Molecular Characterization of bla(NDM)-Carrying IncX3 Plasmids: bla(NDM-16b) Likely Emerged from a Mutation of bla(NDM-5) on IncX3 Plasmid

Dissemination of bla(NDM), which is carried on the IncX3 plasmid, among Enterobacterales has been reported worldwide. In particular, bla(NDM-5)-carrying IncX3 plasmids can spread among several hosts, facilitating their dissemination. Other variants, such as bla(NDM-17)-, bla(NDM-19)-, bla(NDM-20)-, bla(NDM-21)-, and bla(NDM-33)-carrying IncX3 plasmids, have also been reported. Here, we characterized, using whole-genome sequencing (WGS), a bla(NDM-16b)-carrying IncX3 plasmid harbored by Escherichia coli strain TA8571, which was isolated from a urine specimen of a hospital inpatient in Tokyo, Japan. The bla(NDM-16b) differed in sequence from bla(NDM-5) (C > T at site 698, resulting in an Ala233Val substitution). This bla(NDM-16b)-carrying IncX3 plasmid (pTMTA8571-1) is 46,161 bp in length and transferred via conjugation. Transconjugants showed high resistance to β-lactam antimicrobials (except for aztreonam). Because pTMTA8571-1, which carries the Tn125-related region containing bla(NDM) and conjugative transfer genes, was similar to the previously reported IncX3 plasmids, we performed phylogenetic analysis based on the sequence of 34 shared genes in 142 bla(NDM)-carrying IncX3 plasmids (22,846/46,923 bp). Comparative analysis of the shared genes revealed short branches on the phylogenetic tree (average of 1.08 nucleotide substitutions per shared genes), but each bla(NDM) variant was divided into separate groups, and the structure of the tree correlated with the flowchart of bla(NDM) nucleotide substitutions. The bla(NDM)-carrying IncX3 plasmids may thereby have evolved from the same ancestral plasmid with subsequent mutation of the bla(NDM). Therefore, pTMTA8571-1 likely emerged from a bla(NDM-5)-carrying IncX3 plasmid. This study suggested that the spread of bla(NDM)-carrying IncX3 plasmids may be a hotbed for the emergence of novel variants of bla(NDM). IMPORTANCE bla(NDM)-carrying IncX3 plasmids have been reported worldwide. Harbored bla(NDM) variants were mainly bla(NDM-5), but there were also rare variants like bla(NDM-17), bla(NDM-19), bla(NDM-20), bla(NDM-21), and bla(NDM-33), including bla(NDM-16b) detected in this study. For these plasmids, previous reports analyzed whole genomes or parts of sequences among a small number of samples, whereas, in this study, we performed an analysis of 142 bla(NDM)-carrying IncX3 plasmids detected around the world. The results showed that regardless of the bla(NDM) variants, bla(NDM)-carrying IncX3 plasmids harbored highly similar shared genes. Because these plasmids already spread worldwide may be a hotbed for the emergence of rare or novel variants of bla(NDM), increased attention should be paid to bla(NDM)-carrying IncX3 plasmids in the future.