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Zhang X, Ye J, Wang L, Zhang L, Wang L, Jin H. Nanopore Sequencing Technology: A Reliable Method for Pathogen Diagnosis in Elderly Patients with Community-Acquired Pneumonia. Infect Drug Resist 2024; 17:3659-3667. [PMID: 39205800 PMCID: PMC11352510 DOI: 10.2147/idr.s475861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 08/19/2024] [Indexed: 09/04/2024] Open
Abstract
Purpose Next-generation sequencing of the metagenome (mNGS) is gaining traction as a valuable tool for diagnosing infectious diseases. Compared to mNGS, pathogen detection based on Oxford Nanopore Technology further shortens the detection time. This study seeks to assess the efficacy of Nanopore sequencing in identifying pathogens associated with community-acquired pneumonia (CAP) among elderly individuals in China. Patients and Methods From January 2023 to June 2023, elderly patients with CAP were prospectively recruited from Hangzhou First People's Hospital. A comprehensive set of clinical data was gathered, and bronchoalveolar lavage (BAL) fluid samples were collected. Concurrently, pathogen identification was performed using conventional microbiological diagnostic methods, Illumina sequencing, and Nanopore sequencing, and the diagnostic efficacy of pathogen detection was compared. Results The study included a total of 29 patients. The diagnostic positivity rates of traditional microbiological detection, Illumina sequencing, and Nanopore sequencing were 24.1%, 51.7%, and 48.3%, respectively. Their diagnostic specificities were 91.7%, 50%, and 75%, respectively. Compared to traditional microbiological detection, both Nanopore and Illumina sequencing showed significantly increased sensitivity. However, Nanopore sequencing exhibited relatively better consistency with the final clinical comprehensive diagnosis, with a Kappa value of 0.574. This outperformed traditional microbiological detection and Illumina sequencing, which had a Kappa value of 0.296 and 0.402, respectively. In addition, Nanopore sequencing required the shortest turnaround time. Conclusion Nanopore sequencing technology demonstrates as a reliable and rapid method for detecting pathogens in elderly patients with CAP.
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Affiliation(s)
- Xiyue Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Jian Ye
- Department of Respiratory Medicine, Zhejiang Hospital, Hangzhou, People’s Republic of China
| | - Limin Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liuhai Zhang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Liusheng Wang
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
| | - Hualiang Jin
- Department of Respiratory Medicine, Affiliated Hangzhou First People’s Hospital, School of Medicine, Westlake University, Hangzhou, People’s Republic of China
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Duan JL, Li CY, Jiang Y, Liu C, Huang PR, Gao LF, Guan WJ, Cheng LL. Microbiological characteristics of the lower airway in adults with bronchiectasis: a prospective cohort study. Respir Res 2024; 25:283. [PMID: 39020401 PMCID: PMC11253380 DOI: 10.1186/s12931-024-02903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 07/02/2024] [Indexed: 07/19/2024] Open
Abstract
BACKGROUND Microbial infection and colonization are frequently associated with disease progression and poor clinical outcomes in bronchiectasis. Identification of pathogen spectrum is crucial for precision treatment at exacerbation of bronchiectasis. METHODS We conducted a prospective cohort study in patients with bronchiectasis exacerbation onset and stable state. Bronchoalveolar lavage fluid (BALF) was collected for conventional microbiological tests (CMTs) and metagenomic Next-Generation Sequencing (mNGS). Bronchiectasis patients were monitored for documenting the time to the next exacerbation during longitudinal follow-up. RESULTS We recruited 168 eligible participants in the exacerbation cohorts, and 38 bronchiectasis patients at stable state at longitudinal follow-up. 141 bronchiectasis patients at exacerbation onset had definite or probable pathogens via combining CMTs with mNGS reports. We identified that Pseudomonas aeruginosa, non-tuberculous mycobacteria, Haemophilus influenzae, Nocardia spp, and Staphylococcus aureus were the top 5 pathogens with a higher detection rate in our cohorts via combination of CMTs and mNGS analysis. We also observed strong correlations of Pseudomonas aeruginosa, Haemophilus influenzae, non-tuberculous mycobacteria with disease severity, including the disease duration, Bronchiectasis Severity Index, and lung function. Moreover, the adjusted pathogenic index of potential pathogenic microorganism negatively correlated (r = -0.7280, p < 0.001) with the time to the next exacerbation in bronchiectasis. CONCLUSION We have revealed the pathogenic microbial spectrum in lower airways and the negative correlation of PPM colonization with the time to the next exacerbation in bronchiectasis. These results suggested that pathogens contribute to the progression of bronchiectasis.
