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

Lin, Tianlai; Zhao, Jiangman; Huang, Ling; Dai, Xiaodong; Chen, Xiaoling; Xu, Yue; Li, Wushuang; Wang, Yaoyao; Lou, Jingwei; Wu, Shouxin; Zhang, Hongling

doi:10.3389/fcimb.2023.1136588

Cited by 6 publications

(4 citation statements)

References 39 publications

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“…Compared to BALF, sputum affected by open oral environment has complex microbiota. In Tianlai Lin’s study, 21 based on 83 BALF, 89 blood and 33 sputum samples of 205 CAP patients from ICU, the top 3 common bacteria detected by mNGS were Escherichia coli, Mycobacterium tuberculosis and K. pneumoniae , followed by C. striatum and A. baumannii . However, in our study, based on sputum of 180 pneumonia patients from ICU, the top 3 common bacteria detected by mNGS were C. striatum, A. baumannii and Pseudomonas aeruginosa , followed by K. pneumoniae and S. pneumoniae .…”

Section: Discussionmentioning

confidence: 99%

“…For the residual microorganisms, we developed a set of requirements for a positive mNGS result based on prior research. 21 Bacteria (mycobacteria excluded): ≥50 reads mapped to pathogen species and with a reads number no less than 10 times of any other microorganism, 17 or supported by CMT results. 15 Fungus/mycoplasma/chlamydia/virus: the reads mapped to pathogen species with a reads no less than five times of any other fungus, 17 or supported by CMT results.…”

Section: Methodsmentioning

confidence: 99%

“…For the residual microorganisms, we developed a set of requirements for a positive mNGS result based on prior research. 21 1. Bacteria (mycobacteria excluded): ≥50 reads mapped to pathogen species and with a reads number no less than 10 times of any other microorganism, 17 or supported by CMT results.…”

Section: Criteria For a Positive Pathogen Of Mngsmentioning

confidence: 99%

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Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status

Chang,

Wang,

Zhang

et al. 2023

IDR

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Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions. Patients and Methods: A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status. Results: In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, P=9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was Acinetobacter baumannii (42/180, 23.3%) in bacterum level, Candida albicans in fungus level (44/180, 24.4%), and Human herpesvirus 1 (39/180, 27.5%) in virus level. However, for mNGS results, Candida albicans in 34.9% of positive patients, and Human herpesvirus 1 in 7.7% of positive cases were confirmed as pathogens causing pneumonia. Acinetobacter baumannii detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. Pneumocystis jirovecii was more likely to infect immunocompromised patients (P=0.002). Pseudomonas aeruginosa (14.8% vs 0.0%, P=0.008) and Human herpesvirus 1 (26.1% vs 5.3%, P=0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including Streptococcus pneumoniae, Enterococcus faecium, Pneumocystis jirovecii, and majority of viruses. Conclusion: mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.

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Section: Discussionmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

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Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status

Chang,

Wang,

Zhang

et al. 2023

IDR

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“…The possibility of contamination and the inability to differentiate colonization from infection limits its clinical applicability. 41…”

Section: Rapid Diagnostic Toolsmentioning

confidence: 99%

Risk of Multidrug-Resistant Pathogens in Severe Community-Acquired Pneumonia

Campaña-Duel,

Camprubí-Rimblas,

Areny-Balagueró

et al. 2024

Semin Respir Crit Care Med

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Severe community-acquired pneumonia (SCAP) is difficult to treat when caused by difficult-to-treat (DTR) pathogens because of limited treatment options and poorer clinical outcomes. Over time, several predictive scoring systems based on risk factors for infection with multidrug resistant pathogens have been developed. We reviewed the available tools for identifying DTR pathogens as the cause of SCAP, both predictive scoring systems and rapid diagnostic methods, to develop management strategies aimed at early identification of DTR pathogens, reducing broad-spectrum antibiotic use and improving clinical outcomes. The scoring systems reviewed show considerable heterogeneity among them at the level of the region studied, the definition of risk factors, as well as which DTR pathogens are the target pathogens. The models described have shown limited effectiveness in reducing inappropriate antibiotic treatment or improving patient outcomes by themselves. However, predictive models could serve as a first step in identifying DTR pathogen infections as part of a larger detection algorithm. Rapid diagnostic tools, such as multiplex polymerase chain reaction, would be useful for the rapid identification of pneumonia-causing pathogens and their resistance mechanisms. In resource-limited settings, rapid tests should be limited to patients at high risk of developing SCAP due to DTR pathogens. We propose an integrative algorithm based on the different scores, taking into account local epidemiological data, where ideally each center should have an antimicrobial stewardship program.

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Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

Zhao,

Yan

et al. 2023

Journal of Microbiological Methods

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

Cited by 6 publications

References 39 publications

Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status

Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status

Risk of Multidrug-Resistant Pathogens in Severe Community-Acquired Pneumonia

Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients

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