Elizabethkingia bruuniana strain Mich-4: molecular identification, genome analysis, resistome characterization, and virulence profiling

Introduction Elizabethkingia bruuniana is an emerging opportunistic pathogen associated with severe human infections, yet its genomic diversity, antimicrobial resistance mechanisms, and virulence-associated traits remain poorly understood. Methods Here, we performed phenotypic characterization and comparative genomic analyses of E. bruuniana strain Mich-4, isolated from the upper respiratory tract of a patient in Michigan. Results MALDI-TOF MS misidentified the isolate as E. meningoseptica , whereas genome-based analyses using GTDB-Tk, average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and phylogenomics classified it as E. bruuniana . Comparative analysis of 12 E. bruuniana genomes revealed an open pan-genome comprising 6,301 gene clusters, including 3,062 core genes. Analysis based on Heaps’ law indicated substantial genomic plasticity. Further analysis of 47 representative Elizabethkingia genomes identified lineage-specific patterns of antimicrobial resistance and virulence-associated genes. Antimicrobial susceptibility testing showed that Mich-4 exhibited multidrug resistance but remained susceptible to trimethoprim-sulfamethoxazole and ciprofloxacin. Genomic analysis identified conserved intrinsic β-lactamase genes ( blaB , blaGOB , and blaCME ) together with determinants associated with aminoglycoside and chloramphenicol resistance, consistent with the observed β-lactam-resistant phenotype. Comparative analyses also demonstrated widespread conservation of genes involved in oxidative stress resistance, adhesion, capsule formation, lipopolysaccharide biosynthesis, metabolic adaptation, and urease production. A type VI secretion system subtype III (T6SSiii) and conserved ICEEa-like type B conjugative transfer loci were identified in most E. bruuniana genomes. Conclusion Collectively, this study provides a comparative genomic framework for understanding the evolution, antimicrobial resistance, and virulence-associated traits of E. bruuniana , while improving species identification and expanding genomic resources for future epidemiological and functional studies.