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 and 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.