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Qin W, Guo T, You T, Tian R, Cui X, Wang P. Metagenomic next generation sequencing of bronchoalveolar lavage fluids for the identification of pathogens in patients with pulmonary infection: A retrospective study. Diagn Microbiol Infect Dis 2024; 110:116402. [PMID: 38878340 DOI: 10.1016/j.diagmicrobio.2024.116402] [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: 04/14/2024] [Revised: 06/10/2024] [Accepted: 06/11/2024] [Indexed: 07/30/2024]
Abstract
Due to the limitations of traditional laboratory methods (TMs), identification of causative pathogens of numerous pulmonary infections (PIs) remains difficult. This study evaluated the value of metagenomic next generation sequencing (mNGS) in the identification of various respiratory pathogens. A total of 207 patients with TMs and mNGS data were collected for this retrospective study. TMs included sputum culture, blood, and bronchoalveolar lavage fluid (BALF) analysis, or polymerase chain reaction analysis of throat swabs. Otherwise, BALF was collected and analyzed using mNGS. For bacterial pathogens, sensitivities of mNGS as compared to TMs were 76.74 % and 58.14 % (P=0.012). For fungal pathogens, the detection rate of mNGS sensitivity was higher as compared to that of TMs (93.68 % vs 22.11 %; P<0.001). The positive predictive value and negative predictive value were also greater for mNGS. Use of mNGS for BALF analysis offers good specificity and thus facilitates to the clinical diagnosis of PIs.
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Affiliation(s)
- Wenwen Qin
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Tai Guo
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Tiebin You
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Ruixin Tian
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Xiaoman Cui
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China
| | - Ping Wang
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang, 050011, China.
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Vasanthaiah S, Verma R, Kumar A, Bandari AK, George J, Rastogi M, Manjunath GK, Sharma J, Kumar A, Subramani J, Chawla K, Pandey A. Culture-Free Whole Genome Sequencing of Mycobacterium tuberculosis Using Ligand-Mediated Bead Enrichment Method. Open Forum Infect Dis 2024; 11:ofae320. [PMID: 38957687 PMCID: PMC11218775 DOI: 10.1093/ofid/ofae320] [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: 01/17/2024] [Accepted: 06/12/2024] [Indexed: 07/04/2024] Open
Abstract
Background Direct whole genome sequencing (WGS) of Mycobacterium tuberculosis (Mtb) can be used as a tool to study drug resistance, mixed infections, and within-host diversity. However, WGS is challenging to obtain from clinical samples due to low number of bacilli against a high background. Methods We prospectively collected 34 samples (sputum, n = 17; bronchoalveolar lavage, n = 13; and pus, n = 4) from patients with active tuberculosis (TB). Prior to DNA extraction, we used a ligand-mediated magnetic bead method to enrich Mtb from clinical samples and performed WGS on Illumina platform. Results Mtb was definitively identified based on WGS from 88.2% (30/34) of the samples, of which 35.3% (12/34) were smear negative. The overall median genome coverage was 15.2% (interquartile range [IQR], 7.7%-28.2%). There was a positive correlation between load of bacilli on smears and genome coverage (P < .001). We detected 58 genes listed in the World Health Organization mutation catalogue in each positive sample (median coverage, 85% [IQR, 61%-94%]), enabling the identification of mutations missed by routine diagnostics. Mutations causing resistance to rifampicin, isoniazid, streptomycin, and ethambutol were detected in 5 of 34 (14.7%) samples, including the rpoB S441A mutation that confers resistance to rifampicin, which is not covered by Xpert MTB/RIF. Conclusions We demonstrate the feasibility of magnetic bead-based enrichment for culture-free WGS of Mtb from clinical specimens, including smear-negative samples. This approach can also be integrated with low-cost sequencing workflows such as targeted sequencing for rapid detection of Mtb and drug resistance.
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Affiliation(s)
- Shruthi Vasanthaiah
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Renu Verma
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Ajay Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Aravind K Bandari
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - John George
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Mona Rastogi
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Gowrang Kasaba Manjunath
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Jyoti Sharma
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | - Abhishek Kumar
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
| | | | - Kiran Chawla
- Department of Microbiology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Akhilesh Pandey
- Manipal Academy of Higher Education, Manipal, Karnataka, India
- Institute of Bioinformatics, International Technology Park, Bangalore, Karnataka, India
- Department of Laboratory Medicine and Pathology, Center for Individualized Medicine, Mayo Clinic, Rochester, Minnesota, USA
- Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Bangalore, Karnataka, India
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Chen S, Wen L, Ou J, Lai Y, Shen Y. Exploring the Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Unexplained Pulmonary Infection. Int J Gen Med 2024; 17:2465-2474. [PMID: 38826507 PMCID: PMC11141768 DOI: 10.2147/ijgm.s459373] [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: 01/12/2024] [Accepted: 05/16/2024] [Indexed: 06/04/2024] Open
Abstract
Background Pulmonary infections are significant global health burdens, and conventional diagnostic methods (culture and polymerase chain reaction), are often limited by slow results and low sensitivity. Metagenomic next-generation sequencing (mNGS) offers a rapid, comprehensive alternative for identifying diverse pathogens, including rare and mixed infections. Thus, we assessed the diagnostic performance of mNGS in pulmonary infections, compared the findings with those of traditional pathogen detection methods, and explored its potential to enhance clinical diagnostics and patient care. Methods We collected samples from 125 immunocompromised patients diagnosed with pulmonary infection at the Department of Respiratory Medicine of Shenzhen Longgang Central Hospital from March 2020 to July 2022. We compared the rate of pathogen positivity and pathogen distribution between conventional pathogen detection methods and mNGS using samples including sputum, blood, and bronchoalveolar lavage fluid. Results Among the 125 cases of unexplained pulmonary infection, 82 (65.6%) and 40 (32.0%) tested positive for pathogens using mNGS and routine culture, respectively (P < 0.05). Both methods of pathogen detection were positive in 28 (22.4%) cases (complete match, 9; complete mismatch, 13; partial match, 6). However, 43.2% of cases only tested positive using mNGS, 9.4% only tested positive using routine tests, and 24.8% tested negative using both methods. A viral infection was present in 55.2% of cases. The detection rate of mycobacteria using mNGS (12.8%) was higher than that using conventional pathogen detection methods (5.6%). Conclusion mNGS technology enhances pathogen detection in unexplained pulmonary infections, enabling targeted antimicrobial therapy and consequently helping to reduce broad-spectrum antibiotic use, aligning treatments more closely with the causative pathogens. Thus, mNGS offers significant clinical value by improving treatment efficacy and potentially reducing antibiotic resistance in pulmonary infection cases.
