A Nationwide Assessment On The Occurrence Of Plasmid-Borne Mobile Colistin-Resistance Gene, mcr-1, In Escherichia Coli Isolated From Lebanese River Water

Abstract

Colistin, a last resort antibiotic, is used to treat multidrug and extensively drug-resistant Gram-negative infections. However, colistin’s excessive use has led to the emergence of the plasmid-borne mobile colistin-resistance gene; mcr-1. The dissemination of this transmissible genetic marker has been documented in different niches across the globe. Anthropogenic, industrial, and agricultural activities near freshwater resources have significantly polluted river water with antibiotic-resistant organisms and genes. This study aims to determine the dissemination of mcr-1 alongside other antimicrobial resistance genes across 14 major perennial rivers and Ras El Ain water spring in Lebanon (45 sub-rivers). Samples were collected from three sites along the rivers in triplicates yielding 135 freshwater samples. Approximately 98.3% of the samples detected the presence of colistin-resistant E. coli, and a total of 116 mcr-1 positive isolates were recovered from 27 sub-rivers. Other mcr genes (mcr-2, mcr-3, mcr-4, mcr-6, and mcr-8) were also reported in some of the isolates. The antimicrobial characteristics showed colistin’s MIC ranging between 4-64 μg/ml and the phenotypic resistance reported against Penicillin (100%), Ampicillin (77%), Amoxicillin/Clavulanic acid (76%), Cefepime (25%), Cefotaxime (44%), Cephalexin (77%), Cefixime (39%), Doripenem (5%), Meropenem (3%), Imipenem (7%), Gentamicin (35%), Kanamycin (39%), Streptomycin (61%), Tetracycline (68%), Ciprofloxacin (30%), Norfloxacin (25%), Chloramphenicol (39%), and Trimethoprim/Sulfamethoxazole (57%). The majority of the isolate 94% were multidrug-resistant. Moreover, the extended-spectrum β-lactamase genes (ESBL), blaTEM, blaSHV, blaCTX-M were detected in 48%,42%, 36%, of the isolates, respectively. Moreover, the carbapenem-resistance genes blaKPC, blaOXA-48, blaIPM and blaNDM, were also reported in 3%,1%,2% and 4%, respectively. Interestingly, 62% of the mcr-1-positive-E. coli samples harbored the Class-1 Integron gene. The plasmid harboring the mcr-1 gene was successfully transformed into chemically competent JM109 E. coli cells. A variety of plasmid types were detected in the samples, especially the ones responsible for the global dissemination of the mcr-1 gene, IncX4, IncI1 α, and IncI2. Remarkably, 54.3% of the isolates were genotypically diverse. Additionally, the mcr-1 gene persisted in the water matrix for more than 127 days. These findings highlight the high prevalence of the mcr genes and other antibiotic resistance genes in Lebanese river water. This is the first study to highlight the dissemination and characterization of mcr-1-positive-E.coli in the Lebanese river water