Diagnostic yield and impact of internal transcribed spacer sequencing from clinical specimens on antifungal management in patients with suspected fungal infection.

Internal transcribed spacer (ITS) sequencing has been increasingly used for the diagnosis of fungal infection. However, data on its real-world clinical utility are limited. We retrospectively evaluated the diagnostic yield from direct clinical specimens using the final diagnosis as the gold standard, and studied the impact of ITS sequencing on antifungal management in a university hospital with an unrestricted order setting. A total of 315 specimens were collected from 227 patients between November 2023 and April 2024. Of these, 59 (18.7%) were from fungal infection cases. ITS sequencing demonstrated a sensitivity of 35.6% and specificity of 96.9%. Agreement with fungal culture was 79.7% (κ = 0.583). In our setting, the median turnaround time of the positive results was 12 (12-14) days. ITS sequencing altered clinical management in only 2 patients (0.9%). The culture-negative but ITS sequencing-positive specimens mostly represented colonizers from bronchoalveolar lavage fluid. In an unrestricted setting, ITS sequencing showed low sensitivity and minimal impact on clinical decision-making. To maximize diagnostic benefit and utility, implementation of diagnostic stewardship is necessary. IMPORTANCE: This study provides a real-life evaluation of internal transcribed spacer (ITS) sequencing in an unrestricted clinical setting. We demonstrated fair sensitivity and minimal impact on antifungal alteration. We identified critical implementation barriers, including prolonged turnaround times and the frequent detection of colonizers, which fail to guide acute decision-making. These findings are vital for informing hospital policy and advocating for strict diagnostic stewardship to maximize clinical benefit.