Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on bla(NDM) Transmission

Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing Enterobacterales are increasing globally, resulting in a great burden to public health. The carbapenem-resistant Enterobacterales (CRE) were collected from Henan, China during 2013–2016. The bla(NDM)-positive strains were characterized using PCR, antimicrobial susceptibility testing, conjugation assay, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blot, whole-genome sequencing (WGS), and bioinformatics analysis. Eighty-one NDM-producing strains were identified among 391 nonduplicate CRE strains. Among them, four strains cocarried mcr and bla(NDM) genes, and two carried bla(IMP-4) and bla(NDM) genes. The coexistence of bla(NDM-5) and mcr-9 in Enterobacter hormaechei was found for the first time. In total, four bla(NDM) subtypes were identified. Among them, bla(NDM-1) and bla(NDM-5) were predominant. There was an obvious increasing trend in bla(NDM-5) from 2013 to 2016. Thirteen different bacterial species were found among the 81 strains, and Escherichia coli was the dominant strain. bla(NDM) genes were located on nine different Inc-type plasmids, most of them on the IncX3 plasmids, except for the Pr-15-2-50 strain, which was located on the chromosome. We characterized two novel plasmids: the IncHI5-like plasmid carrying bla(NDM-9) found in K. pneumonia, and the IncI1 bla(NDM-5)-positive plasmid. These findings provide the genomic basis for the widespread transmission of bla(NDM) and pave the way for the formulation of more effective monitoring and control methods. IMPORTANCE To control the emergence and transmission of CRE, it is important to perform retrospective genomic investigations. It is important to evaluate the plasmid diversity, genetic environment, and evolutionary relationships of the bla(NDM)-positive clinical strains in the early transmission stages. This study conducted an in-depth analysis of bla(NDM)-positive pathogens during a 4-year period using different methods for observing the high prevalence and active transmission of bla(NDM)-positive CRE. Moreover, we also explored the coexistence of the bla(NDM) and mcr, a clinically important mobile colistin resistance gene. This study shows that the prevalence of bla(NDM)-positive pathogens in Henan is high and the isolation rates increase each year. Moreover, plasmid-mediated horizontal transfer plays an important role in bla(NDM) dissemination. The co-occurrence of multiple resistance genes highlighted a long-lasting evolutionary pathway. Therefore, we have suggested the long-term continuous surveillance of clinical pathogens carrying bla(NDM) to learn the future transmission trend and curb the public health risk caused by CRE.