Multi-Drug Resistance Profiling and Mutational Analysis of mcr-1 Gene among Salmonella enterica subsp. enterica serovar Typhimurium Isolated from Chicken Farms of Khanewal, Pakistan

Salmonella enterica subspecies enterica (S. enterica) bacterium causes infections in poultry chicken birds every year and possess economic losses to the poultry farming. This study aimed to isolate and identify multi-drug resistant (MDR) S. enterica from local chicken farms and to detect any emerging novel variant of mobile colistin resistance (mcr) gene. A total of 150 samples from 5 commercial chicken farms were collected including; dead bird’s tissue (50), cloacal swabs/feces (50) and farm’s environment (50). Isolation of S. enterica was carried out by culturing on MacConkey and Salmonella-Shigella agar, followed by rapid API 20E kits for biochemical characterization and Kirby-Bauer disc diffusion method for screening of multi-drug resistant (MDR) strains. Polymerase chain reaction (PCR) assay performed to amplify 16S rRNA, invasion (invA) and mobile colisitin resistance (mcr-1) genes followed by in-silico analysis. Out of 150 collected samples, 16% S. enterica strains were isolated (n=24/150), including further categorically from; lesions (n= 8/24; 33%), cloaca/feces (n=11/24; 46%), and water (n= 5/24; 21%). Out of 24 S. enterica isolates, 88% (n=21/24) were MDR, including further categorically from; lesions (n= 8/21; 38%), cloaca/feces (n=10/21; 48%), and water (n=3/21; 14%). S. enterica isolates were resistant against polymyxin B (n=23/24; 96%), co-trimoxazole (sulfamethoxazole-trimethoprim) (n=21/24; 88%), nalidixic acid (n=20/24; 83%), and ampicillin (n=17/24; 72%), whereas antibiotic susceptibility was recorded against ceftriaxone (n=20/24; 83%) and ceftazidime (n=19/24; 79%). 16S rRNA gene sequencing and phylogenetic analysis confirmed isolates as Salmonella enterica subsp. enterica serovar Typhimurium, whereas mcr-1 gene sequence analysis revealed that no novel genetic mutation was detected in this study. In conclusion, presence of multi-drug resistant bacterial strains in the local poultry chicken farming is alarming in addition to irrational use of antibiotics specifically last-resort antibiotics usage is worrisome as a serious public health concern. There is a need to spread awareness among farmers regarding use of the alternatives to antibiotics in order to control spread of superbugs in food chain and “keep antibiotics working”.