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

Abstract

BackgroundPneumocystis jirovecii 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 Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring.Method34 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 P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods.ResultsWe 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 P. jirovecii 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 P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups.ConclusionsAn 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 P. jirovecii 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.

Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia

“…Since Pneumocystis cannot be cultured, in this study, all patients infected with P. jirovecii were diagnosed by mNGS. Our study demonstrated that mNGS could quickly and accurately diagnose P. jirovecii pneumonia, which was also approved by other reseachers (Liu et al, 2021;Lu X. et al, 2022;Sun et al, 2022;Wang et al, 2022;Zhao et al, 2022). A combination of clinical symptoms, laboratory testing, and imaging examination is suggested to make a comprehensive judgment along with the mNGS test.…”

Diagnostic performance of metagenomic next-generation sequencing for Pneumocystis jirovecii pneumonia

“…The clinical manifestations of PJP are not specific, and definite diagnosis requires direct test of pathogens in lung tissues or lower respiratory secretions [1,21]. Currently, diagnosis of PJP relies on the detection of pathogenic microorganisms from induced sputum and/or BALF by cytological staining, quantitative PCR, or immunofluorescence [22].…”

Diagnosis of invasive fungal infections: challenges and recent developments

“…Based on the results, the team has advocated the need to add PCP prophylaxis to the Diagnosis and Treatment Guideline of IFIs in Solid Organ Transplant Recipients in China. There have been other studies as well that have reported the successful use of mNGS to diagnose pulmonary infections involving P. jirovecii [ 177 , 185 – 187 ], highlighting the inadequate sensitivity of microscopic examination of samples and serum BDG assay for diagnosing PCP.…”