Genomic patterns and characterizations of chromosomally-encoded mcr-1 in Escherichia coli populations

Abstract

The emergence and transmission of the mobile colistin resistance gene (mcr-1) threatened the extensive use of polymyxin antimicrobials. Accumulated evidence showed that the banning of colistin additive in livestock feed efficiently reduce mcr-1 prevalence, not only in animals but also in humans and environments. However, our previous study has revealed that a small proportion of Escherichia coli could continually carry chromosomally-encoded mcr-1. The chromosomally-encoded events, indicated the existence of stabilized heritage of mcr-1 and revealed a potential threat in the antimicrobial stewardship interventions, are yet to be investigated. In this study, we systematically investigated the genetic basis of chromosomally-encoded mcr-1 in prevalence and potential mechanisms of lineage, plasmid, insertion sequence, and phage. Our results demonstrated that the emergence of chromosomally-encoded mcr-1 could originate from multiple mechanisms, but mainly derived through the recombination of ISApl1/Tn6330. We reported a specific transmission mechanism, which is a phage-like region without lysogenic components, could associate with the emergence and stabilization of chromosomally-encoded mcr-1. These results highlighted the potential origin and risks of chromosomally-encoded mcr-1, which could be a heritable repository and thrive again when confronted with new selective pressures. To the best of our knowledge, this is the first study to systematically reveal the genomic basis of chromosomally-encoded mcr-1, and report a specific transmission pattern involved in phage-like region. Overall, we demonstrate the origin mechanisms and risks of chromosomally-encoded mcr-1. It highlights the need of public attention on chromosome-encoded mcr-1 to prevent from its reemergence.

Genomic characterization of antimicrobial resistance in mcr-carrying ESBL-producing Escherichia coli from pigs and humans

“…While mcr-3 are mostly localized on plasmids, mcr-1.1 could be either chromosomally located or plasmid mediated. The latter was supported by a previous study showing that mcr-1 was initially discovered on Tn6330, which could mobilize between chromosome and plasmid [52,53]. Therefore, the localization and route of transmission of mcr-1.1 in this study remained unclear.…”

Prevalence and Relatedness of mcr-1-Mediated Colistin-Resistant Escherichia coli Isolated From Livestock and Farmers in Japan

“…There is also a possibility of mcr-1 -coding gene transfer across different species and strains by horizontal gene transfer, such as conjugation and transformation. A recent study reported that E. coli strains harboring chromosomally encoded mcr-1 were isolated from 3.5% of mcr-1 -positive E. coli in China from 2016 to 2018 ( Shen et al, 2020 ). Therefore, the whole genome of the other 25 strains of mcr-1 -positive E. coli should be analyzed to characterize the genetic construction and determine whether the mcr-1 gene is encoded on a plasmid or chromosome in the future.…”

High diversity of pathogenic Escherichia coli clones carrying mcr‐1 among gulls underlines the need for strategies at the environment–livestock–human interface

“…A similar genetic environment, although with one or two copies of IS Apl1 upstream mcr‐1 ‐ pap2 , was already described in the chromosome of E . coli isolates (Shen et al, 2020). In fact the occurrence of the mcr‐1 gene in diverse genetic contexts (e.g.…”