Isolation of mobile colistin-resistance (mcr) gene-harboring gram-negative bacteria from chicken droppings in Dhaka

Abstract

The use of antibiotics in poultry industries across low and middle-income countries is increasing rapidly, contributing to the emergence of antibiotic resistance and leading to a public health threat. This study aimed to investigate the prevalence of Mobile Colistin Resistance (mcr) genes in Escherichia coli, Klebsiella pneumoniae and Acinetobacter baumannii isolated from the fecal samples of broiler chickens in Dhaka city. A total of 100 fresh poultry droppings were collected from 8 different raw markets in Dhaka. The samples were processed and streaked onto HiCrome UTI Agar to presumptively isolate E. coli and K. pneumoniae and Leeds Acinetobacter Agar for A. baumannii. The isolates were further confirmed by polymerase chain reaction (PCR). Detection of mcr genes was performed by employing two sets of multiplex PCR targeting mcr-1 to mcr-5, and mcr-6 to mcr-10. A total of 84 E. coli and 14 K. pneumoniae isolates were confirmed by PCR. The mcr-3 gene was the most abundant, being present in 83.7% of isolates, among which 74 were from E. coli and 8 from K. pneumoniae. The mcr-8 gene was the second most prevalent, being present in 40 (40.8%) isolates, among which 39 were from E. coli, and 1 from K. pneumoniae. None of the isolates tested positive for mcr-2, mcr-4, mcr-5 or mcr-10. Co-occurrence of two or more mcr gene variants occurred in 41.8% of E. coli isolates. Phenotypic colistin resistance was conducted on 15 E. coli isolates using the broth microdilution method to measure the minimum inhibitory concentration, and 14 isolates showed resistance to colistin. Discrepancies were observed between phenotypic and genotypic resistance to colistin. To our knowledge, this study marks the first report of mcr-3 in Bangladeshi poultry, and the first report of mcr-6, mcr-8, and mcr-9 in Bangladesh overall. The high prevalence of various mcr genes, notably mcr-3 and mcr-8, indicated industrial poultry as a potential source of multidrug-resistant pathogens.