Dataset Information

Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections.

ABSTRACT: Objectives: To evaluate metagenomic next-generation sequencing (mNGS) as a diagnostic tool in detecting pathogens from osteoarticular infection (OAI) samples. Methods: 130 samples of joint fluid, sonicate fluid, and tissue were prospectively collected from 92 patients with OAI. The performance of mNGS and microbiology culture was compared pairwise. Results: The overall sensitivity of mNGS was 88.5% (115/130), significantly higher than that of microbiological culture, which had a sensitivity of 69.2% (90/130, p < 0.01). Sensitivity was significantly higher for joint fluid (mNGS: 86.7% vs. microbiology culture: 68.7%, p < 0.01) and sonicate fluid (mNGS: 100% vs. microbiology culture: 66.7%, p < 0.05) samples. mNGS detected 12 pathogenic strains undetected by microbiological culture. Additional pathogens detected by mNGS were Coagulase-negative Staphylococci, Gram-negative Bacillus, Streptococci, Anaerobe, non-tuberculosis mycobacterium, MTCP (p > 0.05), and Mycoplasma (OR = ?, 95% confidence interval, 5.12-?, p < 0.001). Additionally, sensitivity by mNGS was higher in antibiotic-treated samples compared to microbiological culture (89.7 vs. 61.5%, p < 0.01). Conclusions: mNGS is a robust diagnostic tool for pathogenic detection in samples from OAI patients, compared to routine cultures. The mNGS technique is particularly valuable to diagnose pathogens that are difficult to be cultured, or to test samples from patients previously treated with antibiotics.

SUBMITTER: Huang ZD

PROVIDER: S-EPMC7527540 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections.

Huang Zi-da ZD Zhang Zi-Jie ZJ Yang Bin B Li Wen-Bo WB Zhang Chong-Jing CJ Fang Xin-Yu XY Zhang Chao-Fan CF Zhang Wen-Ming WM Lin Jian-Hua JH

Frontiers in cellular and infection microbiology 20200917

Objectives: To evaluate metagenomic next-generation sequencing (mNGS) as a diagnostic tool in detecting pathogens from osteoarticular infection (OAI) samples. Methods: 130 samples of joint fluid, sonicate fluid, and tissue were prospectively collected from 92 patients with OAI. The performance of mNGS and microbiology culture was compared pairwise. Results: The overall sensitivity of mNGS was 88.5% (115/130), significantly higher than that of microbiological culture, which h ...[more]

PMID: 33042860

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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.

Project description:IntroductionMetagenomic next-generation sequencing (mNGS) assay for detecting infectious agents is now in the stage of being translated into clinical practice. With no approved approaches or guidelines available, laboratories adopt customized mNGS assays to detect clinical samples. However, the accuracy, reliability, and problems of these routinely implemented assays are not clear.ObjectivesTo evaluate the performance of 90 mNGS laboratories under routine testing conditions through analyzing identical samples.MethodsEleven microbial communities were generated using 15 quantitative microbial suspensions. They were used as reference materials to evaluate the false negatives and false positives of participating mNGS protocols, as well as the ability to distinguish genetically similar organisms and to identify true pathogens from other microbes based on fictitious case reports.ResultsHigh interlaboratory variability was found in the identification and the quantitative reads per million reads (RPM) values of each microbe in the samples, especially when testing microbes present at low concentrations (1 × 103 cell/ml or less). 42.2% (38/90) of the laboratories reported unexpected microbes (i.e. false positive problem). Only 56.7% (51/90) to 83.3% (75/90) of the laboratories showed a sufficient ability to obtain clear etiological diagnoses for three simulated cases combined with patient information. The analysis of the performance of mNGS in distinguishing genetically similar organisms in three samples revealed that only 56.6% to 63.0% of the laboratories recovered RPM ratios (RPM S. aureus /RPM S. epidermidis ) within the range of a 2-fold change of the initial input ratios (indicating a relatively low level of bias).ConclusionThe high interlaboratory variability found in both identifying microbes and distinguishing true pathogens emphasizes the urgent need for improving the accuracy and comparability of the results generated across different mNGS laboratories, especially in the detection of low-microbial-biomass samples.

Dataset Information

Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections.

Publications

Pathogenic Detection by Metagenomic Next-Generation Sequencing in Osteoarticular Infections.

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