in animal production appears to be the origin of MDR and super-MDR isolates, the latter being closely associated with the β-lactamase genes blaCTX-M, blaOXA-1-like, and blaTEM-1-like. Carried by chickens, ST17 (S. Indiana) is an emerging super-MDR clone whose associated resistance genes are expanding to other ST clones and serotypes being transmitted to animals and humans.