Identification of Ustilago spp infection in a paediatric patient undergoing open-chest extracorporeal membrane oxygenation (ECMO) through Whole Genome Sequencing

Introduction: Immunocompromised patients, particularly those undergoing extracorporeal membrane oxygenation (ECMO), are susceptible to nosocomial infections, including fungal diseases. While Candida and Aspergillus species are commonly implicated, other fungal pathogens are emerging. We present a case of a 3-year-old male, born preterm, with history of pulmonary hypertension, and bronchopulmonary dysplasia, who was hospitalized for respiratory failure during influenza A and RSV infection and required open-chest ECMO support. Due to radiological worsening and high risk of fungal infection, tests for identification of these microorganisms were requested. After standard methods and molecular techniques failed to identify the cause of infection, Whole Genome Sequencing (WGS) revealed the presence of a fungus belonging to the Ustilago genus, a group of fungi commonly found in the environment, but rarely causing human diseases. Materials and Methods: Whole blood samples and blood cultures were sent to our laboratory, and the latter were used for T2Candida panel (T2 Biosystems). Blood cultures resulted positive after 4 days and positivity for fungi was confirmed by Gram staining. The blood cultures were then plated on agar media and the microorganism was isolated from blood agar and Sabouraud dextrose agar. The fungus underwent typing using Bruker MALDI-TOF MS System and Autobio Autof ms1000. WGS was finally performed on both blood and suspension samples. Results: Although the T2Candida panel returned negative, empirical antifungal treatment with caspofungin was started due to positive findings from blood cultures. No identification was obtained by mass spectrometry. Notably, the fungus exhibited a mucoid phenotype on Sabouraud dextrose agar. Despite caspofungin treatment, there was no improvement in the patient's conditions. Finally, WGS analysis, coupled with phylogenetic analysis based on Universal Fungal Core Genes, identified the presence of a species belonging to Ustilago genus. Despite the paucity of literature describing treatments for Ustilago spp infections, adjustements to therapy, including the addition of ambisome and voriconazole, led to a positive response and eradication of the Ustilago spp. Discussion and Conclusions: This case underscores the importance of correct identification of fungal infections in immunocompromised patients and emphasizes the need for research addressing emerging fungal pathogens. It also highlights the importance of advanced molecular techniques like WGS in the identification of these microorganisms, allowing for correct diagnosis and improved patient care. Moreover, following WGS identification, we acquired the mass spectrometry spectrum in order to allow future identification of this pathogen.