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Wang Y, He X, Liu S, Li X. Pneumocystis jirovecii and Nocardia pneumonia in a middle-aged male with Nephrotic syndrome: a case report and literature review. BMC Infect Dis 2024; 24:1071. [PMID: 39350124 PMCID: PMC11440764 DOI: 10.1186/s12879-024-09987-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 09/23/2024] [Indexed: 10/04/2024] Open
Abstract
INTRODUCTION Nephrotic syndrome (NS) is a common chronic kidney disease that is often accompanied by a state of immunodeficiency. Immunosuppression increases the risk of infections, with Pneumocystis jirovecii and Nocardia brasiliensis being two opportunistic pathogens that can cause severe infections in patients with compromised immune function. This study presents a case of a middle-aged male patient with NS concurrently infected with Pneumocystis jirovecii and Nocardia brasiliensis. It aims to synthesize the pertinent diagnostic approaches and treatment experiences. Notably, there have been no reported cases of NS occurring simultaneously with both Pneumocystis jirovecii pneumonia and Nocardia pneumonia. CASE PRESENTATION A 58-year-old male farmer presented to the hospital with a one-week history of persistent fever, cough, and sputum production. His maximum body temperature was recorded at 39 °C, and he produced yellow viscous sputum. This patient had a one-year history of NS, managed with long-term oral corticosteroid and cyclophosphamide therapy. Admission chest computed tomography displayed interstitial changes in both lungs. After failing to detect any pathogens through routine etiological tests, we successfully identified Nocardia brasiliensis, Pneumocystis jirovecii, and Lodderomyces elongisporus using bronchoscopy-guided sputum samples through metagenomic next-generation sequencing (mNGS) technology. Subsequently, we initiated a combined treatment regimen for the patient using trimethoprim-sulfamethoxazole, meropenem, and moxifloxacin, which yielded remarkable therapeutic outcomes. CONCLUSION The adoption and promotion of mNGS technologies have significantly resolved the difficulty in early pathogen detection, guiding clinicians from empirical to genomic diagnosis, achieving prevention before treatment, and thereby enhancing patient survival rates.
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Affiliation(s)
- Yaqing Wang
- Graduate School of Chengde Medical University, Chengde, Hebei, 067000, China
| | - Xiaojie He
- Graduate School of Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Shuangyan Liu
- Graduate School of Hebei Medical University, Shijiazhuang, Hebei, 050017, China
| | - Xiaodong Li
- Department of Nephrology, Baoding No 1 Central Hospital of Hebei Medical University, Baoding Great Wall North Street No 320, Baoding, Hebei, 071000, China.
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Wei M, Mao S, Li S, Gu K, Gu D, Bai S, Lu X, Li M. Comparing the diagnostic value of targeted with metagenomic next-generation sequencing in immunocompromised patients with lower respiratory tract infection. Ann Clin Microbiol Antimicrob 2024; 23:88. [PMID: 39350160 PMCID: PMC11443791 DOI: 10.1186/s12941-024-00749-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Accepted: 09/20/2024] [Indexed: 10/04/2024] Open
Abstract
BACKGROUND Accurate identification of the etiology of lower respiratory tract infections (LRTI) is crucial, particularly for immunocompromised patients with more complex etiologies. The advent of next-generation sequencing (NGS) has enhanced the effectiveness of pathogen detection. However, assessments of the clinical diagnostic value of targeted NGS (tNGS) in immunocompromised patients with LRTI are limited. METHODS To evaluate the diagnostic value of tNGS in immunocompromised patients with LRTI, a total of 88 patients, of whom 54 were immunocompromised, were enrolled. These patients underwent tNGS testing of bronchoalveolar lavage fluid (BALF). Results from both metagenomic next-generation sequencing (mNGS) and conventional microbiological tests (CMT) were also available for all participants. The performance of tNGS was assessed by comparing its findings against mNGS, CMT, and the clinical composite diagnosis. RESULTS In the cohort of 88 patients, tNGS showed comparable diagnostic value to mNGS and was significantly superior to CMT. Compared to CMT and composite reference standard, tNGS showed sensitivity of 94.55% and 90.48%, respectively. In immunocompromised patients, despite a more diverse pathogen variety, tNGS maintained similar sensitivity to mNGS and outperformed CMT. tNGS positively influenced etiologic diagnosis and antibiotic decision-making in 72.72% of cases, leading to a change in antibiotic regimen in 17.05% of cases. We also compared the detection of microbial nucleic acids by tNGS with mNGS and found that tNGS could identify 87.99% of the microbial nucleic acids identified by mNGS. CONCLUSION In summary, our study demonstrated that tNGS offers promising clinical diagnostic accuracy in immunocompromised patients, as evidenced by its favorable comparison with CMT, the composite reference standard, and mNGS.
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Affiliation(s)
- Muyun Wei
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai, China.
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Shaowei Mao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shuangshuang Li
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai, China
| | - Kangyi Gu
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai, China
| | - Dejian Gu
- Geneplus-Beijing Co., Ltd, Beijing, China
| | | | - Xinhua Lu
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, No.160 Pujian Road, Shanghai, China.
- Jiading Branch, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Faculty of Medical Laboratory Science, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wang C, Hu ZW, Li ZY, Zhao MH, Little MA, Chen M. Advantages of metagenomic next-generation sequencing in the management of ANCA-associated vasculitis patients with suspected pulmonary infection as a rule-out tool. BMC Pulm Med 2024; 24:478. [PMID: 39334057 PMCID: PMC11438174 DOI: 10.1186/s12890-024-03301-5] [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: 02/26/2024] [Accepted: 09/19/2024] [Indexed: 09/30/2024] Open
Abstract
OBJECTIVE Pulmonary infection is one of the leading causes of death in patients with ANCA-associated vasculitis (AAV). It is sometimes difficult to differentiate pulmonary infection from pulmonary involvement of vasculitis in AAV patients. Fiberoptic bronchoscopy and bronchoalveolar lavage fluid (BALF) assays are useful diagnostic methods. In addition to conventional microbiological tests (CMTs), metagenomic next-generation sequencing (mNGS) facilitates rapid and sensitive detection of various pathogens. The current study aimed to evaluate the advantages of additional BALF mNGS in the management of pulmonary infection in AAV patients. METHODS 27 patients with active AAV and suspected pulmonary infection whose BALF samples were tested by mNGS and CMTs and 17 active AAV patients whose BALF were tested by CMTs alone were retrospectively recruited. The results of microbiological tests, and adjustments of treatment following BALF mNGS, were described. The durations of antimicrobial treatment and in-hospital mortality in patients were compared. RESULTS Among the 27 patients whose BALF samples were tested by mNGS, 25.9% of patients did not have evidence of pathogenic microorganism in their BALF samples, 55.6% had polymicrobial infections, including bacteria, fungi and viruses. Of these 27 patients, 40.7% did not have evidence of pathogenic microorganism in their BALF or serum samples according to CMTs. Patients in the BALF mNGS/CMT group received a significantly shorter duration of antibacterial and total antimicrobial treatment than patients in the CMT alone group (17.3 ± 14.7 vs. 27.9 ± 19.0 days, P = 0.044; 18.9 ± 15.0 vs. 29.5 ± 17.7 days, P = 0.040, respectively). Fewer patients in the BALF mNGS/CMT group died than in the CMT alone group (4/27 vs. 7/17, P = 0.049). CONCLUSION Compared with CMT alone, additional mNGS tests may shorten the duration of antimicrobial treatment and possibly decrease death from severe infection by providing precise and quick diagnosis of infection.
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Affiliation(s)
- Chen Wang
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, NO.8 Xishiku Street, Xicheng District, Beijing, 100034, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
| | - Zhan-Wei Hu
- Respiratory Division, Department of Medicine, Peking University First Hospital, Beijing, China
| | - Zhi-Ying Li
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, NO.8 Xishiku Street, Xicheng District, Beijing, 100034, China.
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China.
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China.
| | - Ming-Hui Zhao
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, NO.8 Xishiku Street, Xicheng District, Beijing, 100034, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Beijing, China
| | - Mark A Little
- Irish Centre for Vascular Biology, Trinity Kidney Centre, Trinity Translational Medicine Institute, Trinity College Dublin, Trinity College Dublin, Dublin, Ireland
| | - Min Chen
- Renal Division, Department of Medicine, Peking University First Hospital, Peking University Institute of Nephrology, NO.8 Xishiku Street, Xicheng District, Beijing, 100034, China
- Key Laboratory of Renal Disease, Ministry of Health of China, Beijing, China
- Key Laboratory of Chronic Kidney Disease Prevention and Treatment (Peking University), Ministry of Education, Beijing, China
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Quarton S, Livesey A, Jeff C, Hatton C, Scott A, Parekh D, Thickett D, McNally A, Sapey E. Metagenomics in the Diagnosis of Pneumonia: Protocol for a Systematic Review. JMIR Res Protoc 2024; 13:e57334. [PMID: 39293053 PMCID: PMC11447427 DOI: 10.2196/57334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 07/16/2024] [Accepted: 07/18/2024] [Indexed: 09/20/2024] Open
Abstract
BACKGROUND Causative pathogens are currently identified in only a minority of pneumonia cases, which affects antimicrobial stewardship. Metagenomic next-generation sequencing (mNGS) has potential to enhance pathogen detection due to its sensitivity and broad applicability. However, while studies have shown improved sensitivity compared with conventional microbiological methods for pneumonia diagnosis, it remains unclear whether this can translate into clinical benefit. Most existing studies focus on patients who are ventilated, readily allowing for analysis of bronchoalveolar lavage fluid (BALF). The impact of sample type on the use of metagenomic analysis remains poorly defined. Similarly, previous studies rarely differentiate between the types of pneumonia involved-community-acquired pneumonia (CAP), hospital-acquired pneumonia (HAP), or ventilator-associated pneumonia (VAP)-which have different clinical profiles. OBJECTIVE This study aims to determine the clinical use of mNGS in CAP, HAP, and VAP, compared with traditional microbiological methods. METHODS We aim to review all studies (excluding case reports of a series of fewer than 10 people) of adult patients with suspected or confirmed pneumonia that compare metagenomic analysis with traditional microbiology techniques, including culture, antigen-based testing, and polymerase chain reaction-based assays. Relevant studies will be identified through systematic searches of the Embase, MEDLINE, Scopus, and Cochrane CENTRAL databases. Screening of titles, abstracts, and subsequent review of eligible full texts will be done by 2 separate reviewers (SQ and 1 of AL, CJ, or CH), with a third clinician (ES) providing adjudication in case of disagreement. Our focus is on the clinical use of metagenomics for patients with CAP, HAP, and VAP. Data extracted will focus on clinically important outcomes-pathogen positivity rate, laboratory turnaround time, impact on clinical decision-making, length of stay, and 30-day mortality. Subgroup analyses will be performed based on the type of pneumonia (CAP, HAP, or VAP) and sample type used. The risk of bias will be assessed using the QUADAS-2 tool for diagnostic accuracy studies. Outcome data will be combined in a random-effects meta-analysis, and where this is not possible, a narrative synthesis will be undertaken. RESULTS The searches were completed with the assistance of a medical librarian on January 13, 2024, returning 5750 records. Screening and data extraction are anticipated to be completed by September 2024. CONCLUSIONS Despite significant promise, the impact of metagenomic analysis on clinical pathways remains unclear. Furthermore, it is unclear whether the use of this technique will alter depending on whether the pneumonia is a CAP, HAP, or VAP or the sample type that is collected. This systematic review will assess the current evidence base to support the benefit of clinical outcomes for metagenomic analysis, depending on the setting of pneumonia diagnosis or specimen type used. It will identify areas where further research is needed to advance this methodology into routine care. TRIAL REGISTRATION PROSPERO CRD42023488096; https://tinyurl.com/3suy7cma. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID) DERR1-10.2196/57334.
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Affiliation(s)
- Samuel Quarton
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Alana Livesey
- National Institute for Health Research Welcome Trust Clinical Research Facility, University Hospitals Birmingham, Birmingham, United Kingdom
| | - Charlotte Jeff
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
| | - Christopher Hatton
- National Institute for Health Research Midlands Patient Safety Research Collaboration, University of Birmingham, Birmingham, United Kingdom
| | - Aaron Scott
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
| | - Dhruv Parekh
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
| | - David Thickett
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, United Kingdom
| | - Alan McNally
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
| | - Elizabeth Sapey
- National Institute for Health Research Birmingham Biomedical Research Centre, Birmingham, United Kingdom
- National Institute for Health Research Midlands Patient Safety Research Collaboration, University of Birmingham, Birmingham, United Kingdom
- National Institute for Health Research Midlands Applied Research Collaborative, University of Birmingham, Birmingham, United Kingdom
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Zheng YR, Chen XH, Chen Q, Cao H. Comparison of targeted next-generation sequencing and metagenomic next-generation sequencing in the identification of pathogens in pneumonia after congenital heart surgery: a comparative diagnostic accuracy study. Ital J Pediatr 2024; 50:174. [PMID: 39267108 PMCID: PMC11395185 DOI: 10.1186/s13052-024-01749-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 08/31/2024] [Indexed: 09/14/2024] Open
Abstract
BACKGROUND This study aimed to compare targeted next-generation sequencing (tNGS) with metagenomic next-generation sequencing (mNGS) for pathogen detection in infants with severe postoperative pneumonia after congenital heart surgery. METHODS We conducted a retrospective observational study using data from the electronic medical record system of infants who developed severe pneumonia after surgery for congenital heart disease from August 2021 to August 2022. Infants were divided into tNGS and mNGS groups based on the pathogen detection methods. The primary outcome was the efficiency of pathogen detection, and the secondary outcomes were the timeliness and cost of each method. RESULTS In the study, 91 infants were included, with tNGS detecting pathogens in 84.6% (77/91) and mNGS in 81.3% (74/91) of cases (P = 0.55). No significant differences were found in sensitivity, specificity, PPA, and NPA between the two methods (P > 0.05). tNGS identified five strains with resistance genes, while mNGS detected one strain. Furthermore, tNGS had a faster detection time (12 vs. 24 h) and lower cost ($150 vs. $500) compared to mNGS. CONCLUSION tNGS offers similar sensitivity to mNGS but with greater efficiency and cost-effectiveness, making it a promising approach for respiratory pathogen detection.
