Co-occurrence of plasmid-mediated colistin resistance gene, mcr-1 and blaCTX−M in multidrug-resistant Escherichia coli isolates from calves in Iran

Colistin, a “last-resort” antibiotic for treatment of human infections caused by multidrug-resistant (MDR) Gram-negative bacteria, has been widely used in veterinary medicine for decades. Farm animals have been identified as a significant reservoir of mcr-1-carrying bacteria with potential zoonotic transmission. This study aimed to characterize mcr-1-positive Escherichia coli isolates obtained from calves in Iran. Rectal swab samples were collected from both diarrhetic and healthy calves and screened for colistin-resistant bacteria. The presence of colistin resistance genes mcr-1 to 5 was examined using PCR. The genomic features of 15 out of 82 colistin resistant isolates were further studied by whole -genome sequencing. All isolates carried mcr-1.1 variant and belonged to ST224 (n = 3), ST162 (n = 2), ST167 (n = 2), ST1642 (n = 2), ST949 (n = 2), ST617, ST5229, ST88 and ST2345 (n = 1 each). These isolates exhibited high rates of resistance to ceftazidime, cefepime, and sulfamethoxazole-trimethoprim (100%), followed by tetracyclines, chloramphenicol, gentamicin, ciprofloxacin (≥ 80%) and amikacin (60%) mediated by the presence of blaCTX−M, sul and dfrA variants, tetA/B/M, floR/cmlA1, aac(3)-IId/a or ant(2’’)-Ia, qnrS, aac(6’)-Ib-cr, gyrA (S83L, D87N), and parC (S80I) mutations and rmtB gene. All isolates were susceptible to tigecycline, nitrofurantoin and imipenem. The IncI2 (delta) replicon was the most prevalent plasmid type among the studied isolates, suggesting it may play a key role in mcr-1 dissemination. The mcr-1- associated elements and colistin resistance phenotype remained stable following 10 days of passage in the absence of colistin pressure. This study reports isolation of mcr-1-bearing-MDR E. coli isolates co-harboring blaCTX−M and rmtB genes from animal sources. The observed clonal diversity among mcr-1-positive-isolates suggests a potential role for epidemic plasmids including IncI2, in the dissemination of mcr-1 gene in farm animals.