A case of Ustilago spp. infection identified by whole genome sequencing in a pediatric patient undergoing open-chest extracorporeal membrane oxygenation

• Published in: International journal of infectious diseases 2025-02, Vol.151, p.107320, Article 107320
• Main Authors: Fox, Valeria, Vrenna, Gianluca, Foglietta, Gianluca, Colagrossi, Luna, Lucignano, Barbara, Onori, Manuela, Cortazzo, Venere, Agosta, Marilena, Rossitto, Martina, Pereyra Boza, Maria del Carmen, Fini, Vanessa, Granaglia, Annarita, Paglietti, Maria Giovanna, Verrillo, Elisabetta, Cutrera, Renato, Bernaschi, Paola, Perno, Carlo Federico
• Format: Article
• Language: English
• Subjects: ECMO; MALDI TOF; Rare pathogen; Ustilago; WGS
• ISSN: 1201-9712; 1878-3511; 1878-3511
• DOI: 10.1016/j.ijid.2024.107320

•Standard diagnostic methods may underestimate the presence of rare fungal pathogens.•Pediatric patient on extracorporeal membrane oxygenation with fungal infection not identified by standard techniques.•Matrix-assisted laser desorption ionization-time of flight mass spectrometry databases did not allow an identification with reliable scores.•A fungus of the Ustilago genus, commonly found in the environment, was found by whole genome sequencing.•Identification allowed tailored treatment, leading to pathogen eradication. Patients undergoing extracorporeal membrane oxygenation (ECMO) are susceptible to fungal infections, also from rare or emerging pathogens. We present a case of a 3-year-old male patient hospitalized for respiratory failure and subjected to open-chest ECMO support, with a fungal infection from a pathogen not identifiable by standard methods. Although T2Candida panel (T2 Biosystems) resulted negative, blood cultures resulted positive for fungi after 4 days, confirmed by Gram staining. The fungus underwent typing using Bruker matrix-assisted laser desorption ionization-time of flight mass spectrometry system and Autobio Autof ms1000, which could not precisely identify the microorganism. Ultimately, whole genome sequencing (WGS) was performed directly on blood culture. WGS analysis revealed in 5 days the presence of a fungus belonging to the Ustilago genus, a group of fungi commonly found in the environment but rarely causing human diseases. To the best of our knowledge, we presented the first case of an Ustilago spp infection in a pediatric patient undergoing ECMO, not identified by standard techniques but only by WGS performed directly on a blood sample in 5 days. Despite the paucity of literature on Ustilago spp infections treatment, therapy adjustments led to the eradication of the pathogen, underscoring the importance of advanced molecular techniques for the correct and timely identification of these microorganisms.