Phenotypic and genotypic profile of antimicrobial resistance in Klebsiella pneumoniae, Salmonella enterica and coagulase-negative Staphylococcus

Abstract

Antimicrobial resistance is a major concern in both human and veterinary medicine. Agents such as Klebsiella pneumoniae, Salmonella enterica and coagulase-negative Staphylococcus (CNS) are subject of researches involving detection and identification of antimicrobial resistance genes. The present study aimed to establish the phenotypic and genotypic resistance profile in: (i) S. enterica isolated from domestic animals and human patients from São Paulo State; (ii) K. pneumoniae isolated from bovine feces and milk in Brazilian dairy herds and; (iii) CNS samples isolated from lactating cows in Canadian dairy herds. Still, study associations between resistance profiles and different sources, barn types, bulk tank somatic cell count and to establish associations between antimicrobial usage and resistance in CNS. In this project, 166 K. pneumoniae isolates from 24 dairy farms, 153 S. enterica isolates originating from broiler carcasses and human patients and 1,859 CNS isolates from Canadian dairy herds were subjected to antimicrobial susceptibility tests and molecular detection of resistance genes according to the respective phenotypic profile. Still, associations between resistance profile and the origin of the isolates were determined. For S. enterica, non-susceptibility was commonly observed for streptomycin, tetracycline, sulfamethoxazole and amoxicillin. Genes commonly observed according to the distinct profiles were aadA, tetC, sul1 and blactx-m according to the respective profile. For our knowledge, this is the first report of the presence of qnrB gene in S. enterica isolated from human patients in Brazil. Profiles were distinct for human and animal isolates, with the first showing a higher proportion of non-susceptibility for several drugs. For K. pneumoniae isolates, it was observed an association between the source (milk; feces) and non-susceptibility for streptomycin, chloramphenicol, tetracycline and sulfamethoxazole. Multidrug resistance (MDR) was observed only for clinical mastitis isolates. Genes commonly observed included tetD, tetB and sul2. For CNS isolates, non-susceptibility to sulfonamides was the most commonly observed (18.65%) followed by penicillin, tetracycline and erythromycin (11.95, 11.29 and 6.5% of isolates tested, respectively). Alberta showed the lowest prevalence of sulfonamides non-susceptibility, although the prevalence of MDR isolates was constant across different Provinces. Samples from tie-stalls had higher odds of being MDR than samples from free-stalls. Antimicrobial usage was associated with the presence of MDR, especially for chloramphenicol and macrolides. blaZ and mecA (beta-lactams), str and aadE (aminoglycosides), ermA and ermC (macrolides), tetK and tetL (tetracyclines) genes were the most commonly observed.