Genomic characterization of plasmid-borne colistin resistance variants, mcr-1.1 and mcr-1.26, in multidrug-resistant Escherichia coli isolated from backyard farm animals

Colistin remains a high-priority, critically important antimicrobial that is used for treating severe infections caused by multidrugresistant (MDR) Gram-negative bacteria.However, colistin resistance and the emergence of the mobile colistin resistance ( mcr) genes have been increasingly documented in clinical and community settings, including in humans, animals, and the environment [ 1-3 ], which severely limits available antimicrobial options for addressing critical infections.Previous studies have reported that the wide dissemination of mcr-1 across Lebanon, an East Mediterranean country, is a major concern, especially in agricultural areas.Recently, we have identified a novel mcr variant, mcr-1.26, which appears to be spreading in Lebanon and is rarely reported abroad.This variant has been detected in hospitalised patients [ 4 ], otherwise healthy people [ 2 ], and birds [ 3 , 5 ] in Lebanon.Mcr-1.26harbouringbacteria appear to concurrently exhibit resistance to other clinically and agriculturally important antimicrobials.Subsequently, we aimed to assess the faecal carriage and antimicrobial susceptibility patterns of colistin-resistant E. coli in backyard food animals in largely disenfranchised areas of North and South Lebanon.Many individuals in Lebanese rural and agricultural areas own backyard food animals that constitute an important source of nutrition and income.This is vital for disenfranchised communities that face critical socioeconomic challenges and have limited resources that are further weakened by the ongoing economic crisis in Lebanon.The latter has resulted in a lack of government subsidies and restricted access to affordable veterinary supportive care [ 6 ].This prevailing situation often compels individuals to resort to self-prescribing practices, driven by the need to reduce costs and cope with limited access to affordable veterinary services.Consequently, it is necessary to investigate the spread of resistance to colistin and other antimicrobials in these settings [ 6 ].Thirty-three fresh faecal swab samples were collected from different animals from 16 farms in July 2022.The samples were homogenised and spread onto RAPID' E. coli 2 Medium (Bio-Rad, Hercules, CA, USA) plates supplemented with colistin (3.5 mg/L) (Supplementary data 1) .After incubation for 24 hours at 37 °C under aerobic conditions, putatively colistin-resistant E. coli colonies were selected and purified.The identity of the isolates was further confirmed using MALDI-TOF VITEK MS (bioMérieux, Marcy L'Etoile, France).We successfully detected the presence of the MCR-1 protein in four colistin-resistant E. coli isolates using the NG-Test® MCR-1 (NG Biotech, Guipry, France) lateral flow immunoassay (LFA).These isolates were characterised by minimum