No genetic link between E. coli isolates carrying mcr-1 in bovines and humans in France.

Abstract

Background: Colistin is a last-line antibiotic used to treat severe human infections caused by carbapenemase-producing Gram-negative bacteria. In parallel, colistin has massively been used in the veterinary field so that mcr-1-positive E. coli have spread worldwide in livestock, potentially constituting a reservoir of colistin-resistant isolates that can be further transmitted to humans.

Objectives: In France, the mcr-1 gene was frequently identified in E. coli of bovine origin. This genomic study assessed whether French human mcr-1-positive E. coli might originate or derive from the bovine reservoir.

Material and methods: Human (n=24) and bovine (n=127) isolates collected between 2011-2019 were included and colistin-resistance was confirmed by MICs. The detection of mcr-1 was performed by PCR. Isolates were short-read whole-genome sequenced and a cgMLST-based phylogeny was constructed. The genetic support of mcr-1 was identified using short-read sequences or Southern blots.

Results: The mcr-1 gene was carried by a high diversity of genetic backgrounds, among which ST167 and ST10 were the most widespread. No clonally-related isolates between bovines and humans were observed. In bovines, mcr-1 was identified on IncHI2 and IncX4 plasmids and increasingly on the chromosome, while it was also found on IncI2 and p0111 plasmids in humans.

Conclusion: Although similar STs (ST744 and ST88) and plasmid types (IncHI2, IncX4) carried mcr-1, no hypothesis of a transfer from bovines to humans could be supported by the data. Furthermore, the increasing chromosomal location of mcr-1 over time may reflect an animal-specific evolutionary pathway deserving further investigation.