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Affiliation(s)
- Yi-Rong Zheng
- Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
| | - Xiu-Hua Chen
- Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
| | - Qiang Chen
- Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
| | - Hua Cao
- Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China.
- College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China.
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Hu W, Li X, Guo W, Shangguan Y, Xia J, Feng X, Sheng C, Ji Z, Ding C, Xu K. The Utility of Real-Time PCR, Metagenomic Next-Generation Sequencing, and Culture in Bronchoalveolar Lavage Fluid for Diagnosis of Pulmonary Aspergillosis. J Mol Diagn 2024; 26:832-842. [PMID: 38972592 DOI: 10.1016/j.jmoldx.2024.06.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 03/31/2024] [Accepted: 06/11/2024] [Indexed: 07/09/2024] Open
Abstract
Timely detection of Aspergillus infection is crucial given the high mortality rate of pulmonary aspergillosis (PA). Here, the diagnostic performances for PA of mycological culture, Aspergillus real-time PCR, and metagenomic next-generation sequencing (mNGS) assay from bronchoalveolar lavage fluid, were evaluated. In total, 139 patients with suspected fungal pneumonia were enrolled between December 2021 and July 2023, collecting 139 bronchoalveolar lavage fluid samples for real-time PCR and culture, with 87 undergoing mNGS assay. The sensitivity, specificity, positive predictive value, negative predictive value, and area under the curve with 95% CIs of these assays for PA were as follows: 35.3% (14.2%-61.7%), 100.0% (94.0%-100.0%), 100.0% (54.1%-100.0%), 84.5% (79.3%-88.6%), and 0.676 (0.560-0.779), respectively, for culture; 82.4% (56.6%-96.2%), 98.3% (91.1%-100.0%), 93.3% (66.4%-99.0%), 95.2% (87.6%-98.2%), and 0.903 (0.815-0.959), respectively, for same diagnostic performance of real-time PCR and mNGS; and 94.1% (71.3%-99.9%), 96.7% (88.5%-99.6%), 88.9% (67.1%-96.9%), 98.3% (89.6%-99.7%), and 0.954 (0.880-0.989), respectively, for real-time PCR combining mNGS; real-time PCR, mNGS, and their combination significantly improved in area under the curve values over culture (P < 0.001), but real-time PCR testing and mNGS had no significant difference with each other and their combination. Overall, the performance of culture was limited by low sensitivity; both real-time PCR and mNGS assays as single diagnostic tests are promising compared with culture and combined tests.
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Affiliation(s)
- Wenjuan Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Xiaomeng Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Wanru Guo
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Yanwan Shangguan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Jiafeng Xia
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Xuewen Feng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Chengmin Sheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Zhongkang Ji
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Cheng Ding
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China
| | - Kaijin Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou City, China.
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Fu R, Xu J, Fan Z, Qu H, Jiang Y, Xiong W, Huang F, Xuan L, Xu N, Liu H, Wang Z, Sun J, Liu Q, Lin R. Metagenomic Next-Generation Sequencing in the Diagnosis of Pulmonary Infections after Allogeneic Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2024:S2666-6367(24)00607-9. [PMID: 39197493 DOI: 10.1016/j.jtct.2024.08.014] [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: 05/25/2024] [Revised: 07/27/2024] [Accepted: 08/19/2024] [Indexed: 09/01/2024]
Abstract
Early and accurate identification of pathogens in pulmonary infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT) is critically important. The clinical usefulness of metagenomic next-generation sequencing (mNGS) in the diagnosis of pulmonary infections after allo-HSCT remains under discussion. This multicenter retrospective study was conducted to compare mNGS and conventional microbiological tests (CMTs) in identifying the pathogens of pulmonary infections in allo-HSCT recipients. One hundred forty allo-HSCT recipients with suspected pulmonary infections who underwent bronchoscopy were included. mNGS and CMTs performed on bronchoalveolar lavage fluid specimens showed 71.4% positivity on mNGS compared to 55.0% positivity on CMTs. mNGS identified 182 pathogens, including bacteria (n = 88), fungi (n = 35) and viruses (n = 59), compared to 106 pathogens detected by CMTs (bacteria, n = 31; fungi, n = 24; viruses, n = 51). Pulmonary infection was finally diagnosed in 98 patients, including 22 bacterial, 7 fungal, 18 viral, and 48 mixed infections and 3 infections with an unknown pathogen. Mixed infections were identified in 50.5% of the patients with pulmonary infection. The sensitivity of mNGS and CMTs for diagnosing pulmonary infections was 88.8% and 69.4%, respectively (P = .001), and the specificity were 81.0% and 85.7%, respectively (P = .688). Our findings suggest that mNGS may be a promising technology for diagnosing pulmonary infections in allo-HSCT recipients.
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Affiliation(s)
- Rong Fu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jun Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhiping Fan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hong Qu
- The Affiliated Panyu Central Hospital of Guangzhou Medical University, Infection Medicine Research Institute of Panyu District, Guangzhou, China
| | | | - Wenjie Xiong
- Foresea Life Insurance Guangzhou General Hospital, Guangzhou, China
| | - Fen Huang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Li Xuan
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Na Xu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Hui Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Zhixiang Wang
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Jing Sun
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Qifa Liu
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China
| | - Ren Lin
- Department of Hematology, Nanfang Hospital, Southern Medical University, Clinical Medical Research Center of Hematological Diseases of Guangdong Province, Guangzhou, China.
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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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Zhang P, Lu Z, Cao L, Fu L, Chen H, Sun Y. Diagnostic performance of pancreatic fluid aspiration through metagenomic next-generation sequencing for suspected infected pancreatic necrosis. Dig Liver Dis 2024:S1590-8658(24)00918-6. [PMID: 39155203 DOI: 10.1016/j.dld.2024.07.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 07/07/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024]
Abstract
AIMS This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) with pancreatic fluid aspiration for the detection of infected pancreatic necrosis (IPN). METHODS This retrospective observational study included 66 patients with suspected IPN. The participants simultaneously underwent pancreatic fluid aspiration mNGS, and microbial and blood culture. We compared the diagnostic performance of mNGS with that of culture in the detection of pathogens associated with IPN. RESULTS Of the 66 patients, 45 (68.2 %) were confirmed to have IPN. Pancreatic fluid aspiration mNGS yielded positive results in 32 of these patients (71.1 %), significantly outperforming microbial culture results (25 patients, 55.6 %; P = 0.039); however, both methods exhibited similar specificity (95.2% vs. 100 %). The results of pancreatic fluid aspiration mNGS and microbial culture matched in 73.3 % (33/45) of patients with IPN. The turnaround time for the mNGS results was significantly shorter than that for the microbial culture method (P < 0.001). In addition, survival analysis demonstrated that a positive mNGS result was not associated with increased mortality (hazard ratio, 0.652; 95 % confidence interval 0.157-2.699, P = 0.555). CONCLUSIONS Our study highlights the potential of mNGS for diagnosing IPN, with implications for improving patient care by facilitating early and accurate diagnosis, guiding appropriate interventions, and possibly improving patient outcomes.
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Affiliation(s)
- Pinjie Zhang
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China
| | - Zhonghua Lu
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China
| | - Lijun Cao
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China
| | - Lu Fu
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China
| | - Hu Chen
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China
| | - Yun Sun
- The First Department of Critical Care Medicine, the Second Affiliated Hospital of Anhui Medical University, No. 678, Furong Road, Hefei Economic Development Zone, Hefei 230601, Anhui Province, China.
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10
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Huang SS, Qiu JY, Li SP, Ma YQ, He J, Han LN, Jiao LL, Xu C, Mao YM, Zhang YM. Microbial signatures predictive of short-term prognosis in severe pneumonia. Front Cell Infect Microbiol 2024; 14:1397717. [PMID: 39157177 PMCID: PMC11327560 DOI: 10.3389/fcimb.2024.1397717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 07/15/2024] [Indexed: 08/20/2024] Open
Abstract
Objective This retrospective cohort study aimed to investigate the composition and diversity of lung microbiota in patients with severe pneumonia and explore its association with short-term prognosis. Methods A total of 301 patients diagnosed with severe pneumonia underwent bronchoalveolar lavage fluid metagenomic next-generation sequencing (mNGS) testing from February 2022 to January 2024. After applying exclusion criteria, 236 patients were included in the study. Baseline demographic and clinical characteristics were compared between survival and non-survival groups. Microbial composition and diversity were analyzed using alpha and beta diversity metrics. Additionally, LEfSe analysis and machine learning methods were employed to identify key pathogenic microorganism associated with short-term mortality. Microbial interaction modes were assessed through network co-occurrence analysis. Results The overall 28-day mortality rate was 37.7% in severe pneumonia. Non-survival patients had a higher prevalence of hypertension and exhibited higher APACHE II and SOFA scores, higher procalcitonin (PCT), and shorter hospitalization duration. Microbial α and β diversity analysis showed no significant differences between the two groups. However, distinct species diversity patterns were observed, with the non-survival group showing a higher abundance of Acinetobacter baumannii, Klebsiella pneumoniae, and Enterococcus faecium, while the survival group had a higher prevalence of Corynebacterium striatum and Enterobacter. LEfSe analysis identified 29 distinct terms, with 10 potential markers in the non-survival group, including Pseudomonas sp. and Enterococcus durans. Machine learning models selected 16 key pathogenic bacteria, such as Klebsiella pneumoniae, significantly contributing to predicting short-term mortality. Network co-occurrence analysis revealed greater complexity in the non-survival group compared to the survival group, with differences in central genera. Conclusion Our study highlights the potential significance of lung microbiota composition in predicting short-term prognosis in severe pneumonia patients. Differences in microbial diversity and composition, along with distinct microbial interaction modes, may contribute to variations in short-term outcomes. Further research is warranted to elucidate the clinical implications and underlying mechanisms of these findings.
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Affiliation(s)
- Shen-Shen Huang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Jia-Yong Qiu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
- Department of Respiratory and Critical Care Medicine, The Second Hospital of Hebei Medical University, Shijiazhuang, China
| | - Shuang-Ping Li
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Ya-Qing Ma
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Jun He
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Li-Na Han
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Long-Long Jiao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Chong Xu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yi-Min Mao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
| | - Yong-Mei Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, and College of Clinical Medicine of Henan University of Science and Technology, Luoyang, China
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Yu JM, Liang ZY, Fu YH, Peng XL, Zheng YP, Dong YJ, He JS. Coexistence of adeno-associated virus 2 with adenovirus 18 or herpesvirus may be associated with severe lingual papillomatosis in an immunocompromised individual. Virol Sin 2024; 39:705-707. [PMID: 38914259 PMCID: PMC11401458 DOI: 10.1016/j.virs.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 06/19/2024] [Indexed: 06/26/2024] Open
Affiliation(s)
- Jie-Mei Yu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Ze-Yin Liang
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China
| | - Yuan-Hui Fu
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Xiang-Lei Peng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yan-Peng Zheng
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China
| | - Yu-Jun Dong
- Department of Hematology, Peking University First Hospital, Beijing, 100034, China.
| | - Jin-Sheng He
- College of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, 100044, China.
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12
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Cao H, Chen Y, Ge L, Kwong JSW, Lai H, Hu F, Zhang R, Zhao H, Hu L, He R, Zheng W, Zhang J. An umbrella review of the diagnostic value of next-generation sequencing in infectious diseases. Int J Clin Pharm 2024; 46:780-794. [PMID: 38570474 DOI: 10.1007/s11096-024-01704-2] [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: 12/15/2023] [Accepted: 01/18/2024] [Indexed: 04/05/2024]
Abstract
BACKGROUND An increasing number of systematic reviews (SRs) have evaluated the diagnostic values of next-generation sequencing (NGS) in infectious diseases (IDs). AIM This umbrella analysis aimed to assess the potential risk of bias in existing SRs and to summarize the published diagnostic values of NGS in different IDs. METHOD We searched PubMed, Embase, and the Cochrane Library until September 2023 for SRs assessing the diagnostic validity of NGS for IDs. Two investigators independently determined review eligibility, extracted data, and evaluated reporting quality, risk of bias, methodological quality, and evidence certainty in the included SRs. RESULTS Eleven SRs were analyzed. Most SRs exhibited a moderate level of reporting quality, while a serious risk of bias was observed in all SRs. The diagnostic performance of NGS in detecting pneumocystis pneumonia and periprosthetic/prosthetic joint infection was notably robust, showing excellent sensitivity (pneumocystis pneumonia: 0.96, 95% CI 0.90-0.99, very low certainty; periprosthetic/prosthetic joint infection: 0.93, 95% CI 0.83-0.97, very low certainty) and specificity (pneumocystis pneumonia: 0.96, 95% CI 0.92-0.98, very low certainty; periprosthetic/prosthetic joint infection: 0.95, 95% CI 0.92-0.97, very low certainty). NGS exhibited high specificity for central nervous system infection, bacterial meningoencephalitis, and tuberculous meningitis. The sensitivity to these infectious diseases was moderate. NGS demonstrated moderate sensitivity and specificity for multiple infections and pulmonary infections. CONCLUSION This umbrella analysis indicates that NGS is a promising technique for diagnosing pneumocystis pneumonia and periprosthetic/prosthetic joint infection with excellent sensitivity and specificity. More high-quality original research and SRs are needed to verify the current findings.
