Molecular identification and diagnostic challenges of Kodamaea ohmeri fungemia in a neonate - first report from Pakistan

Abstract

Background and Objectives: Kodamaea ohmeri is an uncommon opportunistic yeast increasingly recognized as a cause of invasive infections, particularly in immunocompromised individuals and neonates. We report the first case of Kodamaea ohmeri fungemia in a neonate from Pakistan, highlighting the diagnostic challenges posed by its close resemblance to more common Candida species.
Materials and Methods: A one-month-old female neonate with suspected fungal sepsis yielded a yeast isolate. Initial identification was performed using API 20C AUX, followed by colony morphology assessment on Sabouraud Dextrose Agar. Molecular investigations included PCR amplification of the ITS1–5.8S rRNA–ITS2 region, restriction fragment length polymorphism (RFLP) with MspI, and definitive Sanger sequencing. Antifungal susceptibility testing was conducted using standard methods.
Results: The isolate was initially misidentified as Candida guilliermondii by API 20C AUX. Colony characteristics suggested an unusual yeast, prompting molecular analysis. PCR produced a ~400 bp amplicon, and RFLP yielded an undigested band, initially suggestive of Candida auris or Candida haemulonii. Sanger sequencing confirmed the organism as K. ohmeri with 99.8% identity. Antifungal testing showed low minimum inhibitory concentrations (MICs) for echinocandins and azoles, while fluconazole demonstrated a higher MIC.
Conclusion: This case emphasizes the limitations of conventional methods in identifying rare fungal pathogens, the critical role of molecular confirmation, and the importance of antifungal stewardship in guiding treatment. Reporting such cases contributes to global awareness, surveillance, and improved management of emerging yeast infections.