Genomic Characteristics of NDM-Producing Enterobacteriaceae Isolates in Australia and Their blaNDM Genetic Contexts

Abstract

blaNDM has been reported in different Enterobacteriaceae species and on numerous plasmid replicon types (Inc). Plasmid replicon typing, in combination with genomic characteristics of the bacterial host (e.g., sequence typing), is used to infer the spread of antimicrobial resistance determinants between genetically unrelated bacterial hosts. The genetic context of blaNDM is heterogeneous. In this study, we genomically characterized 12 NDM-producing Enterobacteriaceae isolated in Australia between 2012 and 2014: Escherichia coli (n = 6), Klebsiella pneumoniae (n = 3), Enterobacter cloacae (n = 2) and Providencia rettgeri (n = 1). We describe their blaNDM genetic contexts within Tn125, providing insights into the acquisition of blaNDM into Enterobacteriaceae. IncFII-type (n = 7) and IncX3 (n = 4) plasmids were the most common plasmid types found. The IncHI1B (n = 1) plasmid was also identified. Five different blaNDM genetic contexts were identified, indicating four particular plasmids with specific blaNDM genetic contexts (NGCs), three of which were IncFII plasmids (FII-A to -C). Of note, the blaNDM genetic context of P. rettgeri was not conjugative. Epidemiological links between our NDM-producing Enterobacteriaceae were established by their acquisition of these five particular plasmid types. The combination of different molecular and genetic characterization methods allowed us to provide insight into the spread of plasmids transmitting blaNDM.

FIG 1

Schematic representation of all the NGCs in the study and the reference sequence pNDM-BJ01 (GenBank accession no. JQ001791). The bla_NDM genetic contexts and their GenBank accession numbers are as follows: IncFII plasmids with NGC type FII-A (pCR53-EC-NDM-4 [KP826711], pWA1-EC-NDM-4 [KP826707], pACT1-EC-NDM-1 [KP826702], and pCR7-EC-NDM-1 [KP826713]), with NGC type FII-B (pCR16-ECL-NDM-1 [KP826704] and pCR63-KP-NDM-1 [KP826712]), and with NGC type FII-C (pCR38-KP-NDM-1 [KP826710]); IncX3 plasmids with NGC type X3-A (pCR37-ECL-NDM-7 [KP826705], pWA2-KP-NDM-7 [KP826708], and pCR15-EC-NDM-4 [KP826709]); and an IncHI1B plasmid with NGC type HI1B-A (pCR58-PR-NDM-1 [KP826706]). Δ, truncated gene. IS elements are represented as block arrows. The vertical black arrows indicate insertion of IS elements. Reference sequences from GenBank for each genetic context are in boldface: pGUE-NDM (GenBank accession no. NC_019089), pECL3-NDM-1 (GenBank accession no. KC887917), pKOX-NDM-1 (GenBank accession no. JQ314407), pNDM_MGR194 (GenBank accession no. KF220657), pTR3 (GenBank accession no. JQ349086), and PittNDM01 (GenBank accession no. CP006799). The gray box highlights bla_NDM in each genetic context.