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Affiliation(s)
- Jie-Lin Duan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, Department of Allergy and Clinical Immunology, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
| | - Cai-Yun Li
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, People's Republic of China
| | - Ying Jiang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
- Guangzhou National Laboratory, Guangzhou, China
| | - Chao Liu
- Medical Department, Hangzhou Matridx Biotechnology Co., Ltd, Hangzhou, People's Republic of China
| | - Pan-Rui Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
- Guangzhou National Laboratory, Guangzhou, China
| | - Li-Fen Gao
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
- Guangzhou National Laboratory, Guangzhou, China
| | - Wei-Jie Guan
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China
- Guangzhou National Laboratory, Guangzhou, China
| | - Lin-Ling Cheng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Department of Respiratory and Critical Care Medicine, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, P.R. China.
- Guangzhou National Laboratory, Guangzhou, China.
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Gao Q, Li L, Su T, Liu J, Chen L, Yi Y, Huan Y, He J, Song C. A single-center, retrospective study of hospitalized patients with lower respiratory tract infections: clinical assessment of metagenomic next-generation sequencing and identification of risk factors in patients. Respir Res 2024; 25:250. [PMID: 38902783 PMCID: PMC11191188 DOI: 10.1186/s12931-024-02887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 06/17/2024] [Indexed: 06/22/2024] Open
Abstract
INTRODUCTION Lower respiratory tract infections(LRTIs) in adults are complicated by diverse pathogens that challenge traditional detection methods, which are often slow and insensitive. Metagenomic next-generation sequencing (mNGS) offers a comprehensive, high-throughput, and unbiased approach to pathogen identification. This retrospective study evaluates the diagnostic efficacy of mNGS compared to conventional microbiological testing (CMT) in LRTIs, aiming to enhance detection accuracy and enable early clinical prediction. METHODS In our retrospective single-center analysis, 451 patients with suspected LRTIs underwent mNGS testing from July 2020 to July 2023. We assessed the pathogen spectrum and compared the diagnostic efficacy of mNGS to CMT, with clinical comprehensive diagnosis serving as the reference standard. The study analyzed mNGS performance in lung tissue biopsies and bronchoalveolar lavage fluid (BALF) from cases suspected of lung infection. Patients were stratified into two groups based on clinical outcomes (improvement or mortality), and we compared clinical data and conventional laboratory indices between groups. A predictive model and nomogram for the prognosis of LRTIs were constructed using univariate followed by multivariate logistic regression, with model predictive accuracy evaluated by the area under the ROC curve (AUC). RESULTS (1) Comparative Analysis of mNGS versus CMT: In a comprehensive analysis of 510 specimens, where 59 cases were concurrently collected from lung tissue biopsies and BALF, the study highlights the diagnostic superiority of mNGS over CMT. Specifically, mNGS demonstrated significantly higher sensitivity and specificity in BALF samples (82.86% vs. 44.42% and 52.00% vs. 21.05%, respectively, p < 0.001) alongside greater positive and negative predictive values (96.71% vs. 79.55% and 15.12% vs. 5.19%, respectively, p < 0.01). Additionally, when comparing simultaneous testing of lung tissue biopsies and BALF, mNGS showed enhanced sensitivity in BALF (84.21% vs. 57.41%), whereas lung tissues offered higher specificity (80.00% vs. 50.00%). (2) Analysis of Infectious Species in Patients from This Study: The study also notes a concerning incidence of lung abscesses and identifies Epstein-Barr virus (EBV), Fusobacterium nucleatum, Mycoplasma pneumoniae, Chlamydia psittaci, and Haemophilus influenzae as the most common pathogens, with Klebsiella pneumoniae emerging as the predominant bacterial culprit. Among herpes viruses, EBV and herpes virus 7 (HHV-7) were most frequently detected, with HHV-7 more prevalent in immunocompromised individuals. (3) Risk Factors for Adverse Prognosis and a Mortality Risk Prediction Model in Patients with LRTIs: We identified key risk factors for poor prognosis in lower respiratory tract infection patients, with significant findings including delayed time to mNGS testing, low lymphocyte percentage, presence of chronic lung disease, multiple comorbidities, false-negative CMT results, and positive herpesvirus affecting patient outcomes. We also developed a nomogram model with good consistency and high accuracy (AUC of 0.825) for predicting mortality risk in these patients, offering a valuable clinical tool for assessing prognosis. CONCLUSION The study underscores mNGS as a superior tool for lower respiratory tract infection diagnosis, exhibiting higher sensitivity and specificity than traditional methods.
