Detection and identification of fungi in bronchoalveolar lavage fluid from immunocompromised patients using panfungal PCR

Context.— Direct visualization of Pneumocystis jiroveci organisms, using Gomori methenamine silver (GMS) staining in bronchoalveolar lavage fluid (BAL), is a historical gold standard that has been widely used for the diagnosis of P jiroveci pneumonia (PJP). However, the stain may be less sensitive in human immunodeficiency virus (HIV)–negative immunocompromised patients owing to a lower burden of organisms. Objectives.— To assess the sensitivity of the GMS stain on BAL fluid for the diagnosis of PJP in HIV-negative immunocompromised patients as compared to HIV-positive patients. Design.— We conducted a retrospective review from 2012 to 2018 to identify immunocompromised patients (≥18 years old) who underwent bronchoscopy with BAL GMS staining for the diagnosis of PJP. To assess for sensitivity, we sought to identify BAL GMS-positive cases and BAL GMS-negative cases of PJP. The BAL GMS-negative cases were categorized into proven and probable PJP. Results.— We identified 45 adult immunocompromised patients with proven and probable PJP, including 24 HIV-negative (11 BAL GMS-positive and 13 BAL GMS-negative) and 21 HIV-positive cases (all were BAL GMS-positive). The sensitivity of BAL GMS for the diagnosis of PJP in HIV-negative immunocompromised patients was 11 of 24 (46%) versus 21 of 21 (100%) in HIV-positive patients (CD4: median, 10 cells/mL; range, 3–300 cells/mL). Delayed or missed diagnoses were seen in 3 cases of BAL GMS-negative PJP. Re-examination of BAL GMS slides showed rare P jiroveci cysts in 1 case. Conclusions.— BAL GMS has poor sensitivity for PJP in HIV-negative immunocompromised patients. Using BAL GMS as a sole method for PJP may result in missed or delayed diagnoses in this population.

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Diagnostic Value of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid for the Diagnosis of Suspected Pneumonia in Immunocompromised Patients

10.21203/rs.3.rs-1201244/v1 ◽

2022 ◽

Author(s):

Pengcheng Lin ◽

Yi Chen ◽

Shanshan Su ◽

Wengang Nan ◽

Lingping Zhou ◽

...

Keyword(s):

Next Generation Sequencing ◽

Diagnostic Accuracy ◽

Bronchoalveolar Lavage ◽

Detection Rate ◽

Bronchoalveolar Lavage Fluid ◽

Lavage Fluid ◽

Diagnostic Value ◽

Immunocompromised Patients ◽

Suspected Pneumonia ◽

Generation Sequencing

Abstract Background: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in immunocompromised patients for the diagnosis of suspected pneumonia in comparation to that of conventional microbiological tests (CMTs).Methods: Sixty-nine immunocompromised patients with suspected pneumonia received both CMTs and mNGS of BALF were analyzed retrospectively. The diagnostic value was compared between CMTs and mNGS, using the clinical composite diagnosis as the reference standard. Results: Sixty patients were diagnosed of pneumonia including fifty-two patients with identified pathogens and eight patients with probable pathogens. The overall detection rate of mNGS for pathogens were higher than that of CMTs. However, a comparable diagnostic accuracy of mNGS and CMTs were found for bacterial and viral infections. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs (78% vs. 54%, P＜0.05), which mainly because of the high sensitivity of mNGS in patients with Pneumocystis jirovecii pneumonia (PJP) (100% vs. 28%, P＜0.05). Among fifty-two patients with definite pathogens, nineteen patients (37%) were identified as pulmonary mixed infection, mNGS test showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in mixed infection. Moreover, Pneumocystis jirovecii was the most common pathogen in mix infection and mNGS have identified much more co-pathogens of PJP than CMTs.Conclusions: mNGS of BALF improved the microbial detection rate of pathogens and exhibited remarkable advantages in detecting PJP and identifying mixed infections in immunocompromised patients.

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