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Affiliation(s)
- Hong Cao
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Yan Chen
- School of Pharmaceutical Sciences, Guizhou University, 2708 South of Huaxi Avenue Road, Guiyang, Guizhou Province, China
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Long Ge
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Joey Sum-Wing Kwong
- Global Health Nursing, Graduate School of Nursing Science, St. Luke's International University, 10-1 Akashi-Cho, Chuo-Ku, Tokyo, 104-0044, Japan
| | - Honghao Lai
- Evidence-Based Social Science Research Center, School of Public Health, Lanzhou University, Lanzhou, China
- Key Laboratory of Evidence Based Medicine and Knowledge Translation of Gansu Province, No. 199, Donggang West Road, Chengguan District, Lanzhou City, Gansu Province, China
| | - Fangfang Hu
- Department of Laboratory, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, 550002, Guizhou Province, China
| | - Rui Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Huaye Zhao
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Linfang Hu
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China
| | - Rui He
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Wenyi Zheng
- Experimental Cancer Medicine, Department of Laboratory Medicine, Karolinska Institute, Room 601, Novum PI 6, Hälsovägen 7, Huddinge, 14157, Stockholm, Sweden
| | - Jiaxing Zhang
- Department of Pharmacy, Guizhou Provincial People's Hospital, No.83 Zhongshandong Road, Guiyang, Guizhou Province, China.
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He M, Xie J, Rui P, Li X, Lai M, Xue H, Chen C. Clinical efficacy of macrolide antibiotics in mycoplasma pneumoniae pneumonia carrying a macrolide-resistant mutation in the 23 S rRNA gene in pediatric patients. BMC Infect Dis 2024; 24:758. [PMID: 39085799 PMCID: PMC11292884 DOI: 10.1186/s12879-024-09612-6] [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: 05/06/2024] [Accepted: 07/15/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND The global prospective surveillance data showed the re-emergence of mycoplasma pneumoniae pneumonia (MPP) in Europe and Asia after the coronavirus disease 2019 pandemic. We sought to observe the effect of macrolide antibiotics in the treatment of MPP carrying a macrolide-resistant mutation gene and the potential of targeted next-generation sequencing (tNGS) as a front-line diagnostic in MPP patients. METHODS The baseline characteristics of 91 children with MPP hospitalized from January to October 2023 were retrospectively analyzed. They were divided into two groups according to whether carrying the macrolide-resistant mutation or not. The logistic and linear regression analyses were used to determine whether the mutation was a standalone predictive predictor of the duration of fever and hospital length of stay. RESULTS First, no patients had a fever for ≥ 7 days after macrolide treatment. But length of stay and hormone concentration were significantly different between the two groups (P < 0.05). There were also no statistical association between the mutation and the duration of fever and hospital length of stay. CONCLUSION Macrolides can be administered to MPP children carrying a macrolide-resistant mutation. tNGS can be seen as a front-line diagnostic in MPP.
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Affiliation(s)
- Mengyuan He
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Junfeng Xie
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Pu Rui
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Xiaoyu Li
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Min Lai
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Hongman Xue
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Chun Chen
- Pediatric Hematology Laboratory, Division of Hematology/Oncology, Department of Pediatrics, The Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China.
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14
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Yang Z, Tang Y, Shan S. Bronchial lavage tNGS in the diagnosis of pulmonary tuberculosis. Technol Health Care 2024:THC240823. [PMID: 39093094 DOI: 10.3233/thc-240823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
BACKGROUND Tuberculosis (TB), primarily caused by Mycobacterium tuberculosis, remains a significant global health concern. Targeted Next-Generation Sequencing (tNGS) has emerged as a rapid and comprehensive diagnostic tool for tuberculosis, offering advantages over traditional methods and serving as an effective alternative for drug susceptibility testing and the detection of drug-resistant tuberculosis. OBJECTIVE This study aimed to retrospectively analyze the clinical characteristics of pulmonary tuberculosis patients. After explore the application value of targeted next-generation sequencing technology in this patient population, providing valuable insights for clinical diagnosis and treatment. METHODS In this retrospective study, we analyzed data from 65 patients with laboratory-confirmed tuberculosis admitted to Tianjin Baodi Hospital from November 14, 2020, to February 1, 2023. Patients underwent bronchoalveolar lavage fluid (BALF) testing, including acid-fast staining, culture, and tNGS. Biopsies and histopathological examinations were performed on some patients, along with comprehensive radiological assessments for all. RESULTS Among the 65 pulmonary tuberculosis patients, targeted next-generation sequencing detected pathogens in bronchoalveolar lavage fluid with a positivity rate of 93.8%, significantly higher than traditional methods such as acid-fast staining, culture, and pathology. Compared to bronchoalveolar lavage fluid smear, targeted next-generation sequencing demonstrated significantly higher diagnostic sensitivity (98.46% vs. 26.15%) and accuracy (98.46% vs. 26.15%). CONCLUSION Targeted next-generation sequencing, with its high sensitivity and specificity compared to traditional methods, provides unique advantages in detecting pathogens among these patients, highlighting its importance in disease management.
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Affiliation(s)
- Zhongpeng Yang
- Department of Respiratory and Critical Care Medicine, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
| | - Yucong Tang
- Department of Respiratory and Critical Care Medicine, Tianjin Medical University, Tianjin, China
| | - Shuxiang Shan
- Department of Respiratory and Critical Care Medicine, Tianjin Baodi Hospital, Baodi Clinical College of Tianjin Medical University, Tianjin, China
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15
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Jiang L, Liang TW, Al-Odaini N, Hu Y, Huang M, Wei L, Li XY, Pan KS, Zheng DY, Jiang ZW, Wei G, Cao CW. Metagenomic Next-Generation Sequencing as an Effective Diagnostic Tool for Talaromycosis in HIV-Negative Patients. Mycopathologia 2024; 189:63. [PMID: 38985209 DOI: 10.1007/s11046-024-00866-x] [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: 02/04/2024] [Accepted: 06/05/2024] [Indexed: 07/11/2024]
Abstract
The diagnosis of Talaromyces marneffei infection in HIV-negative patients remains challenging. There is an urgent need for rapid and convenient methods to diagnose this complicated disease. The aim of this study was to evaluate the diagnostic efficiency of metagenomic next-generation sequencing (mNGS) for talaromycosis in non-HIV-infected patients by comparing mNGS with traditional microbial culture. In total, 66 samples from 57 patients were analyzed via both mNGS and microbial culture. The ROC curve showed a sensitivity for mNGS of 97.22%, which was greater than that of microbial culture (61.11%). Samples from the respiratory tract, infectious skin lesions, and lymph nodes are recommended as routine samples for talaromycosis detection via mNGS. Furthermore, mNGS significantly reduced the diagnostic time compared to microbial culture. Overall, our study demonstrated that mNGS is a promising tool for rapid and accurate pathogenic detection in HIV-negative patients with talaromycosis.
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Affiliation(s)
- Li Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Tian-Wei Liang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Najwa Al-Odaini
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Yuan Hu
- Richardson Medical Fungal Laboratory, Guangzhou Centre for Fungal Diagnostics and Research, Guangzhou, China
| | - Minli Huang
- Department of Ophthalmology, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China
| | - Lili Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Xiu-Ying Li
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Kai-Su Pan
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Dong-Yan Zheng
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Zhi-Wen Jiang
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China
| | - Gao Wei
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
| | - Cun-Wei Cao
- Department of Dermatology and Venereology, The First Affiliated Hospital of Guangxi Medical University, Nanning, 530021, Guangxi, China.
- Fangchenggang Wanqing Institute of Mycosis Prevention and Control, Fangchenggang, China.
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16
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Zhu Z, Wang Y, Ning W, Liu C, Chen C. Torquetenovirus from bronchoalveolar lavage fluid as a biomarker for lung infection among immunocompromised hosts. Biomark Med 2024; 18:581-591. [PMID: 38982729 PMCID: PMC11370955 DOI: 10.1080/17520363.2024.2366148] [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: 01/01/2024] [Accepted: 05/08/2024] [Indexed: 07/11/2024] Open
Abstract
Aim: Torquetenovirus (TTV) was a promising biomarker for immunity, while lung regional TTV for evaluating the opportunistic infection among immunocompromised hosts (ICH) was unclear.Materials & methods: In the ICH and non-ICH populations, we compared the susceptibility to opportunistic infections, clinical severity and the prognosis between subgroups, respectively.Results: ICH with detectable bronchoalveolar lavage fluid (BALF)-TTV were more susceptible to lung aspergillosis and Mycobacterium infections. Furthermore, our data demonstrated that the ICH cohort with detectable BALF-TTV represented a higher clinical severity and a worse prognosis, while the above findings were not found in the non-ICH population.Conclusion: Our findings demonstrated that the BALF-TTV could act as an effective predictor for opportunistic infection for ICH that complemented the CD4+ T cell counts.
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Affiliation(s)
- Ziwen Zhu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou215006, China
| | - Yang Wang
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou215006, China
| | - Weiwei Ning
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou215006, China
| | - Chao Liu
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou215006, China
| | - Cheng Chen
- Department of Respiratory & Critical Medicine, The First Affiliated Hospital of Soochow University, 899 Pinghai Road, Suzhou215006, China
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17
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Quarton S, Livesey A, Pittaway H, Adiga A, Grudzinska F, McNally A, Dosanjh D, Sapey E, Parekh D. Clinical challenge of diagnosing non-ventilator hospital-acquired pneumonia and identifying causative pathogens: a narrative review. J Hosp Infect 2024; 149:189-200. [PMID: 38621512 DOI: 10.1016/j.jhin.2024.02.029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/12/2024] [Accepted: 02/21/2024] [Indexed: 04/17/2024]
Abstract
Non-ventilated hospital-acquired pneumonia (NV-HAP) is associated with a significant healthcare burden, arising from high incidence and associated morbidity and mortality. However, accurate identification of cases remains challenging. At present, there is no gold-standard test for the diagnosis of NV-HAP, requiring instead the blending of non-specific signs and investigations. Causative organisms are only identified in a minority of cases. This has significant implications for surveillance, patient outcomes and antimicrobial stewardship. Much of the existing research in HAP has been conducted among ventilated patients. The paucity of dedicated NV-HAP research means that conclusions regarding diagnostic methods, pathology and interventions must largely be extrapolated from work in other settings. Progress is also limited by the lack of a widely agreed definition for NV-HAP. The diagnosis of NV-HAP has large scope for improvement. Consensus regarding a case definition will allow meaningful research to improve understanding of its aetiology and the heterogeneity of outcomes experienced by patients. There is potential to optimize the role of imaging and to incorporate novel techniques to identify likely causative pathogens. This would facilitate both antimicrobial stewardship and surveillance of an important healthcare-associated infection. This narrative review considers the utility of existing methods to diagnose NV-HAP, with a focus on the significance and challenge of identifying pathogens. It discusses the limitations in current techniques, and explores the potential of emergent molecular techniques to improve microbiological diagnosis and outcomes for patients.
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Affiliation(s)
- S Quarton
- National Institute for Health Research Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK.
| | - A Livesey
- National Institute for Health Research/Wellcome Trust Clinical Research Facility, University Hospitals Birmingham, Birmingham, UK
| | - H Pittaway
- Queen Elizabeth Hospital Birmingham, University Hospitals Birmingham, Birmingham, UK
| | - A Adiga
- Warwick Hospital, South Warwickshire University NHS Foundation Trust, Warwick, UK
| | - F Grudzinska
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - A McNally
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - D Dosanjh
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
| | - E Sapey
- National Institute for Health Research Birmingham Biomedical Research Centre, University of Birmingham, Birmingham, UK; National Institute for Health Research Midlands Patient Safety Research Collaboration, University of Birmingham, Birmingham, UK; National Institute for Health Research Midlands Applied Research Collaborative, University of Birmingham, Birmingham, UK
| | - D Parekh
- Institute of Inflammation and Ageing, University of Birmingham, Birmingham, UK
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18
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Wang D, Zhang Z, Shen H, Jin F, Liang J, Shen D, Song H, Zhang J, Xu W, Tang Y, Xu X. Comparison of plasma and blood cell samples in metagenomic next-generation sequencing for identification of the causative pathogens of fever. Heliyon 2024; 10:e31677. [PMID: 38841453 PMCID: PMC11152940 DOI: 10.1016/j.heliyon.2024.e31677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 05/19/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) of plasma DNA has become an attractive diagnostic method for infectious diseases; however, the rate of false-positive results is high. This study aims to evaluate the diagnostic accuracy of mNGS in plasma versus blood cell samples for immunocompromised children with febrile diseases. Methods The results of conventional microbiological test (CMT) and mNGS using plasma and blood cells in 106 patients with 128 episodes of febrile diseases from the Department of Hematology/Oncology were analyzed and described. Results The positivity rates for CMT and mNGS of plasma and blood cells were 35.9 %, 84.4 % and 46.9 %, respectively (P < 0.001). Notably, mNGS identified multiple pathogens in a single specimen in 68.5 % of plasma samples and 38.3 % of blood cell samples (P < 0.001). Furthermore, plasma and blood cell mNGS identified causative pathogens in 58 and 46 cases, accounting for 53.7 % and 76.7 % of the mNGS-positive cases for each sample type, respectively (P = 0.002). By integrating results from both plasma and blood cell samples, causative pathogens were identified in 77 cases (60.2 %), enhancing sensitivity to 87.5 % but reducing specificity to 15.0 %, compared to plasma (65.9 % sensitivity and 20.0 % specificity) and blood cell samples (52.3 % sensitivity and 80.0 % specificity). Conclusions mNGS of plasma is sensitive but has a high false-positive rate, while mNGS of blood cells has low sensitivity but higher specificity.