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Affiliation(s)
- Qinghua Gao
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Lingyi Li
- Department of Medical, Hangzhou Matridx Biotechnology, Hangzhou, 311100, China
| | - Ting Su
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Jie Liu
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Liping Chen
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Yongning Yi
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Yun Huan
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China
| | - Jian He
- Department of Pulmonary and Critical Care Medicine, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China.
| | - Chao Song
- Department of Medical Imaging, Anning First People's Hospital Affiliated to Kunming University of Science and Technology, Kunming, 650302, China.
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Atto B, Anteneh Y, Bialasiewicz S, Binks MJ, Hashemi M, Hill J, Thornton RB, Westaway J, Marsh RL. The Respiratory Microbiome in Paediatric Chronic Wet Cough: What Is Known and Future Directions. J Clin Med 2023; 13:171. [PMID: 38202177 PMCID: PMC10779485 DOI: 10.3390/jcm13010171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/13/2023] [Accepted: 12/17/2023] [Indexed: 01/12/2024] Open
Abstract
Chronic wet cough for longer than 4 weeks is a hallmark of chronic suppurative lung diseases (CSLD), including protracted bacterial bronchitis (PBB), and bronchiectasis in children. Severe lower respiratory infection early in life is a major risk factor of PBB and paediatric bronchiectasis. In these conditions, failure to clear an underlying endobronchial infection is hypothesised to drive ongoing inflammation and progressive tissue damage that culminates in irreversible bronchiectasis. Historically, the microbiology of paediatric chronic wet cough has been defined by culture-based studies focused on the detection and eradication of specific bacterial pathogens. Various 'omics technologies now allow for a more nuanced investigation of respiratory pathobiology and are enabling development of endotype-based models of care. Recent years have seen substantial advances in defining respiratory endotypes among adults with CSLD; however, less is understood about diseases affecting children. In this review, we explore the current understanding of the airway microbiome among children with chronic wet cough related to the PBB-bronchiectasis diagnostic continuum. We explore concepts emerging from the gut-lung axis and multi-omic studies that are expected to influence PBB and bronchiectasis endotyping efforts. We also consider how our evolving understanding of the airway microbiome is translating to new approaches in chronic wet cough diagnostics and treatments.
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Affiliation(s)
- Brianna Atto
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
| | - Yitayal Anteneh
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
| | - Seweryn Bialasiewicz
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, QLD 4072, Australia;
| | - Michael J. Binks
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- SAHMRI Women and Kids, South Australian Health and Medical Research Institute, Adelaide, SA 5000, Australia
| | - Mostafa Hashemi
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
| | - Jane Hill
- Department of Chemical and Biological Engineering, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada; (M.H.); (J.H.)
- Spire Health Technology, PBC, Seattle, WA 98195, USA
| | - Ruth B. Thornton
- Centre for Child Health Research, University of Western Australia, Perth, WA 6009, Australia;
- Wesfarmers Centre of Vaccines and Infectious Diseases, Telethon Kids Institute, Perth, WA 6009, Australia
| | - Jacob Westaway
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
- Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, QLD 4811, Australia
| | - Robyn L. Marsh
- School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Child and Maternal Health Division, Menzies School of Health Research, Charles Darwin University, Darwin, NT 0811, Australia; (Y.A.); (M.J.B.); (J.W.)
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