Uncommon Pathogens in Common Presentations: Genetic Profiling and Virulence Determinants of Vibrio alginolyticus Isolated from a Case of External Otitis

<b>Backgrunod/Objectives</b>: Routine identification of common bacterial pathogens is typically efficient, utilizing standardized, cost-effective methods. However, the diagnostic process becomes significantly more complex when dealing with rare or unexpected microorganisms, especially as they can be considered colonizers in many cases. <b>Methods</b>: This study presents diagnostic details of an uncommon pathogen, <i>Vibrio alginolyticus</i>, isolated from auricular discharge in a patient with non-Hodgkin lymphoma diagnosed with persistent otitis externa and explores its identification through both conventional and modern laboratory approaches. Sequential ear discharge cultures resulted in phenotypically similar but genomically different <i>Vibrio alginolyticus</i> isolates. We complemented classical methods like conventional culture (on Columbia agar and CLED agar), Vitek2 Compact identification, and EUCAST disk diffusion antimicrobial susceptibility testing (following the EUCAST version 12.0 guidelines) with MALDI-TOF mass spectrometry and Illumina/Nanopore whole genome sequencing. Comparative analysis of the genomes was performed with the PeGAS pipeline, Unicycler, and 1928Diagnostics SNP analysis. <b>Results</b>: The Vitek2 analysis identified both isolates as <i>V. alginolyticus</i> with 99% confidence, and this was supported by the MALDI-TOF MS results. The first isolate (A) was fully susceptible to the antibiotics tested, while the second (B) showed resistance to ciprofloxacin. Whole genome sequencing revealed 99.23% and 98.60% nucleotide identity to the <i>V. alginolyticus</i> reference genome for isolates A and B, respectively, with a 99.8% match between them. Isolate B acquired a <i>gyrA</i> (c.1870C>T) mutation that correlates with the ciprofloxacin resistance (MIC > 0.5 mg/L). Both genomes carry <i>hlyA</i> (hemolysin), <i>toxR</i> (cholera toxin regulator), genes involved in biofilm formation (<i>rpoN</i>, <i>relA</i>, <i>spoT</i>, <i>opp</i>), <i>luxS</i> (motility), <i>proA</i>, <i>vacB</i> (virulence factors), and <i>tet(34)</i> (oxytetracycline resistance). A core genome SNP distance of <100 indicates clonal relatedness. Our integrated (phenotypic and genomic) diagnostic approach confirmed <i>V. alginolyticus</i> and documented host resistance evolution, with a virulence repertoire that could explain the clinical evolution. <b>Conclusions</b>: This case highlights the utility of molecular methods in confirming species identity, detecting resistance markers, characterizing virulence determinants, and differentiating a pathogen from a colonizer, supporting targeted clinical management.