Comparative Genomic Characterization of a Megaplasmid-harboring Multidrug-Resistant Raoultella ornithinolytica from a Septic Diabetic Patient in Uganda.

Raoultella ornithinolytica is an emerging Gram-negative pathogen implicated in nosocomial infections. However, it remains understudied, especially in low-resource regions, including East Africa. Here, we sought to unravel genomic virulence and antimicrobial resistance (AMR) profiles of a strain (RSM7096), isolated from a Ugandan patient with sepsis and diabetes mellitus. We combined antimicrobial susceptibility testing (AST) based on CLSI M100, 2022, with minimum inhibitory concentration (MIC) to determine its susceptibility/resistance to 16 antibiotics. Then we sequenced its genome (Illumina NovaSeq 6000) and performed multiple bioinformatic analyses to establish its clinical relevance. The BD Phoenix™ system classified the isolate as ESBL phenotype (code 1505), consistent with the presence of blaCTX-M-15, blaTEM-1B and blaOXA-1. The isolate was susceptible to imipenem, gentamicin, tigecycline, levofloxacin, and colistin but resistant to 11 antibiotics, including ceftriaxone and piperacillin/tazobactam used for treatment. Using PathogenFinder, the strain was predicted as a human pathogen (97.63% confidence). Virulence profiling revealed siderophore gene clusters for yersiniabactin and enterobactin, as well as capsular (type KL115) and O-antigen (OL2α.3; serotype O2αγ) loci, suggesting potential immune evasion capacity based on genomic predictions. Further, our detailed genomic analysis enabled us to reconstruct a megaplasmid (pRSM7096p5), which harbored 10 AMR genes, including blaCTX-M-15, blaTEM-1B, and blaOXA-1, responsible for the ESBL phenotype. The megaplasmid also harbors multiple mobile genetic elements, including the transposon Tn3 and insertion sequence ISec9 (ISec9), which are associated with high rates of interspecies horizontal antimicrobial resistance gene transfer. Our results demonstrate that Raoultella ornithinolytica poses a significant health risk, especially to patients with comorbidities. We advocated for rigorous surveillance to monitor and mitigate its impact, particularly in low-resource healthcare settings.