In Silico Characterization of blaNDM-Harboring Conjugative Plasmids in Acinetobacter Species

Abstract

New Delhi metallo-β-lactamase (NDM)-producing clinical strains in Acinetobacter spp. have been recently reported in many countries and have received considerable attention. The vast majority of bla_NDM cases occur on conjugative plasmids, which play a vital role in disseminating bla_NDM. To characterize the conjugative plasmids bearing bla_NDM genes in Acinetobacter spp., we analyzed the variants of bla_NDM, conjugative transfer regions, genetic contexts of bla_NDM, and the phylogenetic pattern of the 62 predicted bla_NDM-positive plasmids, which were selected from 1,191 plasmids of Acinetobacter species from GenBank. We identified 30 conjugative plasmids from the 62 bla_NDM-harboring plasmids in Acinetobacter species, with the oriT sites similar to plasmid pNDM-YR7 in our study, genes coding for relaxases of the MOB_Q family, genes encoding type IV coupling proteins (T4CPs) of the TrwB/TraD subfamily, and VirB-like type IV secretion system (T4SS) gene clusters. The genome sizes of all 30 pNDM-YR7-like plasmids ranged from 39.36 kb to 49.65 kb, with a median size of 44.56 kb. The most common species of Acinetobacter containing the bla_NDM-positive conjugative plasmids was A. baumannii, followed by Acinetobacter lwoffii and Acinetobacter indicus. Notably, pNDM-YR7 is the first report on a bla_NDM-positive conjugative plasmid in Acinetobacter junii. Moreover, all 30 bla_NDM-positive conjugative plasmids in Acinetobacter species were found to contain genetic contexts with the structure ISAba14-aph(3')-VI-ISAba125-bla_NDM-ble. Our findings provide important insights into the phylogeny and evolution of bla_NDM-positive plasmids of Acinetobacter species and further address their role in acquiring and spreading bla_NDM genes in Acinetobacter species. IMPORTANCE Conjugative plasmids harboring the bla_NDM gene play a vital role in disseminating carbapenem resistance. In this study, we first report a conjugative plasmid, pNDM-YR7, in Acinetobacter junii. Based on the genomic characteristics of the bla_NDM-positive pNDM-YR7, we performed in silico typing and comparative analysis of bla_NDM-positive plasmids using the 1,191 plasmids of Acinetobacter species available in the NCBI RefSeq database. We analyzed the characteristics of bla_NDM-positive plasmids, including the variants of bla_NDM, genetic features associated with bla_NDM, conjugative transfer regions, and the phylogenetic pattern of the bla_NDM-positive plasmids. All 30 bla_NDM-positive conjugative plasmids were found to contain an ISAba14-aph(3')-VI-ISAba125-bla_NDM-ble region. This study provides novel insights into the phylogeny and evolution of bla_NDM-harboring conjugative plasmids and contributes to the repertoire of knowledge surrounding bla_NDM-positive plasmids in the genus Acinetobacter.

Keywords: Acinetobacter; New Delhi metallo-β-lactamase; conjugative; plasmid.