The co-transfer of plasmid-borne colistin-resistant genes mcr-1 and mcr-3.5, the carbapenemase gene blaNDM-5 and the 16S methylase gene rmtB from Escherichia coli

Haiyan Long,Alan Mcnally,Zhiyong Zong,Ke Ma,Lu Liu,Yu Feng

doi:10.1038/s41598-018-37125-1

Abstract

We found an unusual Escherichia coli strain with resistance to colistin, carbapenem and amikacin from sewage. We therefore characterized the strain and determined the co-transfer of the resistance determinants. Whole genome sequencing was performed using both Illumina HiSeq X10 and MinION sequencers. Short and long reads were subjected to de novo hybrid assembly. Sequence type, antimicrobial resistance genes and plasmid replicons were identified from the genome sequences. Phylogenetic analysis of all IncHI2 plasmids carrying mcr-1 available in GenBank was performed based on core genes. Conjugation experiments were performed. mcr-3.5 was cloned into E. coli DH5α. The strain belonged to ST410, a type with a global distribution. Two colistin-resistant genes, mcr-1.1 and mcr-3.5, a carbapenemase gene blaNDM-5, and a 16S methylase gene rmtB were identified on different plasmids of IncHI2(ST3)/IncN, IncP, IncX3 and IncFII, respectively. All of the four plasmids were self-transmissible and mcr-1.1, mcr-3.5, blaNDM-5 and rmtB were transferred together. mcr-1-carrying IncHI2 plasmids belonged to several sequence types with ST3 and ST4 being predominant. MIC of colistin (4 μg/ml) for DH5α containing mcr-3.5 was identical to that containing the original mcr-3 variant. In conclusion, carbapenem resistance, colistin resistance and high-level aminoglycoside resistance can be transferred together even when their encoding genes are not located on the same plasmid. The co-transfer of multiple clinically-important antimicrobial resistance represents a particular challenge for clinical treatment and infection control in healthcare settings. Isolates with resistance to both carbapenem and colistin are not restricted to a given sequence type but rather are diverse in clonal background, which warrants further surveillance. The amino acid substitutions of MCR-3.5 have not altered its activity against colistin.

Highlights

Colistin is the last resort antimicrobial agent to treat infections caused by most Gram-negative bacteria commonly seen in clinical settings, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa[1,2]
BlaNDM-5 in another E. coli strain, which was recovered from hospital sewage, belonging to a different sequence type (ST410)
Compared with amikacin-susceptible strain WCHEC020123 carrying mcr-1.1, mcr-3.5 and blaNDM-511, strain WCHEC025943 had rmtB, which could explain its high-level resistance to amikacin

Summary

Introduction

Colistin is the last resort antimicrobial agent to treat infections caused by most Gram-negative bacteria commonly seen in clinical settings, including Escherichia coli, Klebsiella pneumoniae, Acinetobacter baumannii and Pseudomonas aeruginosa[1,2]. In addition to mutations or interruptions in certain chromosomal genes, acquired resistance to colistin has occurred due to plasmid-borne genes[1]. The co-existence of two plasmid-borne colistin-resistant genes in bacterial isolates is uncommon, but recently, we reported the co-existence of mcr-1 and mcr-3 plus the carbapenemase gene blaNDM-5 in an E. coli clinical strain, WCHEC020123, of phylogenetic group A and sequence type 206 (ST206)[11]. Correspondence and requests for materials should be addressed to Z.Z. blaNDM-5 in another E. coli strain, which was recovered from hospital sewage, belonging to a different sequence type (ST410). BlaNDM-5 in another E. coli strain, which was recovered from hospital sewage, belonging to a different sequence type (ST410) This strain has an even broader antimicrobial resistance spectrum than the extensive drug resistant WCHEC020123

Methods

Results

Conclusion