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Affiliation(s)
- Di Wang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Zihan Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
| | - Heping Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Fenfen Jin
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Juan Liang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Diying Shen
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Hua Song
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Jingying Zhang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Weiqun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Yongmin Tang
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
| | - Xiaojun Xu
- Division/Center of Hematology-Oncology, Children's Hospital of Zhejiang University School of Medicine, PR China
- Pediatric Leukemia Diagnostic and Therapeutic Technology Research Center of Zhejiang Province, National Clinical Research Center for Child Health, PR China
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Zeng W, Liang Y, He X, Chen F, Xiong J, Wen Z, Tang L, Chen X, Zhang J. Exploring the pathogen diagnosis and prognostic factors of severe COVID-19 using metagenomic next-generation sequencing: A retrospective study. J Med Biochem 2024; 43:528-536. [PMID: 39139158 PMCID: PMC11318844 DOI: 10.5937/jomb0-49102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 03/21/2024] [Indexed: 08/15/2024] Open
Abstract
Background This study aimed to identify pathogens and factors that predict the outcome of severe COVID-19 by utilizing metagenomic next-generation sequencing (mNGS) technology. Methods We retrospectively analyzed data from 56 severe COVID-19 patients admitted to our hospital between December 2022 and March 2023. We analyzed the pathogen types and strains detected through mNGS and conventional microbiological testing and collected general patient information. Results In this study, 42 pathogens were detected using mNGS and conventional microbiological testing. mNGS had a significantly higher detection rate of 90.48% compared to 71.43% for conventional testing (P=0.026). A total of 196 strains were detected using both methods, with a significantly higher detection rate of 70.92% for mNGS compared to 49.49% for conventional testing (P=0.000). The 56 patients were divided into a survival group (33 cases) and a death group (23 cases) based on clinical outcomes. The survival group had significantly lower age, number of pathogens detected by mNGS, number of pathogens detected by conventional testing, APACHE-II score, SOFA score, high-sensitivity troponin, creatine kinase-MB subtype, and lactate dehydrogenase compared to the death group (P<0.05). Multivariate logistic regression analysis showed that these factors were risk factors for mortality in severe COVID-19 patients (P<0.05). In contrast, ROC curve analysis revealed that these factors had diagnostic values for mortality, with AUC values ranging from 0.657 to 0.963. The combined diagnosis of these indicators had an AUC of 0.924. Conclusions The use of mNGS technology can significantly enhance the detection of pathogens in severe cases of COVID-19 and also has a solid ability to predict clinical outcomes.
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Affiliation(s)
- Weizhong Zeng
- Zhuzhou Central Hospital, Department of Intensive Care Unit, Zhuzhou, China
| | - Yanchao Liang
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Xiaoyuan He
- Zhuzhou Central Hospital, Nursing Department, Zhuzhou, China
| | - Fangwei Chen
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Jiali Xiong
- Zhuzhou Central Hospital, Department of Respiratory and Critical Care Medicine, Zhuzhou, China
| | - Zhenhua Wen
- Zhuzhou Central Hospital, Department of Rheumatology and Immunology, Zhuzhou, China
| | - Liang Tang
- Zhuzhou Central Hospital, Department of General Internal Medicine, Zhuzhou, China
| | - Xun Chen
- Zhuzhou Central Hospital, Department of Hepatobiliary and Pancreatic Surgery, Zhuzhou, China
| | - Juan Zhang
- Zhuzhou Central Hospital, Reproductive center, Zhuzhou, China
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20
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Liu Y, Ma Y. Clinical applications of metagenomics next-generation sequencing in infectious diseases. J Zhejiang Univ Sci B 2024; 25:471-484. [PMID: 38910493 PMCID: PMC11199093 DOI: 10.1631/jzus.b2300029] [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: 01/09/2023] [Accepted: 06/06/2023] [Indexed: 05/23/2024]
Abstract
Infectious diseases are a great threat to human health. Rapid and accurate detection of pathogens is important in the diagnosis and treatment of infectious diseases. Metagenomics next-generation sequencing (mNGS) is an unbiased and comprehensive approach for detecting all RNA and DNA in a sample. With the development of sequencing and bioinformatics technologies, mNGS is moving from research to clinical application, which opens a new avenue for pathogen detection. Numerous studies have revealed good potential for the clinical application of mNGS in infectious diseases, especially in difficult-to-detect, rare, and novel pathogens. However, there are several hurdles in the clinical application of mNGS, such as: (1) lack of universal workflow validation and quality assurance; (2) insensitivity to high-host background and low-biomass samples; and (3) lack of standardized instructions for mass data analysis and report interpretation. Therefore, a complete understanding of this new technology will help promote the clinical application of mNGS to infectious diseases. This review briefly introduces the history of next-generation sequencing, mainstream sequencing platforms, and mNGS workflow, and discusses the clinical applications of mNGS to infectious diseases and its advantages and disadvantages.
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Affiliation(s)
- Ying Liu
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China
| | - Yongjun Ma
- Department of Clinical Laboratory, Affiliated Jinhua Hospital, Zhejiang University School of Medicine, Jinhua 321000, China.
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21
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Zheng YR, Chen XH, Chen Q, Cao H. Metagenomic Next-generation Sequencing for Pathogen Identification in Bronchoalveolar Lavage Fluid From Neonates Receiving Extracorporeal Membrane Oxygenation. Pediatr Infect Dis J 2024; 43:371-377. [PMID: 38306604 DOI: 10.1097/inf.0000000000004250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2024]
Abstract
BACKGROUND Neonates on extracorporeal membrane oxygenation (ECMO) are at high risk of infection. Rapid and accurate identification of pathogens is essential to improve the prognosis of children on ECMO. Metagenome next-generation sequencing (mNGS) has been used in recent years to detect pathogenic bacteria, but evidence for its use in neonates on ECMO is lacking. METHODS This retrospective study was conducted using an electronic medical record system. We analyzed the results of mNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid of neonates receiving ECMO support with pulmonary infections in our hospital from July 2021 to January 2023. RESULTS We screened 18 ECMO-supported neonates with pneumonia for inclusion in the study. The median age of the included children was 2 (1-4) days, the median gestational age was 38.3 (33-40 +4 ) weeks, and the median weight was 3.3 (2.2-4.8) kg. The detection rate of mNGS was 77.8% (14/18), higher than the 44.4% (8/18) of CMT ( P = 0.04). A total of 20 pathogens were detected in mNGS, with the top 3 most common pathogens being Klebsiella pneumoniae , Acinetobacter baumannii and Escherichia coli . Mixed infections were found in 14 cases (77.8%), including 13 cases (72.2%) with mixed infections detected by mNGS and 7 cases (27.8%) with mixed infections detected by CMT. A total of 9 children underwent treatment changes based on mNGS results and all of them experienced relief of symptoms. CONCLUSION Compared with CMT, mNGS can detect pathogens earlier and more sensitively, and may play an important role in ECMO-supported neonatal pneumonia pathogen detection and optimization of antibiotic therapy.
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Affiliation(s)
- Yi-Rong Zheng
- From the Department of Cardiac Surgery, College of Clinical Medicine for Obstetrics & Gynecology and Pediatrics, Fujian Medical University, Fujian Children's Hospital (Fujian Branch of Shanghai Children's Medical Center), Fuzhou, China
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22
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Tian Y, Duan Y, Gao R, Gao W, Xu S, Wang S, Li F, Fang F, Su R, Chen Y, Xu N, Li W, Zhang L, Zhou JX. DIAGNOSTIC PERFORMANCE OF CENTRAL NERVOUS SYSTEM INFECTIONS IN PATIENTS WITH NEUROSURGICAL INTENSIVE CARE USING METAGENOMIC NEXT-GENERATION SEQUENCING: A PROSPECTIVE OBSERVATIONAL STUDY. Shock 2024; 61:375-381. [PMID: 38517267 DOI: 10.1097/shk.0000000000002320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
ABSTRACT Background. Identifying the causative pathogens of central nervous system infections (CNSIs) is crucial, but the low detection rate of traditional culture methods in cerebrospinal fluid (CSF) has made the pathogenic diagnosis of CNSIs a longstanding challenge. Patients with CNSIs after neurosurgery often overlap with inflammatory and bleeding. Metagenomic next-generation sequencing (mNGS) has shown some benefits in pathogen detection. This study aimed to investigate the diagnostic performance of mNGS in the etiological diagnosis of CNSIs in patients after neurosurgery. Methods. In this prospective observational study, we enrolled patients with suspected CNSIs after neurosurgical operations who were admitted to the intensive care unit of Beijing Tiantan Hospital. All enrolled patients' CSF was tested using mNGS and pathogen culture. According to comprehensive clinical diagnosis, the enrolled patients were divided into CNSIs group and non-CNSIs group to compare the diagnostic efficiency of mNGS and pathogen culture. Results. From December 2021 to March 2023, 139 patients were enrolled while 66 in CNSIs group and 73 in non-CNSIs. The mNGS exceeded culture in the variety and quantity of pathogens detected. The mNGS outperformed traditional pathogen culture in terms of positive percent agreement (63.63%), accuracy (82.01%), and negative predictive value (75.00%), with statistically significant differences ( P < 0.05) for traditional pathogen culture. The mNGS also detected bacterial spectrum and antimicrobial resistance genes. Conclusions. Metagenomics has the potential to assist in the diagnosis of patients with CNSIs who have a negative culture.
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Affiliation(s)
- Ying Tian
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Duan
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ran Gao
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Wei Gao
- Department of Microbiology and Immunology, Peter Doherty Institute, University of Melbourne, Melbourne, Australia
| | - Shanshan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Shuya Wang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Fangqiang Li
- Department of Clinical Diagnosis, Laboratory of Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Rui Su
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Yuqing Chen
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Ningyuan Xu
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | | | - Linlin Zhang
- Department of Critical Care Medicine, Beijing Tiantan Hospital, Capital Medical University, Beijing, China
| | - Jian-Xin Zhou
- Beijing Shijitan Hospital, Capital Medical University, Beijing, China
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23
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Wang C, Yin X, Ma W, Zhao L, Wu X, Ma N, Cao Y, Zhang Q, Ma S, Xu L, Wang X. Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia. Respir Res 2024; 25:68. [PMID: 38317206 PMCID: PMC10840150 DOI: 10.1186/s12931-023-02654-5] [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: 10/13/2023] [Accepted: 12/25/2023] [Indexed: 02/07/2024] Open
Abstract
OBJECTIVE Metagenomic next-generation sequencing (mNGS), as an emerging technique for pathogen detection, has been widely used in clinic. However, reports on the application of mNGS in cancer patients with severe pneumonia remain limited. This study aims to evaluate the diagnostic performance of bronchoalveolar lavage fluid (BALF) mNGS in cancer patients complicated with severe pneumonia. METHODS A total of 62 cancer patients with severe pneumonia simultaneously received culture and mNGS of BALF were enrolled in this study. We systematically analyzed the diagnostic significance of BALF mNGS. Subsequently, optimization of anti-infective therapy based on the distribution of pathogens obtained from BALF mNGS was also assessed. RESULTS For bacteria and fungi, the positive detection rate of mNGS was significantly higher than culture method (91.94% versus 51.61%, P < 0.001), especially for poly-microbial infections (70.97% versus 12.90%, P < 0.001). Compared with the culture method, mNGS exhibited a diagnostic sensitivity of 100% and a specificity of 16.67%, with the positive predictive value (PPV) and negative predictive value (NPV) being 56.14% and 100%, respectively. The agreement rate between these two methods was 59.68%, whereas kappa consensus analysis indicated a poor concordance (kappa = 0.171). After receipt of BALF mNGS results, anti-infective treatment strategies in 39 out of 62 cases (62.90%) were optimized. Moreover, anti-tumor therapy was a high-risk factor for mixed infections (87.18% versus 65.22%, P = 0.04). CONCLUSIONS The present study showed that cancer patients with severe pneumonia, especially those received anti-tumor therapy, were more likely to have poly-microbial infections. BALF mNGS can provide a rapid and comprehensive pathogen distribution of pulmonary infection, making it a promising technique in clinical practice, especially for optimizing therapeutic strategies for cancer patients.
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Affiliation(s)
- Chao Wang
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xiaojuan Yin
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Wenqing Ma
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Li Zhao
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China
| | - Xuhong Wu
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Nan Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Yuepeng Cao
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Quanli Zhang
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China
| | - Shuliang Ma
- Department of Critical Care Medicine, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China
| | - Lin Xu
- Department of Thoracic Surgery, Jiangsu Cancer Hospital, Jiangsu Institute of Cancer Research, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, Jiangsu, 210009, China.
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, 42 Baiziting Road, Xuanwu District, Nanjing, Jiangsu, 210009, China.
| | - Xuerong Wang
- Department of Pharmacology, Nanjing Medical University, 101 Longmian Boulevard, Nanjing, Jiangsu, 210029, China.
