The unprecedented surge of antimicrobial resistance (AMR) in bacteria is a major global threat to public health. One of the clinically critical AMR organisms is a Gram-negative Pseudomonas aeruginosa bacterium. This leading opportunistic pathogen exhibits a multitude of virulence factors and is extraordinarily resistant to a gamut of clinically significant antibiotics. In this study, the genome of an extremely resistant P. aeruginosa CDN118 isolated from a bacteremia patient was analyzed. We hypothesize that CDN118 acquired the resistant factors via horizontal gene transfer. The DNA sequence was generated using a hybrid of Illumina and PacBio platforms, and a novel approach to sequence assembly generated one single complete genome of 6.8 Mbp. Annotations of the genome using two platforms, RAST and Prokka, were manually combined and curated. Comparative analysis of CDN118 genome with two prototypic sequenced genomes of PAO1 and PA14 showed the presence of a novel 1.1 Mbp inversion. The sequencing of the junctions of the chromosomal inversion reconfirmed its presence and uniqueness. The inversion is flanked by duplicated genomic islands (GIs) containing resistant determinates for aminoglycosides, spectinomycin, streptomycin, trimethoprim, bicyclomycin, β -lactams, sulfonamide, mercury, and tetracycline. Analyses using seven GI prediction tools followed by manual curation identified a total 52 GIs in the CDN118 genome. Four of these GIs harbor genes that confer resistance to quinolones, carbapenems, cephalosporins, fluoroquinolones, monobactams, and polymyxins. Overall, CDN118 genome harbors the genetic determinants to be extremely resistant to antibiotics.
