Biochemical and genomic characterization of last-resort antibiotic resistance and oxidant tolerance in environmental E. coli

Colistin is currently reserved as a last-resort antibiotic for multidrug-resistant Gram-negative bacteria such as pan-resistant Escherichia coli. Colistin-resistant E. coli strains have been detected in wastewater, clinical, and agricultural sites, and this resistance is mediated by the plasmid-borne mcr-1 gene, which can spread into other sectors, including the food chain. Herein, we isolated several E. coli strains from mixed wastewater that showed varying resistance to colistin with IC50 values ranging from 6.5 to 27.3 mu g/ml as compared to 0.5 mu g/mL for the wild-type strain. The strains all contained the mcr-1 gene, and there is no gene duplication to account for the increased resistance to colistin. In addition, the strains displayed resistance to several other antibiotics belonging to different classes, including ciprofloxacin, sulfamethoxazole, and tetracycline, while maintaining wild-type sensitivity to other antibiotics such as tazocin and meropenem. Interestingly, some of the strains showed resistance to the powerful DNA-damaging agents, ultraviolet radiation and hydrogen peroxide, used for eradicating bacteria. Measurement of catalase activity, which decomposes hydrogen peroxide, was not significantly elevated, excluding the possibility that catalase is involved in the resistance of the strains to H2O2. However, we found that H2O2 treatment caused the accumulation of fragmented chromosomal DNA in the wild-type, but not in one of the representative H2O2-resistant strains. Analysis of whole genome sequencing data revealed that the H2O2-resistant strains harbour a high level of missense mutations in several genes, including DNA repair genes that could encode variant proteins with elevated capacity to repair damaged DNA.