Introduction

This study aimed to evaluate the utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus-infected patients.

Methods

We conducted a retrospective study. A total of 60 non-human immunodeficiency virus-infected PJP patients and 134 patients diagnosed with non-PJP pneumonia were included. P. jirovecii and other co-pathogens identified by mNGS in bronchoalveolar lavage fluid and/or blood samples were analyzed. Using clinical composite diagnosis as the reference standard, we compared the diagnostic performance of mNGS in PJP with conventional methods, including Gomori methenamine silver staining and serum (1,3)-β-d-glucan. Modifications of antimicrobial treatment for PJP patients after the report of mNGS results were also reviewed.

Results

mNGS reached a sensitivity of 100% in diagnosing PJP, which was remarkably higher than Gomori methenamine silver staining (25.0%) and serum (1,3)-β-d-glucan (67.4%). The specificity of mNGS (96.3%) significantly surpassed serum (1,3)-β-d-glucan (81.4%). Simultaneous mNGS of bronchoalveolar lavage fluid and blood samples was performed in 21 out of 60 PJP patients, and it showed a concordance rate of 100% in detecting P. jirovecii. Besides, mNGS showed good performance in identifying co-pathogens of PJP patients, among which cytomegalovirus and Epstein-Barr virus were most commonly seen. Initial antimicrobial treatment was modified in 71.7% of PJP patients after the report of mNGS results.

Conclusion

mNGS is a useful diagnostic tool with good performance for the diagnosis of PJP and the detection of co-pathogens. mNGS of bronchoalveolar lavage fluid and/or blood samples is suggested in patients with presumptive diagnosis of PJP. Blood samples may be a good alternative to bronchoalveolar lavage fluid for mNGS when bronchoscopic examination is not feasible.

中文翻译：

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宏基因组下一代测序在非 HIV 感染患者中诊断 Pneumocystis jirovecii 肺炎：一项回顾性研究

介绍

本研究旨在评估宏基因组下一代测序 (mNGS ) 在非人类免疫缺陷病毒感染患者中诊断耶氏肺孢子菌肺炎 (PJP)的效用。

方法

我们进行了一项回顾性研究。共纳入 60 例非人类免疫缺陷病毒感染的 PJP 患者和 134 例诊断为非 PJP 肺炎的患者。分析了由 mNGS 在支气管肺泡灌洗液和/或血液样本中鉴定的 P. jirovecii 和其他共病原体。我们以临床复合诊断为参考标准，比较了 mNGS 在 PJP 中的诊断性能与常规方法，包括 Gomori 甲胺银染色和血清 (1,3)-β- d-葡聚糖。还审查了在报告 mNGS 结果后对 PJP 患者的抗菌治疗的修改。

结果

mNGS 在诊断 PJP 方面的敏感性达到 100%，明显高于 Gomori 甲胺银染色 (25.0%) 和血清 (1,3)-β- d-葡聚糖 (67.4%)。mNGS (96.3%) 的特异性显着超过血清 (1,3)-β- d-葡聚糖 (81.4%)。对 60 名 PJP 患者中的 21 名进行了支气管肺泡灌洗液和血液样本的同时 mNGS，在检测P. jirovecii 方面显示出 100% 的一致性。此外，mNGS在鉴定PJP患者的共病原体方面表现出良好的性能，其中以巨细胞病毒和Epstein-Barr病毒最为常见。在报告 mNGS 结果后，71.7% 的 PJP 患者对初始抗菌治疗进行了修改。

结论

mNGS 是一种有用的诊断工具，在诊断 PJP 和检测共病原体方面具有良好的性能。对于推定为 PJP 的患者，建议对支气管肺泡灌洗液和/或血液样本进行 mNGS。当支气管镜检查不可行时，血液样本可能是用于 mNGS 的支气管肺泡灌洗液的良好替代品。