The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients

• Published in: Frontiers in cellular and infection microbiology Vol. 12; p. 1026739
• Main Authors: Zhao, Mengyi, Yue, Ruiming, Wu, Xiaoxiao, Gao, Zhan, He, Miao, Pan, Lingai
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 27.10.2022
• Subjects: Cellular and Infection Microbiology; High-Throughput Nucleotide Sequencing; Humans; immunocompromised; Immunocompromised Host; infection; metagenomic next-generation sequencing (mNGS); Methenamine - therapeutic use; Pneumocystis carinii - genetics; Pneumocystis jirovecii (P. jirovecii); Pneumonia, Pneumocystis - diagnosis; Pneumonia, Pneumocystis - drug therapy; Pneumonia, Pneumocystis - microbiology; transplantation; metagenomic next-generation sequencing (mNGS); infection; Pneumocystis jirovecii (P. jirovecii); immunocompromised; transplantation
• ISSN: 2235-2988; 2235-2988
• DOI: 10.3389/fcimb.2022.1026739

pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring. 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People's Hospital. The clinical performances of mNGS for infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods. We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days . 23days, =0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L .79.56mg/L, =0.016), lactate dehydrogenase (696U/l . 494U/l, =0.030) and procalcitonin (0.09ng/ml . 0.59ng/ml, =0.028) was also statistically significant between the two groups. An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.