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.