Characterization of genetic elements carrying mcr-1 gene in Escherichia coli from the community and hospital setting in Vietnam

We conducted whole-genome sequencing of 94 mcr-1 positive E. coli isolates (Mcr1-Ec) from human and animal faeces, food, and water, in a community cohort (N=87, 2014-2015) and from clinical specimens from a referral hospital (N=7, 2016) in northern Vietnam. We used both short- and long-read sequencing to identify the molecular elements involved in the horizontal transmission of mcr-1. Mcr-1 was plasmid-borne in 71 and chromosomally encoded in 25 (2 isolates contains one copy on a chromosome and one copy on a plasmid) of 94 E. coli isolates from the community and hospital settings. All seven clinical isolates carried mcr-1 on plasmids. Replicon types of mcr-1 encoding plasmids included IncI2, IncP, IncX4, IncFIA, IncHI1B, IncN and IncX1 single replicons and combinations of IncHI2, IncN, IncX1 and IncR multi-replicons. Alignment of a long-read sequence of an IncI2 plasmid from animal faeces with short-read sequences of IncI2 plasmids from a healthy human, water and hospitalized patients showed a highly similar with query cover ranging from 90% to 98%, overall identity >81%. We detected the potential existence of multi-replicon plasmids harbouring mcr-1 in both community and hospital settings and confirmed 10/71 with long-read sequencing. An intact/conserved Tn6330 transposon sequence or its genetic context variants were found in 6/25 Mcr1-Ec with chromosomally encoded mcr-1.