Data Sheet 1_Bronchoalveolar lavage fluid and lung biopsy tissue metagenomic next-generation sequencing in the diagnosis of pulmonary cryptococcosis.xlsx

ObjectiveTo evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in pulmonary cryptococcosis (PC) using bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens.MethodsIn this retrospective study, 321 patients diagnosed with lower respiratory tract diseases who underwent mNGS using BALF and LBT samples, between January 2021 and December 2023 were included. Individuals were classified into PC and non-PC groups according to the diagnostic criteria for PC, and conventional fungal cultures were performed. A serum/BALF cryptococcal antigen (CrAg) test was performed in some patients with PC. The diagnostic efficiencies of three methods for PC (mNGS, conventional culture, and CrAg) were compared. Additionally, two mNGS methods were used in this study: original mNGS (OmNGS, testing time from January 2021 to December 2022) and modified mNGS (MmNGS, testing time from January to December 2023). The diagnostic efficiency of the two mNGS methods on PC was simultaneously compared.ResultsAmong the 321 patients, 23 (7.2%) had PC and 298 (92.8%) did not. Compared with the composite reference standard for PC diagnosis, the sensitivity, specificity, and accuracy of mNGS for PC were 78.3% (95% confidence interval [CI], 55.8%–91.7%), 98.7% (95% CI, 96.4%–99.6%), and 97.2% (95% CI, 94.7%–98.7%), respectively. The sensitivity of mNGS was similar to that of CrAg (80.0%, 12/15) (P > 0.05). The diagnostic sensitivity of both mNGS and CrAg was higher than that of conventional culture (35.0%, 7/20) (P = 0.006, P = 0.016), and the combined detection of mNGS and CrAg further improved the diagnostic sensitivity of PC (93.3%, 14/15). The area under the receiver operating characteristic curve of mNGS was superior to that of conventional culture (0.885 vs. 0.675). In addition, the diagnostic sensitivity of PC was higher than that of OmNGS (P = 0.046).ConclusionThe sensitivity of mNGS is better than that of conventional culture. The combination of mNGS and CrAg improves the testing sensitivity of Cryptococcus. MmNGS could further improve the detection of Cryptococcus. Conventional PC detection methods are indispensable and mNGS can be used as a rapid and accurate auxiliary diagnostic method for PC.

旨在评估利用支气管肺泡灌洗液（BALF）和肺活检组织样本，通过宏基因组下一代测序（mNGS）技术在肺隐球菌病（PC）诊断中的价值。研究方法：本项回顾性研究纳入了2021年1月至2023年12月期间，经mNGS技术检测支气管肺泡灌洗液（BALF）和肺活检组织（LBT）样本诊断为下呼吸道疾病的321位患者。根据肺隐球菌病的诊断标准，将患者分为PC组和非PC组，并进行了常规真菌培养。部分PC患者进行了血清/BALF隐球菌抗原（CrAg）检测。对比了三种PC诊断方法（mNGS、常规培养和CrAg）的诊断效率。此外，本研究中采用了两种mNGS方法：原始mNGS（OmNGS，检测时间从2021年1月至2022年12月）和改进mNGS（MmNGS，检测时间从2023年1月至12月）。同时比较了两种mNGS方法在PC诊断中的效率。研究结果：在321名患者中，23例（7.2%）患有PC，298例（92.8%）未患PC。与PC诊断的复合参考标准相比，mNGS对PC的诊断敏感性、特异性和准确性分别为78.3%（95%置信区间[CI]，55.8%–91.7%）、98.7%（95% CI，96.4%–99.6%）和97.2%（95% CI，94.7%–98.7%）。mNGS的敏感性与CrAg相似（80.0%，12/15）（P > 0.05）。mNGS和CrAg的诊断敏感性均高于常规培养（35.0%，7/20）（P = 0.006，P = 0.016），mNGS与CrAg的联合检测进一步提高了PC的诊断敏感性（93.3%，14/15）。mNGS的受试者工作特征曲线下面积优于常规培养（0.885 vs. 0.675）。此外，PC的诊断敏感性高于OmNGS（P = 0.046）。研究结论：mNGS的敏感性优于常规培养。mNGS与CrAg的结合提高了对隐球菌的检测敏感性。MmNGS可进一步提高隐球菌的检测能力。常规PC检测方法不可或缺，mNGS可作为PC的快速、准确辅助诊断方法。