Clinical Value of Metagenomic Next‐Generation Sequencing Versus Conventional Methods in Diagnosing Cryptococcal Infection After Kidney Transplantation

The aim of this study is to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) for cryptococcal infection after kidney transplantation by comparing its positivity rate, turnaround time, and impact on clinical decision-making with those of conventional diagnostic methods, including India ink staining, culture, and capsular antigen testing.

This retrospective study included 16 kidney transplant recipients diagnosed with cryptococcal infection between January 2017 and July 2025. Among them, 11 had isolated pulmonary infection, 1 had isolated central nervous system (CNS) infection, and 4 had combined pulmonary and CNS involvement. Cerebrospinal fluid and bronchoalveolar lavage fluid samples were analyzed using mNGS and conventional assays. Positivity rates, sensitivity, specificity, and turnaround times were compared using McNemar's exact test for paired data. Confidence intervals (CIs) at 95% were calculated using the Clopper‐Pearson method.

The overall mNGS positivity rate was 93.8% (15/16, 95% CI: 69.8%–99.8%), exceeding the 62.5% (10/16, 95% CI: 35.4%–84.8%) achieved using conventional methods (paired difference, 31.3%; 95% CI: 4.1%–54.6%; McNemar's exact test, p = 0.031). The median turnaround time was significantly shorter for mNGS than for fungal culture (24 vs. 120 h, p < 0.001). In the CNS infection subgroup, mNGS was positive in 4 of 5 cases (80.0%), compared with four of five cases (80.0%) using conventional testing. In the pulmonary infection subgroup, mNGS detected all 15 cases (100%), whereas conventional methods identified 9 of 15 (60.0%). Six patients who tested negative using all conventional methods were diagnosed using mNGS, and all patients received targeted antifungal therapy guided by mNGS results.

In this small exploratory study, mNGS was associated with a higher early detection rate than conventional methods. In six patients with negative results across all conventional tests, mNGS results directly guided antifungal therapy. These findings suggest that mNGS plays an important role in diagnosing cryptococcal infection after kidney transplantation, particularly when conventional tests are negative.