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24
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Liu RT, Zhang D, Li S, Chen Y, Wan XX, Diao ST, Weng L, Peng JM, Du B. Comparison of different criteria of metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in critically ill patients. Diagn Microbiol Infect Dis 2024; 108:116135. [PMID: 38065016 DOI: 10.1016/j.diagmicrobio.2023.116135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/09/2023] [Accepted: 11/11/2023] [Indexed: 01/22/2024]
Abstract
OBJECTIVE To compare different criteria of Metagenomic Next-Generation Sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) for diagnosing invasive pulmonary aspergillosis (IPA). METHODS We compared the diagnostic agreement and performances of six BALF mNGS-derived criteria (SDSMRN>1, SDSMRN≥3, SMRN≥10, SMRN≥50, RPM ratio≥10, and relative abundance of genus>30 %) in pneumonia patients. RESULTS A total of 115 patients were analyzed, with 28 identified with IPA. Diagnostic agreement among the six mNGS-derived criteria was moderate, with a Cohen's kappa of 0.577(P < 0.001). mNGS-derived criteria had low sensitivity ranging from 21.4 % to 57.1 % and high specificity from 88 % to 92 %. The optimal threshold of SDSMRN, SMRN, RPM ratio, and relative abundance of genus for diagnosing IPA were 5, 0.25, 8, and 20 %, respectively. Although using the optimal threshold, the sensitivity of mNGS is lower than 50 %. CONCLUSIONS All mNGS-derived criteria had low sensitivity for diagnosing IPA. A combination of mNGS and conventional mycological tests may be the best diagnostic strategy.
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Affiliation(s)
- Rui-Ting Liu
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China; Department of Critical Care Medicine, The Second Affiliated Hospital of Air Force Medical University, Shaanxi, China
| | - Dong Zhang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Shan Li
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Yan Chen
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Xi-Xi Wan
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Shi-Tong Diao
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Li Weng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
| | - Jin-Min Peng
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China.
| | - Bin Du
- Medical ICU, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Peking, China
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25
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Liang W, Zhang Q, Qian Q, Wang M, Ding Y, Zhou J, Zhu Y, Jin Y, Chen X, Kong H, Song W, Lu X, Wu X, Xu X, Dai S, Sun W. Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections. Ann Clin Microbiol Antimicrob 2024; 23:10. [PMID: 38302964 PMCID: PMC10835912 DOI: 10.1186/s12941-024-00670-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Accepted: 01/20/2024] [Indexed: 02/03/2024] Open
Abstract
OBJECTIVE This study aims to identify the most effective diagnostic method for distinguishing pathogenic and non-pathogenic Gram-negative bacteria (GNB) in suspected pneumonia cases using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples. METHODS The effectiveness of mNGS was assessed on BALF samples collected from 583 patients, and the results were compared with those from microbiological culture and final clinical diagnosis. Three interpretational approaches were evaluated for diagnostic accuracy. RESULTS mNGS outperformed culture significantly. Among the interpretational approaches, Clinical Interpretation (CI) demonstrated the best diagnostic performance with a sensitivity of 87.3%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.3%. CI's specificity was significantly higher than Simple Interpretation (SI) at 37.9%. Additionally, CI excluded some microorganisms identified as putative pathogens by SI, including Haemophilus parainfluenzae, Haemophilus parahaemolyticus, and Klebsiella aerogenes. CONCLUSION Proper interpretation of mNGS data is crucial for accurately diagnosing respiratory infections caused by GNB. CI is recommended for this purpose.
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Affiliation(s)
- Wenyan Liang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Qun Zhang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Qian Qian
- Jiangsu Health Vocational College, Nanjing, 211800, China
| | - Mingyue Wang
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yuchen Ding
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Ji Zhou
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yi Zhu
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Yu Jin
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xuesong Chen
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Hui Kong
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wei Song
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Xin Lu
- Department of Respiratory and Critical Care Medicine, The Affiliated Jiangning Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaodong Wu
- Department of Respiratory and Critical Care Medicine, Shanghai East Hospital, Tongji University, Shanghai, China
| | - Xiaoyong Xu
- Department of respiratory and critical care medicine, The Second Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, Jiangsu, 210000, China
| | - Shanling Dai
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China
| | - Wenkui Sun
- Department of Respirology and Critical Care Medicine, The First Affiliated Hospital of Nanjing Medical University, Nanjing, 210029, China.
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Wanghu H, Li Y, Huang J, Pu K, Guo F, Zhong P, Wang T, Yuan J, Yu Y, Chen J, Liu J, Chen JJ, Hu C. A novel synthetic nucleic acid mixture for quantification of microbes by mNGS. Microb Genom 2024; 10:001199. [PMID: 38358316 PMCID: PMC10926700 DOI: 10.1099/mgen.0.001199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in clinical specimens by mNGS, which co-sequence the target DNA extracted from the specimens along with a set of synthetic dsDNA molecules used as Internal-Standard (IS). The assay facilitates the conversion of microbial reads into their copy numbers based on IS reads utilizing a mathematical model proposed in this study. The performance of KCQ was systemically evaluated using commercial mock microbes with varying IS input amounts, different proportions of human genomic DNA, and at varying amounts of sequence analysis data. Subsequently, KCQ was applied in microbial quantitation in 36 clinical specimens including blood, bronchoalveolar lavage fluid, cerebrospinal fluid and oropharyngeal swabs. A total of 477 microbe genetic fragments were screened using the bioinformatic system. Of these 83 fragments were quantitatively compared with digital droplet PCR (ddPCR), revealing a correlation coefficient of 0.97 between the quantitative results of KCQ and ddPCR. Our study demonstrated that KCQ presents a practical approach for the quantitative analysis of microbes by mNGS in clinical samples.
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Affiliation(s)
- Hailing Wanghu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yingzhen Li
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jin Huang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Kangze Pu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Fengming Guo
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Peiwen Zhong
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Ting Wang
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jianying Yuan
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Yan Yu
- Changsha KingMed Diagnostics Group Co., Ltd., Changsha, Huna, 410000, PR China
| | - Jiachang Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jun Liu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
| | - Jason J. Chen
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
| | - Chaohui Hu
- Guangzhou KingCreate Biotechnology Co., Ltd., Guangzhou, Guangdong, 510005, PR China
- KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, Guangdong, 511436, PR China
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Xu CB, Su SS, Yu J, Lei X, Lin PC, Wu Q, Zhou Y, Li YP. Risk factors and predicting nomogram for the clinical deterioration of non-severe community-acquired pneumonia. BMC Pulm Med 2024; 24:57. [PMID: 38280994 PMCID: PMC10821265 DOI: 10.1186/s12890-023-02813-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 12/11/2023] [Indexed: 01/29/2024] Open
Abstract
BACKGROUND Currently, there remains insufficient focus on non-severe community-acquired pneumonia (CAP) patients who are at risk of clinical deterioration, and there is also a dearth of research on the related risk factors. Early recognition of hospitalized patients at risk of clinical deterioration will be beneficial for their clinical management. METHOD A retrospective study was conducted in The First Affiliated Hospital of Wenzhou Medical University, China, spanning from January 1, 2018 to April 30, 2022, and involving a total of 1,632 non-severe CAP patients. Based on whether their condition worsened within 72 h of admission, patients were divided into a clinical deterioration group and a non-clinical deterioration group. Additionally, all patients were randomly assigned to a training set containing 75% of patients and a validation set containing 25% of patients. In the training set, risk factors for clinical deterioration in patients with non-severe CAP were identified by using LASSO regression analysis and multivariate logistic regression analysis. A nomogram was developed based on identified risk factors. The effectiveness of the nomogram in both the training and validation sets was assessed using Receiver Operating Characteristic (ROC) curves, calibration curves, and decision curve analysis (DCA). RESULTS Age, body mass index (BMI), body temperature, cardiovascular comorbidity, respiratory rate, LDH level, lymphocyte count and D-dimer level were identified as risk factors associated with the clinical deterioration of non-severe CAP within 72 h of admission. The area under curve (AUC) value of the nomogram was 0.78 (95% CI: 0.74-0.82) in the training set and 0.75 (95% CI: 0.67-0.83) in the validation set. Furthermore, the calibration curves for both the training and validation sets indicated that the predicted probability of clinical deterioration aligned with the actual probability. Additionally, DCA revealed clinical utility for the nomogram at a specific threshold probability. CONCLUSION The study successfully identified the risk factors linked to the clinical deterioration of non-severe CAP and constructed a nomogram for predicting the probability of deterioration. The nomogram demonstrated favorable predictive performance and has the potential to aid in the early identification and management of non-severe CAP patients at elevated risk of deterioration.
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Affiliation(s)
- Cheng-Bin Xu
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Shan-Shan Su
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Jia Yu
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Xiong Lei
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Peng-Cheng Lin
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Qing Wu
- The Center of Laboratory and Diagnosis, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, Zhejiang Province, 325015, People's Republic of China
| | - Ying Zhou
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China.
| | - Yu-Ping Li
- The Key Laboratory of Interventional Pulmonology of Zhejiang Province, Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Wenzhou Medical University, South Baixiang, Ouhai District, Wenzhou, Zhejiang Province, 325015, People's Republic of China.
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Guo Q, Xiao Y, Zhang S. Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis. Heliyon 2024; 10:e23188. [PMID: 38148812 PMCID: PMC10750151 DOI: 10.1016/j.heliyon.2023.e23188] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Revised: 10/07/2023] [Accepted: 11/29/2023] [Indexed: 12/28/2023] Open
Abstract
Background Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species. Methods This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies. Results This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4. Conclusion The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.
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Affiliation(s)
- Qiang Guo
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
| | - Yang Xiao
- School of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Shihai Zhang
- Department of Clinical Laboratory, Anhui Provincial Children’s Hospital, Hefei, 230000, Anhui, China
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Yan M, Zou X, Wang Y, Wang C, Wang Y, Liu Z, Shang L, Cui X, Cao B. Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study. J Infect Dis 2024; 229:223-231. [PMID: 37506257 DOI: 10.1093/infdis/jiad296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The impact of metagenomic next-generation sequencing (mNGS) on antimicrobial stewardship in patients with lower respiratory tract infections (LRTIs) is still unknown. METHODS This retrospective cohort study included patients who had LRTIs diagnosed and underwent bronchoalveolar lavage between September 2019 and December 2020. Patients who underwent both mNGS and conventional microbiologic tests were classified as the mNGS group, while those with conventional tests only were included as a control group. A 1:1 propensity score match for baseline variables was conducted, after which changes in antimicrobial stewardship between the 2 groups were assessed. RESULTS A total of 681 patients who had an initial diagnosis of LRTIs and underwent bronchoalveolar lavage were evaluated; 306 patients were finally included, with 153 in each group. mNGS was associated with lower rates of antibiotic escalation than in the control group (adjusted odds ratio, 0.466 [95% confidence interval, .237-.919]; P = .02), but there was no association with antibiotic de-escalation. Compared with the control group, more patients discontinued the use of antivirals in the mNGS group. CONCLUSIONS The use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals, but not contribute to antibiotic de-escalation in patients with LRTIs.
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Affiliation(s)
- Mengwei Yan
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Chenhui Wang
- Department of Anesthesiology, Sanbo Brain Hospital, Capital Medical University, Beijing, China
| | - Yimin Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Zhibo Liu
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Lianhan Shang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Xiaojing Cui
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Capital Medical University, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, National Clinical Research Center for Respiratory Diseases, China-Japan Friendship Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Tsinghua University School of Medicine, Beijing, China
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Yang L, Wang K, Li Y, Li W, Liu D. Joint application of metagenomic next-generation sequencing and histopathological examination for the diagnosis of pulmonary infectious disease. Microbiol Spectr 2024; 12:e0058623. [PMID: 38038451 PMCID: PMC10783098 DOI: 10.1128/spectrum.00586-23] [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: 02/14/2023] [Accepted: 08/28/2023] [Indexed: 12/02/2023] Open
Abstract
IMPORTANCE The diagnosis of some pulmonary infectious diseases and their pathogens is very difficult. A more precise diagnosis of pulmonary infectious diseases can help clinicians use proper antibiotics as well as reduce the development of drug-resistant bacteria. In this study, we performed both mNGS and pathology on lung puncture biopsy tissue from patients and found that combined mNGS and histopathology testing was significantly more effective than histopathology testing alone in detecting infectious diseases and identifying infectious diseases. In addition, the combined approach improves the detection rate of pathogenic microorganisms in infectious diseases and can be used to guide precision clinical treatment.
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Affiliation(s)
- Linhui Yang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Kaige Wang
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yalun Li
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Weimin Li
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Dan Liu
- Department of Pulmonary and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, China
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Zhao L, Formslag CR, Zhang Q, Cowan BC, Mayberry TG, Barnhill AR, Wang Y, Fang Y. Determination of Ideal Factors for Early Adoption and Standardization of Metagenomic Next-generation Sequencing for Respiratory System Infections. Curr Pharm Biotechnol 2024; 25:2266-2277. [PMID: 38347797 DOI: 10.2174/0113892010246350231030042340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 09/07/2023] [Accepted: 09/19/2023] [Indexed: 09/26/2024]
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) demonstrates great promise as a diagnostic tool for determining the cause of pathogenic infections. The standard diagnostic procedures (SDP) include smears and cultures and are typically viewed as less sensitive and more time-consuming when compared to mNGS. There are concerns about the logistics and ease of transition from SDP to mNGS. mNGS lacks standardization of collection processes, databases, and sequencing. Additionally, there is the burden of training clinicians on interpreting mNGS results. OBJECTIVE Until now, few studies have explored factors that could be used as early adoption candidates to ease the transition between SDP and mNGS. This study evaluated 123 patients who had received both SDP and mNGS and compared several variables across a diagnostic test evaluation. METHODS The diagnostic test evaluation observed metrics such as sensitivity, specificity, positive and negative likelihood ratios (PLR, NLR), positive and negative predictive values (PPV, NPV), and accuracy. Factors included various sample sources such as bronchoalveolar lavage fluid (BALF), lung tissue, and cerebral spinal fluid (CSF). An additional factor observed was the patient's immune status. RESULTS Pathogen detection was found to be significantly greater for mNGS for total patients, BALF sample source, CSF sample source, and non-immunocompromised patients (p<0.05). Pathogen detection was found to be insignificant for lung tissue sample sources and immunocompromised patients. Sensitivity, PLR, NLR, PPV, NPV, and accuracy appeared to be higher with mNGS for the total patients, BALF sample source, and non-immunocompromised patients when compared with SDP (p<0.05). CONCLUSION With higher metrics in sensitivity, specificity, PLR, NLR, PPV, NPV, and accuracy for overall patients, mNGS may prove a better diagnostic tool than SDP. When addressing sample sources, mNGS for BALF-collected samples appeared to have higher scores than SDP for the same metrics. When patients were in a non-immunocompromised state, mNGS also demonstrated greater diagnostic benefits to BALF and overall patients compared to SDP. This study demonstrates that using BALF as a sample source and selecting non-immunocompromised patients may prove beneficial as early adoption factors for mNGS standard protocol. Such a study may pave the road for mNGS as a routine clinical method for determining the exact pathogenic etiology of lung infections.
