Whole-genome epidemiology and characterization of mcr-1-encoding Escherichia coli in aquatic bird farms from the Pearl River Delta, China during 2019-2020.

Abstract Due to their unique breeding pattern, aquatic bird farms are gradually considered as a hotspot in the development and spread of antibiotic resistance. However, the number of comprehensive studies addressing the whole-genomic features of colistin resistant bacteria in aquatic bird farms is currently low. Over a period of two years, we conducted surveillance to determine the whole-genome epidemiology and characterization of mcr-1-positive E. coli in aquatic bird farms in southeastern coastal China. A total of 100 mcr-1-producing isolates in 654 E. coli strains were recovered from 781 samples collected in 11 aquatic bird farms and 1 veterinary clinic in the Pearl River Delta area. Higher resistance phenotypes to 17 antibiotics were found in mcr-1 positive isolates than in other isolates. Then, 20 mcr-1-carrying isolates were sequenced to analyse the whole-genomic features. The molecular typing and antibiotic resistance genes (ARGs)/ virulence factors (VFs) profiles of the isolates showed considerable diversity. Three types of genetic backbones of mcr-1 in the isolates were clustered, and identified in diverse broad host range plasmids and bacterial species. The pan-genome analyses revealed a large genetic pool composed of the isolates. Furthermore, phylogenetic trees of both the isolates in this study and a global dataset were built, indicating the spread of the three mcr-1 backbones and the mcr-1 positive isolates among different habitats, farms, and even countries. This study highlighted that aquatic bird farms may act as an important reservoir for mcr-1-producing E. coli, in which colistin resistance may be spread to diverse habitats, different geographical locations, and even across bacterial species.