Genomic Epidemiology Insights on NDM-Producing Pathogens Revealed the Pivotal Role of Plasmids on <i>bla</i> _NDM Transmission

Abstract

Incidences of nosocomial infections mediated by New Delhi metallo-β-lactamase (NDM) enzyme-producing <i>Enterobacterales</i> are increasing globally, resulting in a great burden to public health. The carbapenem-resistant <i>Enterobacterales</i> (CRE) were collected from Henan, China during 2013-2016. The <i>bla</i>_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 <i>mcr</i> and <i>bla</i>_NDM genes, and two carried <i>bla</i>_IMP-4 and <i>bla</i>_NDM genes. The coexistence of <i>bla</i>_NDM-5 and <i>mcr-9</i> in Enterobacter hormaechei was found for the first time. In total, four <i>bla</i>_NDM subtypes were identified. Among them, <i>bla</i>_NDM-1 and <i>bla</i>_NDM-5 were predominant. There was an obvious increasing trend in <i>bla</i>_NDM-5 from 2013 to 2016. Thirteen different bacterial species were found among the 81 strains, and Escherichia coli was the dominant strain. <i>bla</i>_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 <i>bla</i>_NDM-9 found in <i>K. pneumonia</i>, and the IncI1 <i>bla</i>_NDM-5-positive plasmid. These findings provide the genomic basis for the widespread transmission of <i>bla</i>_NDM and pave the way for the formulation of more effective monitoring and control methods. <b>IMPORTANCE</b> 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 <i>bla</i>_NDM-positive clinical strains in the early transmission stages. This study conducted an in-depth analysis of <i>bla</i>_NDM-positive pathogens during a 4-year period using different methods for observing the high prevalence and active transmission of <i>bla</i>_NDM-positive CRE. Moreover, we also explored the coexistence of the <i>bla</i>_NDM and <i>mcr,</i> a clinically important mobile colistin resistance gene. This study shows that the prevalence of <i>bla</i>_NDM-positive pathogens in Henan is high and the isolation rates increase each year. Moreover, plasmid-mediated horizontal transfer plays an important role in <i>bla</i>_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 <i>bla</i>_NDM to learn the future transmission trend and curb the public health risk caused by CRE.