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Affiliation(s)
- Lei Zhao
- The Department of Respiratory Medicine, the Second People's Hospital of Hefei and Hefei Second People's Hospital Affiliated to Bengbu Medical College, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230011, China
| | - Cole R Formslag
- Department of Microbiology, Immunology & Pathology, Des Moines University, Des Moines, IA, 50312, USA
| | - Qing Zhang
- The Department of Respiratory Medicine, the Second People's Hospital of Hefei and Hefei Second People's Hospital Affiliated to Bengbu Medical College, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230011, China
| | - Braydon C Cowan
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Trenton G Mayberry
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Aaron R Barnhill
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO, 65212, USA
| | - Yongsheng Wang
- The Department of Respiratory Medicine, the Second People's Hospital of Hefei and Hefei Second People's Hospital Affiliated to Bengbu Medical College, Hefei Hospital Affiliated to Anhui Medical University, Hefei, Anhui 230011, China
| | - Yujiang Fang
- Department of Microbiology, Immunology & Pathology, Des Moines University, Des Moines, IA, 50312, USA
- Department of Surgery, University of Missouri School of Medicine, Columbia, MO, 65212, USA
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Deng Z, Li C, Wang Y, Wu F, Liang C, Deng W, Wang Y. Targeted next-generation sequencing for pulmonary infection diagnosis in patients unsuitable for bronchoalveolar lavage. Front Med (Lausanne) 2023; 10:1321515. [PMID: 38179267 PMCID: PMC10764475 DOI: 10.3389/fmed.2023.1321515] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 12/04/2023] [Indexed: 01/06/2024] Open
Abstract
Background Targeted next-generation sequencing (tNGS) has emerged as a rapid diagnostic technology for identifying a wide spectrum of pathogens responsible for pulmonary infections. Methods Sputum samples were collected from patients unable or unwilling to undergo bronchoalveolar lavage. These samples underwent tNGS analysis to diagnose pulmonary infections. Retrospective analysis was performed on clinical data, and the clinical efficacy of tNGS was compared to conventional microbiological tests (CMTs). Results This study included 209 pediatric and adult patients with confirmed pulmonary infections. tNGS detected 45 potential pathogens, whereas CMTs identified 23 pathogens. The overall microbial detection rate significantly differed between tNGS and CMTs (96.7% vs. 36.8%, p < 0.001). Among the 76 patients with concordant positive results from tNGS and CMTs, 86.8% (66/76) exhibited full or partial agreement. For highly pathogenic and rare/noncolonized microorganisms, tNGS, combined with comprehensive clinical review, directly guided pathogenic diagnosis and antibiotic treatment in 21 patients. This included infections caused by Mycobacterium tuberculosis complex, certain atypical pathogens, Aspergillus, and nontuberculous Mycobacteria. Among the enrolled population, 38.8% (81/209) of patients adjusted their treatment based on tNGS results. Furthermore, tNGS findings unveiled age-specific heterogeneity in pathogen distribution between children and adults. Conclusion CMTs often fall short in meeting the diagnostic needs of pulmonary infections. This study highlights how tNGS of sputum samples from patients who cannot or will not undergo bronchoalveolar lavage yield valuable insights into potential pathogens, thereby enhancing the diagnosis of pulmonary infections in specific cases.
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Affiliation(s)
- Zhenfeng Deng
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning, China
| | - Chunhong Li
- Clinical Genome Center, Guangxi KingMed Diagnostics, Nanning, China
| | - Yingjin Wang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Fengwen Wu
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Chunfang Liang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Wei Deng
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
| | - Yuanli Wang
- Precision Medicine Laboratory, The First People’s Hospital of Qinzhou, The Tenth Affiliated Hospital of Guangxi Medical University, Qinzhou, China
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Jin D, Le J, Yang Q, Cai Q, Dai H, Luo L, Tong J, Shu W. Pneumocystis jirovecii with high probability detected in bronchoalveolar lavage fluid of chemotherapy-related interstitial pneumonia in patients with lymphoma using metagenomic next-generation sequencing technology. Infect Agent Cancer 2023; 18:80. [PMID: 38057898 DOI: 10.1186/s13027-023-00556-1] [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: 08/22/2023] [Accepted: 11/09/2023] [Indexed: 12/08/2023] Open
Abstract
BACKGROUND Previous studies achieved low microbial detection rates in lymphoma patients with interstitial pneumonia (IP) after chemotherapy. However, the metagenomic next-generation sequencing (mNGS) is a comprehensive approach that is expected to improve the pathogen identification rate. Thus far, reports on the use of mNGS in lymphoma patients with chemotherapy-related IP remain scarce. In this study, we summarized the microbial detection outcomes of lymphoma patients with chemotherapy-related IP through mNGS testing of bronchoalveolar lavage fluid (BALF). METHODS Fifteen lymphoma patients with chemotherapy-related IP were tested for traditional laboratory microbiology, along with the mNGS of BALF. Then, the results of mNGS and traditional laboratory microbiology were compared. RESULTS Of the 15 enrolled patients, 11 received rituximab and 8 were administered doxorubicin hydrochloride liposome. The overall microbial yield was 93.3% (14/15) for mNGS versus 13.3% (2/15) for traditional culture methods (P ≤ 0.05). The most frequently detected pathogens were Pneumocystis jirovecii (12/15, 80%), Cytomegalovirus (4/15, 26.7%), and Epstein-Barr virus (3/15, 20%). Mixed infections were detected in 10 cases. Five patients recovered after the treatment with antibiotics alone without glucocorticoids. CONCLUSION Our findings obtained through mNGS testing of BALF suggested a high microbial detection rate in lymphoma patients with IP after chemotherapy. Notably, there was an especially high detection rate of Pneumocystis jirovecii. The application of mNGS in patients with chemotherapy-related IP was more sensitive.
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Affiliation(s)
- Dian Jin
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Jing Le
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Qianqian Yang
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Qianqian Cai
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Hui Dai
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Liufei Luo
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Jiaqi Tong
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China
| | - Wenxiu Shu
- Department of Hematology, Ningbo Medical Treatment Center Li Huili Hospital, No.1111, Jiangnan road, Ningbo, 315010, China.
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Luo H, Jiang L, Chen J, Wang D, Kong Y, Cao G. Chlamydia psittaci Pneumonia in a patient with motor neuron disease: a case report. BMC Infect Dis 2023; 23:852. [PMID: 38053032 PMCID: PMC10699031 DOI: 10.1186/s12879-023-08860-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Motor neuron disease (MND) is a fatal neurodegenerative disorder that leads to progressive loss of motor neurons. Chlamydia psittaci (C. psittaci) is a rare etiology of community-acquired pneumonia characterized primarily by respiratory distress. We reported a case of C. psittaci pneumonia complicated with motor neuron disease (MND). CASE PRESENTATION A 74-year-old male was referred to the Shaoxing Second Hospital at January, 2022 complaining of fever and fatigue for 2 days. The patient was diagnosed of MND with flail arm syndrome 1 year ago. The metagenomic next-generation sequencing (mNGS) of sputum obtained through bedside fiberoptic bronchoscopy showed C. psittaci infection. Then doxycycline was administrated and bedside fiberoptic bronchoscopy was performed to assist with sputum excretion. Computed Tomography (CT) and fiberoptic bronchoscopy revealed a significant decrease in sputum production. On day 24 after admission, the patient was discharged with slight dyspnea, limited exercise tolerance. One month later after discharge, the patient reported normal respiratory function, and chest CT showed significant absorption of sputum. CONCLUSIONS The mNGS combined with bedside fiberoptic bronchoscopy could timely detect C. psittaci infection. Bedside fiberoptic bronchoscopy along with antibiotic therapy may be effective for C. psittaci treatment.
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Affiliation(s)
- Huade Luo
- Department of Emergency Intensive Care Unit, Shaoxing Second Hospital, Shaoxing, 312000, Zhejiang Province, China
| | - Lingling Jiang
- Department of Blood donation service, Shaoxing blood center, Shaoxing, 312000, Zhejiang Province, China.
| | - Jie Chen
- Department of Emergency Intensive Care Unit, Shaoxing Second Hospital, Shaoxing, 312000, Zhejiang Province, China
| | - Dongying Wang
- Department of Emergency Intensive Care Unit, Shaoxing Second Hospital, Shaoxing, 312000, Zhejiang Province, China
| | - Yingying Kong
- Department of Emergency Intensive Care Unit, Shaoxing Second Hospital, Shaoxing, 312000, Zhejiang Province, China
| | - Guangli Cao
- Department of Emergency Intensive Care Unit, Shaoxing Second Hospital, Shaoxing, 312000, Zhejiang Province, China
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Yao W, Feng S, Yang L, Lin Y, Zhang M, Cai K, Xing L, Yuan K, Lu H, Wang F. Differences caused by blood and secretion samples for the detection of Klebsiella pneumoniae using metagenomic next-generation sequencing: A comparative analysis. J Infect 2023; 87:438-444. [PMID: 37657648 DOI: 10.1016/j.jinf.2023.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Affiliation(s)
- Weiming Yao
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Shiyan Feng
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Liuqing Yang
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Yuanlong Lin
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Mingxia Zhang
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Kanru Cai
- Institute for Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Southern University of Science and Technology, Shenzhen, Guangdong, China
| | - Li Xing
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Ke Yuan
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Hongzhou Lu
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Sou thern University of Science and Technology, Shenzhen, Guangdong, China.
| | - Fuxiang Wang
- Department of Infectious Diseases, National Clinical Research Center for Infectious Disease, Shenzhen Third People's Hospital, The Second Affiliated Hospital, School of Medicine, Sou thern University of Science and Technology, Shenzhen, Guangdong, China.
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He Y, Geng S, Mei Q, Zhang L, Yang T, Zhu C, Fan X, Wang Y, Tong F, Gao Y, Fang X, Bao R, Sheng X, Pan A. Diagnostic Value and Clinical Application of Metagenomic Next-Generation Sequencing for Infections in Critically Ill Patients. Infect Drug Resist 2023; 16:6309-6322. [PMID: 37780531 PMCID: PMC10541086 DOI: 10.2147/idr.s424802] [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: 06/07/2023] [Accepted: 09/14/2023] [Indexed: 10/03/2023] Open
Abstract
Objective To evaluate the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for infections in critically ill patients. Methods Comparison of diagnostic performance of mNGS and conventional microbiological testing for pathogens was analyzed in 234 patients. The differences between immunocompetent and immunocompromised individuals in mNGS-guided anti-infective treatment adjustment were also analyzed. Results The sensitivity and specificity of mNGS for bacterial and fungal detection were 96.6% (95% confidence interval [CI], 93.5%-99.6%) and 83.1% (95% CI, 75.2%-91.1%), and 85.7% (95% CI, 71.9%-99.5%) and 93.2% (95% CI, 89.7%-96.7%), respectively. Overall, 152 viruses were detected by mNGS, but in which 28 viruses were considered causative agents. The proportion of mNGS-guided beneficial anti-infective therapy adjustments in the immunocompromised group was greater than in the immunocompetent group (48.5% vs 30.1%; P=0.008). In addition, mNGS-guided anti-infective regimens with peripheral blood and BALF specimens had the highest proportion (39.0%; 40.0%), but the proportion of patients not helpful due to peripheral blood mNGS was also as high as 22.0%. Conclusion mNGS might be a promising technology to provide precision medicine for critically ill patients with infection.
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Affiliation(s)
- Yuxi He
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Shike Geng
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Qing Mei
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Lei Zhang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Tianjun Yang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Chunyan Zhu
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaoqin Fan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yinzhong Wang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Fei Tong
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Yu Gao
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Xiaowei Fang
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
| | - Renren Bao
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
| | - Ximei Sheng
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
| | - Aijun Pan
- Department of Intensive Care Unit, the First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Affiliated Provincial Hospital of Anhui Medical University, Hefei, Anhui, People’s Republic of China
- Department of Intensive Care Unit, the Training Center of Anhui Provincial Hospital, Wannan Medical College, Wuhu, Anhui, People’s Republic of China
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Lei Y, Guo Q, Liu J, Huang H, Han P. Staphylococcus cohnii infection diagnosed by metagenomic next generation sequencing in a patient on hemodialysis with cirrhotic ascites: a case report. Front Cell Infect Microbiol 2023; 13:1240283. [PMID: 37808911 PMCID: PMC10556727 DOI: 10.3389/fcimb.2023.1240283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023] Open
Abstract
Background Patients with spontaneous bacterial peritonitis (SBP) often just receive empirical antibiotic therapy, as pathogens can be identified in only few patients using the techniques of conventional culture. Metagenomic next generation sequencing (mNGS) is a useful tool for diagnosis of infectious diseases. However, clinical application of mNGS in diagnosis of infected ascites of cirrhotic patients is rarely reported. Case presentation A 53-year-old male with cirrhosis on regular hemodialysis presented with continuous abdominal pain. After treatment with empiric antibiotics, his inflammatory parameters decreased without significant relief of abdominal pain. Finally, based on ascites mNGS detection, he was diagnosed as infection of Staphylococcus cohnii (S.cohnii), a gram-positive opportunistic pathogen. With targeted antibiotic treatment, the bacterial peritonitis was greatly improved and the patient's abdominal pain was significantly alleviated. Conclusions When conventional laboratory diagnostic methods and empirical antibiotic therapy fail, proper application of mNGS can help identify pathogens and significantly improve prognosis and patients' symptoms.
