Genomic features of a carbapenem-resistant OXA-219-positive Acinetobacter baumannii of international ST15 (CC15) from a patient with community-onset urinary tract infection in Chilean Patagonia

Abstract Background Carbapenemase-producing Acinetobacter baumannii has been recognized as a critical priority pathogen by the World Health Organization (WHO). Objective We hereby report the identification and the draft genome sequence of a carbapenem-resistant A. baumannii isolated from a patient with community-onset urinary tract infection, in a Chilean Patagonian city. Methods The whole genome was sequenced on an Illumina NextSeq platform and de novo assembled using Unicycler v.0.4. Resistome analysis and epidemiological investigation (based on MLST data and Pasteur scheme) were performed using bioinformatics tools available from Center for Genomic Epidemiology. Results The genome size was calculated at 3,890,824 bp, with a GC content of 39.1%, and comprising 3,864 total genes, 30 tRNAs, 3 rRNAs, 4 ncRNAs, and 109 pseudogenes. Carbapenem-resistant A. baumannii Ab3_Ch strain belonged to the international sequence type ST15 (clonal complex, CC15), and harboured the ISAba-1-blaOXA-219 gene array, along to blaTEM-1B and blaADC-6 β-lactamase genes, and aac(3)-IIa and aph(3’)-VIa aminoglycoside resistance genes. Additionally, efflux pump encoding genes (abaF, abaQ, abeS, adeI, adeK, adeL, adeN, adeR, adeS, and amvA) were identified, and mutations in the quinolone resistance-determining region (QRDR) of gyrA (Ser81Leu) and parC (Ser84Leu) were considered responsible for fluoroquinolone resistance. Conclusion This genome sequence data could be used for comparative genomic studies of critical priority A. baumannii strains, as well as to understand the specific features of hospital-associated A. baumannii lineages of international clonal complexes emerging in community settings.