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

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 bla(OXA) genes were performed using Harvest and MEGA. The context of bla(OXA-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 bla(NDM-1) and bla(OXA-58), isolate XBB1 has an ESBL gene bla(PER-1) and a few other genes conferring resistance to aminoglycosides, chloramphenicol, rifampicin, sulphonamides and tetracycline. bla(OXA-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 bla(OXA) of XBB1 is a new variant, bla(OXA-311), which is most closely related to bla(OXA-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.