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Affiliation(s)
| | | | | | - Huanjun Huang
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Ping Han
- Department of Gastroenterology, Tongji Hospital of Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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Tekin A, Truong HH, Rovati L, Lal A, Gerberi DJ, Gajic O, O’Horo JC. The Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Diagnosing Pneumocystis Pneumonia: A Systemic Review and Meta-analysis. Open Forum Infect Dis 2023; 10:ofad442. [PMID: 37674635 PMCID: PMC10478158 DOI: 10.1093/ofid/ofad442] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023] Open
Abstract
Background Pneumocystis pneumonia (PCP) is a growing concern as the immunocompromised population expands. Current laboratory approaches are limited. This systematic review aimed to evaluate metagenomic next-generation sequencing (MNGS) tests' performance in detecting PCP. Methods Five databases were searched through December 19, 2022, to identify original studies comparing MNGS with clinically diagnosed PCP. To assess the accuracy, symmetric hierarchical summary receiver operating characteristic models were used. Results Eleven observational studies reporting 1442 patients (424 with PCP) were included. Six studies focused exclusively on recipients of biologic immunosuppression (none with HIV-associated immunosuppression). Six were exclusively on bronchoalveolar lavage, while 1 was on blood samples. The sensitivity of MGNS was 0.96 (95% CI, 0.90-0.99), and specificity was 0.96 (95% CI, 0.92-0.98), with negative and positive likelihood ratios of 0.02 (95% CI, 0.01-0.05) and 19.31 (95% CI, 10.26-36.36), respectively. A subgroup analysis of studies exclusively including bronchoalveolar lavage (BAL) and blood samples demonstrated a sensitivity of 0.94 (95% CI, 0.78-0.99) and 0.93 (95% CI, 0.80-0.98) and a specificity of 0.96 (95% CI, 0.88-0.99) and 0.98 (95% CI, 0.76-1.00), respectively. The sensitivity analysis on recipients of biologic immunosuppression showed a sensitivity and specificity of 0.96 (95% CI, 0.90-0.98) and 0.94 (95% CI, 0.84-0.98), respectively. The overall confidence in the estimates was low. Conclusions Despite the low certainty of evidence, MNGS detects PCP with high sensitivity and specificity. This also applies to recipients of biologic immunosuppression and tests performed exclusively on blood samples without the need for BAL. Further studies are required in individuals with HIV-associated immunosuppression.
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Affiliation(s)
- Aysun Tekin
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Hong Hieu Truong
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Lucrezia Rovati
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- School of Medicine and Surgery, University of Milano-Bicocca, Milan, Italy
| | - Amos Lal
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Danielle J Gerberi
- Mayo Clinic Library Services, Mayo Clinic College of Medicine and Science, Mayo Clinic, Rochester, Minnesota, USA
| | - Ognjen Gajic
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - John C O’Horo
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Division of Infectious Diseases, Mayo Clinic, Rochester, Minnesota, USA
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Guan Y, Yu C, Fei Y, Wang Q, Wang P, Zuo W, Wu H, Qi X, Shi Q. Case Report: Four cases of SARS-CoV-2-associated Guillain-Barré Syndrome with SARS-CoV-2-positive cerebrospinal fluid detected by metagenomic next-generation sequencing: a retrospective case series from China. Front Immunol 2023; 14:1258579. [PMID: 37701436 PMCID: PMC10493301 DOI: 10.3389/fimmu.2023.1258579] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 08/14/2023] [Indexed: 09/14/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often absent or at low levels in the cerebrospinal fluid (CSF) of patients with previous SARS-CoV-2-associated Guillain-Barré syndrome (GBS). This has led to speculation that SARS-CoV-2-associated GBS is more likely mediated by post-infectious immunity or a parainfection. This understanding has influenced the development of treatment regimens for SARS-CoV-2-associated GBS. This paper reports our experience with four Chinese patients with SARS-CoV-2-associated GBS who tested positive for SARS-CoV-2 RNA in the CSF. They developed symptoms of peripheral nerve damage 4-15 days after fever and confirmed SARS-CoV-2 infection, all of whom presented with progressive weakness of both lower limbs; three with autonomic nerve function impairment such as constipation and urination disorder; and one with polycranial neuritis and Miller-Fisher syndrome. Three patients were tested for anti-ganglioside antibodies, and one tested positive for GD1a-IgG. Four patients recovered well after treatment with anti-viral drugs combined with intravenous immunoglobulin. The present results showed that SARS-CoV-2 RNA can be detected via mNGS in the CSF of some patients with SARS-CoV-2-associated GBS, suggesting that SARS-CoV-2-associated GBS may have multiple pathogeneses.
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Affiliation(s)
- Yalin Guan
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Changshen Yu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Yunhan Fei
- Department of Emergency, Tianjin Huanhu Hospital, Tianjin, China
| | - Qiushi Wang
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
| | - Pan Wang
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Wenchao Zuo
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Hao Wu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
| | - Xuemei Qi
- Department of Neurology, The second hospital of tianjin medical university, Tianjin, China
| | - Qiyun Shi
- Infection Business Unit, Tianjin Novogene Med LAB Co., Ltd., Tianjin, China
- Infection Business Unit, Novogene Co., Ltd., Beijing, China
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Jia H, Liu H, Tu M, Wang Y, Wang X, Li J, Zhang G. Diagnostic efficacy of metagenomic next generation sequencing in bronchoalveolar lavage fluid for proven invasive pulmonary aspergillosis. Front Cell Infect Microbiol 2023; 13:1223576. [PMID: 37692168 PMCID: PMC10484620 DOI: 10.3389/fcimb.2023.1223576] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/02/2023] [Indexed: 09/12/2023] Open
Abstract
Objective To assess the diagnostic efficacy of metagenomic next generation sequencing (mNGS) for proven invasive pulmonary aspergillosis (IPA). Methods A total of 190 patients including 53 patients who had been diagnosed with proven IPA were retrospectively analyzed. Using the pathological results of tissue biopsy specimens as gold standard, we ploted the receiver operating characteristic (ROC) curve to determine the optimal cut-off value of mNGS species-specific read number (SSRN) of Aspergillus in bronchoalveolar lavage fluid (BALF)for IPA. Furthermore, we evaluated optimal cut-off value of mNGS SSRN in different populations. Results The optimal cut-off value of Aspergillus mNGS SSRN in BALF for IPA diagnosis was 2.5 for the whole suspected IPA population, and 1 and 4.5 for immunocompromised and diabetic patients, respectively. The accuracy of mNGS was 80.5%, 73.7% and 85.3% for the whole population, immunocompromised and diabetic patients, respectively. Conclusions The mNGS in BALF has a high diagnostic efficacy for proven IPA, superioring to Aspergillus culture in sputum and BALF and GM test in blood and BALF. However, the cut-off value of SSRN should be adjusted when in different population.
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Affiliation(s)
| | | | | | | | | | | | - Guojun Zhang
- Department of Pulmonary and Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
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Shen H, Liu T, Shen M, Zhang Y, Chen W, Chen H, Wang Y, Liu J, Tao J, He L, Lu G, Yan G. Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort. Front Cell Infect Microbiol 2023; 13:1200806. [PMID: 37655299 PMCID: PMC10466250 DOI: 10.3389/fcimb.2023.1200806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/27/2023] [Indexed: 09/02/2023] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples. Methods A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data. Results Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%). Conclusions mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.
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Affiliation(s)
- Huili Shen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Tingyan Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Meili Shen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yi Zhang
- Department of Clinical Epidemiology, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Weiming Chen
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Hanlin Chen
- Medical Department, Nanjing Dinfectome Technology Inc., Nanjing, Jiangsu, China
| | - Yixue Wang
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jing Liu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Jinhao Tao
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Liming He
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Guoping Lu
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
| | - Gangfeng Yan
- Pediatric Intensive Care Unit, Children’s Hospital of Fudan University, National Children’s Medical Center, Shanghai, China
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Zhong J, Liu Y, Luo N, Wei Q, Su Q, Zou J, Wu X, Huang X, Jiang Y, Liang L, Li H, Lin J. Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome. Ann Clin Microbiol Antimicrob 2023; 22:57. [PMID: 37430367 DOI: 10.1186/s12941-023-00608-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 07/05/2023] [Indexed: 07/12/2023] Open
Abstract
BACKGROUND Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens. RESULTS This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People's Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS. CONCLUSIONS In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.
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Affiliation(s)
- Juan Zhong
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China.
| | - Yanfen Liu
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Na Luo
- NanNing Center for Disease Control and Prevention, Nanning, China
| | - Qiu Wei
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | - Qisi Su
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Jun Zou
- The Fourth People's Hospital of Nanning, Nanning, China
| | - Xiaozhong Wu
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | | | - Yuting Jiang
- Department of Traditional Chinese Medicine, The First People's Hospital of Nanning, Nanning, China
| | - Lijuan Liang
- Nanning Yunju Biotechnology Co., Ltd, Nanning, China
| | - Hongmian Li
- The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, China.
| | - Jianyan Lin
- The First People's Hospital of Nanning, Nanning, China.
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Wen S, Peng S, Hu X, Jiang N, Li B, Chen B, Deng S, Yuan Y, Wu Q, Tao Y, Ma J, Li S, Lin T, Wen F, Li Z, Huang R, Feng Z, He C, Wang W, Liang X, Shi W, Xu L, Liu S. Validation of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for diagnosis of suspected pulmonary infections in patients with systemic autoimmune rheumatic diseases receiving immunosuppressant therapy. Front Med (Lausanne) 2023; 10:1161661. [PMID: 37484860 PMCID: PMC10359889 DOI: 10.3389/fmed.2023.1161661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Background The accuracy and sensitivity of conventional microbiological tests (CMTs) are insufficient to identify opportunistic pathogens in patients with systemic autoimmune rheumatic diseases (SARDs). The study aimed to assess the usefulness of metagenomic next-generation sequencing (mNGS) vs. CMTs for the diagnosis of pulmonary infections in patients with SARDs receiving immunosuppressant therapy. Methods The medical records of 40 patients with pulmonary infections and SARDs treated with immunosuppressants or corticosteroids were reviewed retrospectively. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and examined by mNGS and CMTs. Diagnostic values of the CMTs and mNGS were compared with the clinical composite diagnosis as the reference standard. Results Of the 40 patients included for analysis, 37 (92.5%) were diagnosed with pulmonary infections and 3 (7.5%) with non-infectious diseases, of which two were considered primary diseases and one an asthma attack. In total, 15 pathogens (7 bacteria, 5 fungi, and 3 viruses) were detected by CMTs as compared to 58 (36 bacteria, 12 fungi, and 10 viruses) by mNGS. Diagnostic accuracy of mNGS was superior to that of the CMTs for the detection of co-infections with bacteria and fungi (95 vs. 53%, respectively, p < 0.01), and for the detection of single infections with fungi (97.5 vs. 55%, respectively, p < 0.01). Of the 31 patients diagnosed with co-infections, 4 (12.9%) were positive for two pathogens and 27 (87.1%) for three or more. The detection rate of co-infection was significantly higher for mNGS than CMTs (95 vs. 16%, respectively, p < 0.01). Conclusion The accuracy of mNGS was superior to that of the CMTs for the diagnosis of pulmonary infections in patients with SARDs treated with immunosuppressants. The rapid diagnosis by mNGS can ensure timely adjustment of treatment regimens to improve diagnosis and outcomes.
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Affiliation(s)
- Sichun Wen
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Siqi Peng
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
| | - Xuejiao Hu
- Laboratory Medicine, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Nan Jiang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Bohou Li
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Boxi Chen
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shuting Deng
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ye Yuan
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Qiong Wu
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Yiming Tao
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Jianchao Ma
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Sijia Li
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Ting Lin
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Feng Wen
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhuo Li
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Renwei Huang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Zhonglin Feng
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Chaosheng He
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wenjian Wang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Xinling Liang
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Wei Shi
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Lixia Xu
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
| | - Shuangxin Liu
- School of Medicine, South China University of Technology, Guangzhou, Guangdong, China
- Department of Nephrology, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China
- The Second School of Clinical Medicine, Southern Medical University, Guangzhou, China
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Deng Z, Tang Y, Tu Y, Liu M, Cheng Q, Zhang J, Liu F, Li X. BALF metagenomic next-generation sequencing analysis in hematological malignancy patients with suspected pulmonary infection: clinical significance of negative results. Front Med (Lausanne) 2023; 10:1195629. [PMID: 37457591 PMCID: PMC10338636 DOI: 10.3389/fmed.2023.1195629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/01/2023] [Indexed: 07/18/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is gradually being used in hematological malignancy (HM) patients with suspected pulmonary infections. However, negative results are common and the clinical value and interpretation of such results in this patient population require further analysis. Methods Retrospective analysis of 112 HM patients with suspected pulmonary infection who underwent BALF mNGS and conventional microbiological tests. The final diagnosis, imaging findings, laboratory results and treatment regimen of 29 mNGS-negative patients were mainly analyzed. Results A total of 83 mNGS positive and 29 negative patients (15 true-negatives and 14 false-negatives) were included in the study. Compared to false-negative patients, true-negative patients showed more thickening of interlobular septa on imaging (p < 0.05); fewer true-negative patients had acute respiratory symptoms such as coughing or sputum production (p < 0.05) clinically; On the aspect of etiology, drug-related interstitial pneumonia (6/15, 40%) was the most common type of lung lesion in true-negative patients; on the aspect of pathogenesis, false-negative patients mainly missed atypical pathogens such as fungi and tuberculosis (8/14, 57.1%). Regarding treatment, delayed anti-infection treatment occurred after pathogen missing in mNGS false-negative patients, with the longest median time delay observed for anti-tuberculosis therapy (13 days), followed by antifungal therapy (7 days), and antibacterial therapy (1.5 days); the delay in anti-tuberculosis therapy was significantly longer than that in antibacterial therapy (p < 0.05). Conclusion For HMs patients with imaging showing thickening of interlobular septa and no obvious acute respiratory symptoms, lung lesions are more likely caused by drug treatment or the underlying disease, so caution should be exercised when performing BALF mNGS. If BALF mNGS is negative but infection is still suspected, atypical pathogenic infections should be considered.
