Characterization of Acinetobacter johnsonii isolate XBB1 carrying nine plasmids and encoding NDM-1, OXA-58 and PER-1 by genome sequencing

Abstract

Objectives: To obtain the complete genome sequence of an Acinetobacter johnsonii isolate, which encodes the NDM-1 and OXA-58 carbapenemases. Methods: Genome sequencing was performed using the 454 and HiSeq 2000 platforms. Reads were assembled into scaffolds and gaps between scaffolds were filled by PCR and Sanger sequencing. Phylogenetic analyses of A. johnsonii isolates and their intrinsic blaOXA genes were performed using Harvest and MEGA. The context of blaaOXA-58 was analysed in detail. Results: Isolate XBB1 has one 3.5 Mb chromosome (38.5% GC content) and nine plasmids in the range 3.9-398.9 kb. Isolate XBB1 appears to be distinct from other A. johnsonii isolates. Five of the nine plasmids contained genes encoding for mobilization. The largest contains four XerC/XerD-like binding sites and five Re27 regions. Alignment revealed that Re27 regions are variants of XerC/XerD-like sites. Besides blaNDM-1 and blaOXA-58, isolate XBB1 has an ESBL gene blaPER-1 and a few other genes conferring resistance to aminoglycosides, chloramphenicol, rifampicin, sulphonamides and tetracycline. blaOXA-58 is located in a Russian doll-type structure, as it is flanked by ISAba3, then by two copies of a newly identified element ISAjo2 and bracketed by a pair of Re27 regions. The intrinsic blaOXA of XBB1 is a new variant, blaOXA-311, which is most closely related to blaOXA-333 in an Australian A. johnsonii isolate. Conclusions: We present the first completely assembled genome sequence of A. johnsonii. The ability of A. johnsonii to harbour nine plasmids suggests this species could generate various platforms to mediate the dissemination of antimicrobial resistance.