Remarkable Diversity of Escherichia coli Carrying mcr-1 from Hospital Sewage with the Identification of Two New mcr-1 Variants

Abstract

The plasmid-borne colistin-resistant gene <i>mcr-1</i> has rapidly become a worldwide public health concern. This study aims to determine the host bacterial strains, plasmids, and genetic contexts of <i>mcr-1</i> in hospital sewage. A 1-ml hospital sewage sample was cultured. Colistin-resistant bacterial colonies were selected on agar plates and were subjected to whole genome sequencing and subsequent analysis. The transfer of <i>mcr-1</i> between bacterial strains was tested using conjugation. New variants of <i>mcr-1</i> were cloned to test the impact of variations on the function of <i>mcr-1</i>. Plasmids carrying <i>mcr-1</i> were retrieved from GenBank for comparison based on concatenated backbone genes. In the sewage sample, we observed that <i>mcr-1</i> was located in various genetic contexts on the chromosome, or plasmids of four different replicon types (IncHI2, IncI2, IncP, and IncX4), in <i>Klebsiella pneumoniae, Kluyvera</i> spp. and seven <i>Escherichia coli</i> strains of six different sequence types (ST10, ST34, ST48, ST1196, ST7086, and ST7087). We also identified two new variants of <i>mcr-1, mcr-1.4</i> and <i>mcr-1.7</i>, both of which encode an amino acid variation from <i>mcr-1</i>. <i>mcr-1</i>-carrying IncX4 plasmids, which have a global distribution across the <i>Enterobacteriaceae</i>, are the result of global dissemination of a single common plasmid, while IncI2 <i>mcr-1</i> plasmids appear to acquire <i>mcr-1</i> in multiple events. In conclusion, the unprecedented remarkable diversity of species, strains, plasmids, and genetic contexts carrying <i>mcr-1</i> present in a single sewage sample from a single healthcare site highlights the continued evolution and dynamic transmission of <i>mcr-1</i> in healthcare-associated environments.