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Affiliation(s)
- Zuqun Deng
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yishu Tang
- Department of Emergency, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yixuan Tu
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Mei Liu
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qian Cheng
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jian Zhang
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Feiyang Liu
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xin Li
- Department of Hematology, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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Zhu RS, Zhou LH, Cheng JH, Luo Y, Qiu WJ, Huang JT, Jiang YK, Zhao HZ, Wang X, Chen ZQ, Zhu LP. Diagnostic Laboratory Features and Performance of an Aspergillus IgG Lateral Flow Assay in a Chronic Pulmonary Aspergillosis Cohort. Microbiol Spectr 2023; 11:e0026423. [PMID: 37125929 PMCID: PMC10269518 DOI: 10.1128/spectrum.00264-23] [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: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
Chronic pulmonary aspergillosis (CPA) is a chronic and progressive fungal disease with high morbidity and mortality. Avoiding diagnostic delay and misdiagnosis are concerns for CPA patients. However, diagnostic practice is poorly evaluated, especially in resource-constrained areas where Aspergillus antibody testing tools are lacking. This study aimed to investigate the diagnostic laboratory findings in a retrospective CPA cohort and to evaluate the performance of a novel Aspergillus IgG lateral flow assay (LFA; Era Biology, Tianjin, China). During January 2016 and December 2021, suspected CPA patients were screened at the Center for Infectious Diseases at Huashan Hospital. A total of 126 CPA patients were enrolled. Aspergillus IgG was positive in 72.1% with chronic cavitary pulmonary aspergillosis, 75.0% with chronic necrotizing pulmonary aspergillosis, 41.7% with simple aspergilloma, and 30.3% with Aspergillus nodule(s). The cavitary CPA subtypes had significantly higher levels of Aspergillus IgG. Aspergillus IgG was negative in 52 patients, who were finally diagnosed by histopathology, respiratory culture, and metagenomic next-generation sequencing (mNGS). Sputum culture was positive in 39.3% (42/107) of patients and Aspergillus fumigatus was the most common species (69.0%, 29/42). For CPA cohort versus controls, the sensitivity and specificity of the LFA were 55.6% and 92.7%, respectively. In a subgroup analysis, the LFA was highly sensitive for A. fumigatus-associated chronic cavitary pulmonary aspergillosis (CCPA; 96.2%, 26/27). Given the complexity of the disease, a combination of serological and non-serological tests should be considered to avoid misdiagnosis of CPA. The novel LFA has a satisfactory performance and allows earlier screening and diagnosis of CPA patients. IMPORTANCE There are concerns on avoiding diagnostic delay and misdiagnosis for chronic pulmonary aspergillosis due to its high morbidity and mortality. A proportion of CPA patients test negative for Aspergillus IgG. An optimal diagnostic strategy for CPA requires in-depth investigation based on real-world diagnostic practice, which has been rarely discussed. We summarized the clinical and diagnostic laboratory findings of 126 CPA patients with various CPA subtypes. Aspergillus IgG was the most sensitive test for diagnosing CPA. However, it was negative in 52 patients, who were finally diagnosed by non-serological tests, including biopsy, respiratory culture, and metagenomic next-generation sequencing. We also evaluated a novel Aspergillus IgG lateral flow assay, which showed a satisfactory performance in cavitary CPA patients and was highly specific to Aspergillus fumigatus. This study gives a full picture of the diagnostic practice for CPA patients in Chinese context and calls for early diagnosis of CPA with combined approaches.
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Affiliation(s)
- Rong-Sheng Zhu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ling-Hong Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jia-Hui Cheng
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yu Luo
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wen-Jia Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Jun-Tian Huang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying-Kui Jiang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Hua-Zhen Zhao
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xuan Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhong-Qing Chen
- Department of Pathology, Huashan Hospital, Fudan University, Shanghai, China
| | - Li-Ping Zhu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
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Zhao X, Ge Y, Zhang Y, Zhang W, Hu H, Li L, Sha T, Zeng Z, Wu F, Chen Z. Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients. Infect Drug Resist 2023; 16:3293-3303. [PMID: 37260782 PMCID: PMC10228525 DOI: 10.2147/idr.s410593] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/09/2023] [Indexed: 06/02/2023] Open
Abstract
Background Next-generation sequencing of the metagenome (mNGS) is increasingly used in pathogen diagnosis for infectious diseases due to its short detection time. The time for Oxford Nanopore Technologies (ONT) sequencing-based etiology detection is further shortened compared with that of mNGS, but only a few studies have verified the time advantage and accuracy of ONT sequencing for etiology diagnosis. In 2022, a study confirmed that there was no significant difference in sensitivity and specificity between ONT and mNGS in suspected community-acquired pneumonia patients, which there was no clinical study verified in patients with SHAP. Methods From October 24 to November 20, 2022, 10 patients with severe hospital-acquired pneumonia (SHAP) in the Nanfang Hospital intensive care unit (ICU) were prospectively enrolled. Bronchoalveolar lavage fluid (BALF) was collected for ONT sequencing, mNGS, and traditional culture. The differences in pathogen detection time and diagnostic agreement among ONT sequencing, mNGS, traditional culture method, and clinical composite diagnosis were compared. Results Compared with mNGS and the traditional culture method, ONT sequencing had a significant advantage in pathogen detection time (9.6±0.7 h versus 24.7±2.7 h versus 132±58 h, P <0.05). The agreement rate between ONT sequencing and the clinical composite diagnosis was 73.3% (kappa value=0.737, P <0.05). Conclusion ONT sequencing has a potential advantage for rapidly identifying pathogens.
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Affiliation(s)
- Xin Zhao
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- The First Clinical Medical School, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yue Ge
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
- Department of School of Nursing, Southern Medical University, Guangzhou, People’s Republic of China
| | - Yuan Zhang
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - WenJie Zhang
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - HongBin Hu
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - LuLan Li
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Tong Sha
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - ZhenHua Zeng
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - Feng Wu
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
| | - ZhongQing Chen
- Department of Critical Care Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, People’s Republic of China
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Lei C, Ge H, Ding S, Zhou X, Yang B, Yang D, Wang R, Guo T, Yu Y, Luo H. Polybacterial infection in patients with stable bronchiectasis revealed by metagenomic next-generation sequencing. J Infect 2023; 86:e81-e83. [PMID: 36871871 DOI: 10.1016/j.jinf.2023.02.041] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 02/28/2023] [Indexed: 03/07/2023]
Affiliation(s)
- Cheng Lei
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Hu Ge
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan 410005, China
| | - Shuizi Ding
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Xianglin Zhou
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Binyi Yang
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Danhui Yang
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Rongchun Wang
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Ting Guo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China
| | - Yan Yu
- Changsha KingMed Center for Clinical Laboratory, Changsha, Hunan 410005, China.
| | - Hong Luo
- Department of Pulmonary and Critical Care Medicine, the Second Xiangya Hospital, Central South University, Changsha, Hunan 410011, China; Research Unit of Respiratory Disease, Central South University, Changsha, Hunan 410011, China; Hunan Diagnosis and Treatment Center of Respiratory Disease, Changsha, Hunan 410011, China.
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Lin T, Tu X, Zhao J, Huang L, Dai X, Chen X, Xu Y, Li W, Wang Y, Lou J, Wu S, Zhang H. Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia. Front Cell Infect Microbiol 2023; 13:1136588. [PMID: 37009509 PMCID: PMC10061305 DOI: 10.3389/fcimb.2023.1136588] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 02/23/2023] [Indexed: 03/18/2023] Open
Abstract
Background Community-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging. Methods A total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection. Results The positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only. Conclusion mNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.
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Affiliation(s)
- Tianlai Lin
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xueliang Tu
- Department of Clinical Laboratory, Huanghe Sanmenxia Hospital Affiliated to Henan University of Science and Technology, Sanmenxia, China
| | - Jiangman Zhao
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Ling Huang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaodong Dai
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Xiaoling Chen
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
| | - Yue Xu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Wushuang Li
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Yaoyao Wang
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Jingwei Lou
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
- Shanghai Zhangjiang Institute of Medical Innovation, Shanghai, China
| | - Shouxin Wu
- Shanghai Biotecan Pharmaceuticals Co., Ltd., Shanghai, China
| | - Hongling Zhang
- Department of Intensive Care Unit, Quanzhou First Hospital Affiliated to Fujian Medical University, Quanzhou, China
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Li Y, Xiong YZ, Fan HH, Jing LP, Li JP, Lin QS, Xu CH, Li Y, Ye L, Jiao M, Yang Y, Li Y, Yang WR, Peng GX, Zhou K, Zhao X, Zhang L, Zhang FK. [Metagenomic next-generation sequencing of plasma for the identification of bloodstream infectious pathogens in severe aplastic anemia]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:236-241. [PMID: 37356986 PMCID: PMC10119722 DOI: 10.3760/cma.j.issn.0253-2727.2023.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Indexed: 06/27/2023]
Abstract
Objective: To analyze the diagnostic value of cell-free plasma metagenomic next-generation sequencing (mNGS) pathogen identification for severe aplastic anemia (SAA) bloodstream infection. Methods: From February 2021 to February 2022, mNGS and conventional detection methods (blood culture, etc.) were used to detect 33 samples from 29 consecutive AA patients admitted to the Anemia Diagnosis and Treatment Center of the Hematology Hospital of the Chinese Academy of Medical Sciences to assess the diagnostic consistency of mNGS and conventional detection, as well as the impact on clinical treatment benefits and clinical accuracy. Results: ①Among the 33 samples evaluated by mNGS and conventional detection methods, 25 cases (75.76%) carried potential pathogenic microorganisms. A total of 72 pathogenic microorganisms were identified from all cases, of which 65 (90.28%) were detected only by mNGS. ②All 33 cases were evaluated for diagnostic consistency, of which 2 cases (6.06%) were Composite, 18 cases (54.55%) were mNGS only, 2 cases (6.06%) were Conventional method only, 1 case (3.03%) was both common compliances (mNGS/Conventional testing) , and 10 cases (30.3%) were completely non-conforming (None) . ③All 33 cases were evaluated for clinical treatment benefit. Among them, 8 cases (24.24%) received Initiation of targeted treatment, 1 case (3.03%) received Treatment de-escalation, 13 cases (39.39%) received Confirmation, and the remaining 11 cases (33.33%) received No clinical benefit. ④ The sensitivity of 80.77%, specificity of 70.00%, positive predictive value of 63.64%, negative predictive value of 84.85%, positive likelihood ratio of 2.692, and negative likelihood ratio of 0.275 distinguished mNGS from conventional detection methods (21/12 vs 5/28, P<0.001) . Conclusion: mNGS can not only contribute to accurately diagnosing bloodstream infection in patients with aplastic anemia, but can also help to guide accurate anti-infection treatment, and the clinical accuracy is high.
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Affiliation(s)
- Y Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y Z Xiong
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - H H Fan
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - L P Jing
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - J P Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Q S Lin
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - C H Xu
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China Microbiology Laboratory Tianjin Union Precision Medical Diagnostic Co., Ltd, Tianjin 301617, China
| | - Y Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - L Ye
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - M Jiao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - Y Li
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - W R Yang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - G X Peng
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - K Zhou
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - X Zhao
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - L Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
| | - F K Zhang
- State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Haihe Laboratory of Cell Ecosystem, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin 300020, China
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50
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Wei Y, Zhang T, Ma Y, Yan J, Zhan J, Zheng J, Xu Y. Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia. Ital J Pediatr 2023; 49:25. [PMID: 36805803 PMCID: PMC9938609 DOI: 10.1186/s13052-023-01431-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 02/12/2023] [Indexed: 02/19/2023] Open
Abstract
BACKGROUND Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking. METHODS In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT). RESULTS Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication. CONCLUSION mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.
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Affiliation(s)
- Yupeng Wei
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Tongqiang Zhang
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Yuting Ma
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Infection, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China
| | - Jisi Yan
- grid.265021.20000 0000 9792 1228Clinical School of Paediatrics, Tianjin Medical University, Tianjin, China ,grid.417022.20000 0004 1772 3918Department of Respiratory Medicine, Tianjin Children’s Hospital (Tianjin University Children’s Hospital), Tianjin, China ,grid.410626.70000 0004 1798 9265Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China
| | - Jianghua Zhan
- Department of Pediatric Surgery, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
| | - Jun Zheng
- Department of Neonatology, Tianjin Central Hospital of Gynecology Obstetrics, Tianjin, China.
| | - Yongsheng Xu
- Department of Respiratory Medicine, Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China.
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