Coexistence of Two bla(NDM–)(5) Genes Carried on IncX3 and IncFII Plasmids in an Escherichia coli Isolate Revealed by Illumina and Nanopore Sequencing

The emergence of carbapenem-resistant Enterobacteriaceae poses a significant threat to public health worldwide. Here, we reported a multidrug-resistant Escherichia coli strain with two different bla(NDM–)(5)-carrying plasmids from China. Illumina short-read and MinION long-read whole genome sequencing were performed. Genomic analysis found that one bla(NDM–)(5) gene together with mphA was located on a 55-kb IncX3 plasmid, while the other bla(NDM–)(5) gene was on a novel 68-kb IncFII plasmid. Susceptibility testing and quantitative reverse transcription PCR results further indicated that the transconjugants with the IncX3 plasmid exhibited higher-level carbapenem resistance and expression of bla(NDM–)(5) than those with both plasmids or the IncFII plasmid. Two other β-lactamase genes (bla(CTX–M–)(15) and bla(OXA–)(1)) were also detected on another 160-kb IncF plasmid. This is the first report of coexistence of two bla(NDM–)(5)-carrying plasmids in a single bacterial isolate, highlighting the genetic complexity of NDM-5 carbapenemase circulation, and the urgent need for continued active surveillance.