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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  bla  NDM-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 ,  bla  NDM-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.

scientific reports

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