Dataset Information

Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study.

ABSTRACT: Background: We conducted this retrospective study to reveal the accuracy of metagenomic next-generation sequencing (mNGS) for diagnosing osteoarticular infections from fresh abscess specimens obtained from patients in an HIV-naive population. Methods: We retrospectively analyzed hospital records at three participating TB-specialized hospitals for patients admitted with suggestive diagnoses of osteoarticular tuberculosis between January 2018 and August 2019. Abscess specimens obtained from each patient were tested via pathogen culture, GeneXpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF), and mNGS assay. Results: A total of 82 abscess samples were collected from patients with osteoarticular infections, including 53 cases with (64.6%) bacterial, 21 (25.6%) with mycobacterial, 7 (8.5%) with fungal, and 1 (1.2%) with actinomycetal organisms detected. Analysis of mNGS assay results identified potential pathogens in all cases, with M. tuberculosis complex (MTBC) most frequently isolated, followed by Staphylococcus aureus and Brucella melitensis. Conventional culture testing identified causative pathogens in only 48.4% of samples, a significantly lower rate than the mNGS pathogen identification rate (100%, p < 0.01). Culture-positive group specimens yielded significantly greater numbers of sequence reads than did culture-negative group specimens (p < 0.01). Of patients receiving surgical interventions and mNGS-guided treatment, 76 (92.7%) experienced favorable outcomes by the time of follow-up assessment at 3 months post-treatment. Notably, MTBC detection in two patients experiencing treatment failure suggests that they had mixed infections with MTBC and other pathogens. Conclusion: Results presented here demonstrate that mNGS has a greater pathogen detection rate in osteoarticular infections than conventional culture-based methods.

SUBMITTER: Zhao M

PROVIDER: S-EPMC7523410 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study.

Zhao Mingwei M Tang Kai K Liu Fengsheng F Zhou Weidong W Fan Jun J Yan Guangxuan G Qin Shibing S Pang Yu Y

Frontiers in microbiology 20200915

<b>Background</b>: We conducted this retrospective study to reveal the accuracy of metagenomic next-generation sequencing (mNGS) for diagnosing osteoarticular infections from fresh abscess specimens obtained from patients in an HIV-naive population. <b>Methods</b>: We retrospectively analyzed hospital records at three participating TB-specialized hospitals for patients admitted with suggestive diagnoses of osteoarticular tuberculosis between January 2018 and August 2019. Abscess specimens obtain ...[more]

PMID: 33042033

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Project description: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.

Project description:BackgroundMetagenomic next-generation sequencing (mNGS) technology has been widely used to diagnose various infections. Based on the most common pathogen profiles, targeted mNGS (tNGS) using multiplex PCR has been developed to detect pathogens with predesigned primers in the panel, significantly improving sensitivity and reducing economic burden on patients. However, there are few studies on summarizing pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China on large scale.MethodsFrom January 2021 to December 2023, bronchoalveolar lavage fluid (BALF) or sputum samples from 546 immunocompetent and immunocompromised patients with suspected community-acquired pneumonia were collected. Pathogen profiles in those patients on whom mNGS was performed were summarized. Additionally, we also evaluated the performance of tNGS in diagnosing pulmonary infections.ResultsCombined with results of mNGS and culture, we found that the most common bacterial pathogens were Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii in both immunocompromised and immunocompetent patients with high detection rates of Staphylococcus aureus and Enterococcus faecium, respectively. For fungal pathogens, Pneumocystis jirovecii was commonly detected in patients, while fungal infections in immunocompetent patients were mainly caused by Candida albicans. Most of viral infections in patients were caused by Human betaherpesvirus 5 and Human gammaherpesvirus 4. It is worth noting that, compared with immunocompetent patients (34.9%, 76/218), more mixed infections were found in immunocompromised patients (37.8%, 14/37). Additionally, taking final comprehensive clinical diagnoses as reference standard, total coincidence rate of BALF tNGS (81.4%, 48/59) was much higher than that of BALF mNGS (40.0%, 112/280).ConclusionsOur findings supplemented and classified the pathogen profiles of pulmonary infections in immunocompetent and immunocompromised patients in Jilin Province of China. Most importantly, our findings can accelerate the development and design of tNGS specifically used for regional pulmonary infections.

Dataset Information

Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study.

Publications

Metagenomic Next-Generation Sequencing Improves Diagnosis of Osteoarticular Infections From Abscess Specimens: A Multicenter Retrospective Study.

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