First surveillance and draft genome sequences of circulating mcr-1-carrying, multidrug-resistant Escherichia coli in wastewater in Qatar

Objective: The global rise of colistin resistance, primarily mediated by the mcr-1 gene, threatens the efficacy of one of the last-resort treatments for multidrug-resistant Gram-negative infections. While mcr genes have been reported in clinical, veterinary and limited environmental samples in Qatar, there is a notable gap in data regarding their presence in wastewater. Methods: Fifteen composite wastewater samples were collected across multiple rounds in Qatar. Escherichia coli isolates were screened for colistin resistance, and mcr-1–positive strains were identified. Antimicrobial susceptibility testing was performed to determine resistance profiles. Whole-genome sequencing was conducted to characterize plasmid scaffolds harbouring mcr-1. Transformation assays were used to verify the transferability of resistance, and biofilm assays were conducted to evaluate persistence of resistance under biofilm conditions. Results: Out of the 15 composite wastewater samples, only 3 yielded E. coli – one isolate from each sample – and all were positive for the mcr-1 gene. The mcr-1–positive E. coli isolates (DSR2, DNR3 and DSR3) were all further screened and exhibited multidrug resistance while remaining susceptible to selected carbapenems and cephalosporins. Whole-genome sequencing indicated diverse mcr-1–carrying plasmid types: IncI2Δ, IncX4 and IncHI2A. Transformation assays confirmed that these plasmids conferred colistin resistance to recipient strains. In biofilm assays, the IncHI2A-carrying isolate retained colistin-resistant colonies up to day 6, in contrast to the other two plasmid types. Conclusions: This study detected transferable mcr-1–bearing plasmids in wastewater E. coli in Qatar, stressing the value of wastewater surveillance for tracking environmental spread and horizontal transfer of last‐resort antibiotic resistance.