Abstract
BackgroundMetagenomic next-generation sequencing (mNGS) is emerging as a promising technique for pathogens detection. However, reports on the application of mNGS in mixed pulmonary infection remain scarce.MethodsFrom July 2018 to March 2019, 55 cases were enrolled in this retrospective analysis. Cases were classified into mixed pulmonary infection (36 [65.5%]) and non-mixed pulmonary infection (19 [34.5%]) according to primary diagnoses. The performances of mNGS and conventional test on mixed pulmonary infection diagnosis and pathogen identification were compared.ResultsThe sensitivity of mNGS in mixed pulmonary infection diagnosis was much higher than that of conventional test (97.2% vs 13.9%; P < 0.01), but the specificity was the opposite (63.2% vs 94.7%; P = 0.07). The positive predictive value of mNGS was 83.3% (95% CI, 68.0–92.5%), and the negative predictive value was 92.3% (95% CI, 62.1–99.6%). A total of 5 (9.1%) cases were identified as mixed pulmonary infection by both conventional tests and mNGS, however, the pathogens identification results were consistent between these two methods in only 1 (1.8%) case. In summary, the pathogens detected by mNGS in 3 (5.5%) cases were consistent with those by conventional test, and only 1 (1.8%) case was mixed pulmonary infection. According to our data, mNGS had a broader spectrum for pathogen detection than conventional tests. In particular, application of mNGS improved the diagnosis of pulmonary fungal infections. Within the 55 cases, mNGS detected and identified fungi in 31 (56.4%) cases, of which only 10 (18.2%) cases were positive for the same fungi by conventional test. The most common pathogen detected by mNGS was Human cytomegalovirus in our study, which was identified in 19 (34.5%) cases of mixed pulmonary infection. Human cytomegalovirus and Pneumocystis jirovecii, which were detected in 7 (12.7%) cases, were the most common co-pathogens in the group of mixed pulmonary infection.ConclusionsmNGS is a promising technique to detect co-pathogens in mixed pulmonary infection, with potential benefits in speed and sensitivity.Trial registration(retrospectively registered): ChiCTR1900023727. Registrated 9 JUNE 2019.
Highlights
Metagenomic next-generation sequencing is emerging as a promising technique for pathogens detection
Specimen collection and processing Pulmonary biopsy and bronchoalveolar lavage fluid (BALF) of patients with suspected pulmonary infection in Tianjin Medical University General Hospital were collected by bronchoscopy according to standard procedures. 3 to 5 lung biopsy specimens were taken from every patient to meet the needs of pathology and pathogen examination
Patient characteristics and Metagenomic next-generation sequencing (mNGS) results A total of 55 patients were enrolled, including 31 males and 24 females, with an average age of 45 years (11–74 years)
Summary
Metagenomic next-generation sequencing (mNGS) is emerging as a promising technique for pathogens detection. Reports on the application of mNGS in mixed pulmonary infection remain scarce. Mixed pulmonary infection was defined when two or more infectious pathogens were indentified. Wang et al BMC Pulmonary Medicine (2019) 19:252 microbiological testing are manifold, including metagenomic NGS (mNGS), which allows for an unbiased detection of pathogens [5]. When applied to clinical practice, Qing Miao et al reported that the sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7 and 85.7% respectively. MNGS could offer an improved detection of pulmonary infectious pathogens in lung biopsy tissues, with potential benefits in speed and sensitivity [7]. Reports on the use of mNGS in mixed pulmonary infection remain scarce. Most studies on mNGS focused on the diagnosis of single infection
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