Sequencing and Characterization of NDM-1 and ORN-1 -Producing Multi-drug resistant Raoultella ornithinolytica Clinical Isolate from China

Abstract Background Raoultella ornithinolytica poses an urgent threat in antimicrobial resistance threat due to its global emergence, associated high mortality rates, and persistent transmissions. Nevertheless, the resistance and infectivity mechanism, as well as genomic epidemiology, remain poorly understood at present. To elucidate the antibiotic resistance and infectivity mechanisms of R. ornithinolytica, whole genome sequencing was performed on a multi-drug-resistance strain, R. ornithinolytica B1645-1B, isolated from an inpatient. Methods The genome sequence was completed using Illumina Hiseq 4000 and Pacbio RSII procedures. Phylogenetic genomic analysis, combined with a geographical region, isolation source, and host information. The conjugation transfer experiment were performed using the mating-out assay in the intestine of mice. Results The isolate B1645-1B was resistant to five major classes of antibacterial agents including β-lactams, aminoglycosides, chloramphenicols, sulfonamides, and quinolones, but sensitive to tetracyclines. A close phylogenetic relationship was identified between B1645-1B, isolated from blood, and R. ornithinolytica NCTC9164, isolated from pus of the nose, in United Kingdom. A chromosome, designated as chromosome 01, was identified. The annotated chromosomal genome contained 127 genes that were potentially involved in virulence, disease and defense. The isolate B1645-1B contained chromosome-encoded β-lactamase blaORN-1, and plasmid-encoded metallo-β-lactamase blaNDM-1, respectively. A resistance region, designated B1645-1B-RR, carrying the β-lactamase blaORN-1 gene on the chromosome, was identified. The prophage analysis revealed that chromosome 01 contained three intact prophages. The occurrence of the blaORN-1 gene might transfer from R. ornithinolytica B1645-1B to Escherichia coli B1645-1B1 and Klebsiella pneumoniae B1645-1B11 in mice. Conclusions The genomic analysis of R. ornithinolytica B1645-1B partially elucidated its antibiotic resistance mechanisms and virulence factors. Patients at high risk for drug-resistant R. ornithinolytica might require novel therapeutic strategies.