Genotypic and phenotypic analysis of antimicrobial resistance in Salmonella enterica isolates from retail chicken products in Kuwait.

Abstract

Antimicrobial resistance in non-typhoidal Salmonella is recognized as an important threat to food safety and public health. The objectives of this study were to characterize the antimicrobial resistance patterns, molecular epidemiology and agreement between genetic resistance markers and phenotypic susceptibility profiles among Salmonella enterica isolates found in chicken products in Kuwait. Seventy-two Salmonella enterica isolates were tested for susceptibility to eleven antibiotics using the disk-diffusion method. Whole genome sequencing was performed to test the genotypic antibiotic resistance genes and associated mobile genetic elements. Phenotypically, resistance was higher to ampicillin, tetracycline and cefotaxime with rates of 97.1%, 95.7% and 89.9%, respectively. Genomic analysis identified 32 genes with the most common being tetA (98.6%), qacE (87.5%), sul1 (86.1%), floR (81.7%), aac(3)-IV (80.3%) and, blaCTX-M-65 (79.2%). The agreement between the genetic and phenotypic data varied, however, concordance was high for tetracycline (95.5%; k = 0.02), gentamicin (79.7%; k = 0.43), chloramphenicol (78.3%; k = 0.35) and meropenem (100%; k = 1.0), whereas, cefotaxime (10.1%; k = 0.0) and nalidixic acid (30.4%; k = 0.0) showed poor agreement. MLST analysis identified seven sequence types (STs) with ST32 and ST314 being the dominant lineages, representing 33.3% and 31.9% of isolates, respectively. Plasmid analysis showed 79.1% of isolates carried the IncFIB(pN55391) replicon. Integrons (attc & intl) were also identified in 83.3% of isolates. All the isolates were predicted as human pathogens at the confidence level of 95.5-98.5%. In conclusion, the widespread multidrug resistance and high load of resistance genes detected in Salmonella from retail chicken in Kuwait point to an important food safety concern. The findings support the need for routine surveillance in Kuwait that combines whole-genome sequencing with conventional susceptibility testing as a part of a broader One Health approach.