Landscape of bla_NDM genes in Enterobacteriaceae

The blaNDM-1 gene encodes a carbapenemase, New Delhi metallo-β-lactamase (NDM-1), and the ability to produce NDM-1 is spread among Enterobacteriaceae via horizontal gene transfer of plasmids. It has been widely accepted that bla_NDM-1 is regulated by a hybrid promoter (P_ISAba125) consisting of a -10 box from the original bla_NDM-1 and a -35 box from ISAba125. However, the conservation of this promoter and the vertical transmission of bla_NDM genes by chromosomal integration have not been comprehensively analyzed. We retrieved the region containing the ORF of bla_NDM-1 (>95% translated protein identity) and a region 120 bp upstream of the bla_NDM-1 start codon from the complete sequence data of Enterobacteriaceae plasmids (n = 10,914) and chromosomes (n = 4908) deposited in GenBank, and the 310 extracted bla_NDM genes were analyzed by an in-silico approach. The results showed that most bla_NDM genes (99.0%) utilized the promoter, P_ISAba125. Interestingly, two bla_NDM-1 genes from the genus Citrobacter utilized the ISCR1-derived outward-oriented promoters P_OUT (P_ISCR1). Furthermore, the insertion of ISAba125 and ISCR1 occurred upstream of the CCATATTT sequence, which is located upstream of the -10 box. We also confirmed that most of the bla_NDM genes were disseminated by horizontal gene transfer of the plasmid, but 10 cases of the bla_NDM genes were integrated into the chromosome via mobile genetic elements such as IS26, IS150, ISCR1, ICE, and Tn7-like elements. Thus, plasmid-mediated transmission of the P_ISAba125-bla_NDM genes is predominant in Enterobacteriaceae. However, the spread of bla_NDM genes with new promoters and vertical dissemination via chromosomal integrations may pose additional serious clinical problems.