Comparative Genome Analysis of Livestock and Human Colistin-Resistant Escherichia coli Isolates from the Same Household

Abstract

Background

Emergence and dissemination of colistin-resistant bacteria that harbor mobile colistin resistance (mcr) genes pose a dire challenge for the treatment of intractable infections caused by multidrug-resistant bacteria. Current findings on colistin-resistant bacteria in both humans and livestock of the same households highlight the need to identify the dissemination mechanisms of colistin-resistant bacteria.

Methods

In this study, a comparative genome analysis of colistin-resistant Escherichia coli isolates from livestock and humans of the same household was performed to clarify the possible dissemination mechanism of mcr genes among bacteria. Pulsed-field gel electrophoresis and whole-genome sequencing followed by sequence typing of the isolates were performed for assessment of the samples.

Results

The study revealed that two colistin-resistant E. coli isolates, one each from a pig and a chicken, were phylogenetically similar but not identical to the human isolates obtained from the same household. The comparative genome analysis revealed that the chicken isolate and a human isolate shared the same IncHl2 plasmid harboring the mcr transposon (mcr-1-PAP2). The pig isolate and the other human isolate retained the mcr-1 transposon on the chromosome, with the pig isolate carrying the complete mcr transposon (ISApl1-mcr-1-PAP2-ISApl1) and the human isolate carrying the incomplete mcr transposon (ISApl1-mcr-1-PAP2).

Conclusion

The results of the study confirm the distribution of colistin-resistant bacteria and subsequent transmission of the resistance gene-carrying transposon between livestock and humans of the same household. To the best of our knowledge, this is the first report on genomic analysis of colistin-resistant E. coli isolates obtained from livestock and residents of the same household.

Keywords:

• colistin-resistance
• multidrug resistance
• comparative genome analysis
• whole-genome sequencing
• mcr

Abbreviations

COR, colistin-resistant; PFGE, pulsed-field gel electrophoresis; MDR, multidrug resistance; IS, insertion sequence; MLST, multilocus sequence type; ST, sequence type.

Data Sharing Statement

The draft genome sequences of the COR E. coli strains 2018-18.25PC and sequences of the plasmid carrying mcr-1 of strain 2018-18.25CC were deposited in DDBJ/GenBank under the accession numbers AP023286 and LC567843, respectively.

Ethics Approval and Informed Consent

The study was approved by the Ethics Committees of Osaka University (Osaka, Japan) and Thai Binh University of Medicine and Pharmacy (Thai Binh, Vietnam).

Author Contributions

All authors made a significant contribution to the work reported, whether that is in the conception, study design, execution, acquisition of data, analysis and interpretation, or in all these areas; took part in drafting, revising or critically reviewing the article; gave final approval of the version to be published; have agreed on the journal to which the article has been submitted; and agree to be accountable for all aspects of the work.

Disclosure

The authors report no conflicts of interest in this work.