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Affiliation(s)
- Sida Chen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Ling Wen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Jintao Ou
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Yuting Lai
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
| | - Yan Shen
- Department of Respiratory, Shenzhen Longgang Central Hospital, Shenzhen, Guangdong, 518000, People’s Republic of China
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Sun C, Zhou C, Wang L, Wei S, Shi M, Li J, Lin L, Liu X. Clinical application of metagenomic next-generation sequencing for the diagnosis of suspected infection in adults: A cross-sectional study. Medicine (Baltimore) 2024; 103:e37845. [PMID: 38640284 PMCID: PMC11029930 DOI: 10.1097/md.0000000000037845] [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: 07/14/2022] [Revised: 03/15/2024] [Accepted: 03/19/2024] [Indexed: 04/21/2024] Open
Abstract
Metagenomic next-generation sequencing (mNGS) has become an available method for pathogen detection. The clinical application of mNGS requires further evaluation. We conducted a cross-sectional study of 104 patients with suspected infection between May 2019 and May 2021. The risk factors associated with infection were analyzed using univariate logistic analysis. The diagnostic performance of pathogens was compared between mNGS and conventional microbiological tests. About 104 patients were assigned into 3 groups: infected group (n = 69), noninfected group (n = 20), and unknown group (n = 15). With the composite reference standard (combined results of all microbiological tests, radiological testing results, and a summary of the hospital stay of the patient) as the gold standard, the sensitivity, specificity, positive predictive value, negative predictive value of mNGS was 84.9%, 50.0%, 88.6%, and 42.1%, respectively. Compared with conventional microbiological tests, mNGS could detect more pathogens and had obvious advantages in Mycobacterium tuberculosis, Aspergillus, and virus detection. Moreover, mNGS had distinct benefits in detecting mixed infections. Bacteria-fungi-virus mixed infections were the most common in patients with severe pneumonia. mNGS had a higher sensitivity than conventional microbiological tests, especially for M. tuberculosis, Aspergillus, viruses, and mixed infections. We suggest that mNGS should be used more frequently in the early diagnosis of pathogens in critically ill patients in the future.
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Affiliation(s)
- Chunping Sun
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
- Department of Critical Care Medicine, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Peking University Cancer Hospital and Institute, Beijing, China
| | - Chaoe Zhou
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Lina Wang
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Shanchen Wei
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Mingwei Shi
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Jun Li
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Lianjun Lin
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
| | - Xinmin Liu
- Department of Geriatrics, Peking University First Hospital, Peking University, Beijing, China
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Lin Q, Yao Y, Li X, Zhang S, Guo H, Ma X, Chen W, Ru C, Wang L, Wang B, Ma Q, Zhu J, Lin X, Chen Q, Lou H, Chen Q, Chen J, Zeng Z, Zhou J, Chen Y, Yu Y, Zhou H. The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study. Infect Dis (Lond) 2024; 56:128-137. [PMID: 37934028 DOI: 10.1080/23744235.2023.2276785] [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: 08/25/2023] [Accepted: 10/12/2023] [Indexed: 11/08/2023] Open
Abstract
OBJECTIVE To evaluate the value of nanopore targeted sequencing in diagnosing pneumonia pathogens. METHODS This large-scale multicentre prospective study performed in 8 hospitals across China from April to October 2022. Hospitalised patients with a diagnosis of pneumonia at admission were included. Complete clinical data were collected, and bronchoalveolar lavage fluid were obtained from each patient. These samples underwent simultaneous testing using conventional microbial testing, metagenomic next-generation sequencing, and nanopore targeted sequencing. RESULTS A total of 218 patients were included. Among the 168 cases of pulmonary infection, 246 strains of pathogens were confirmed. Nanopore targeted sequencing outperformed conventional microbial testing, identifying more pathogens with a sensitivity increase of 47.9% (77.2% vs. 29.3%). Metagenomic next-generation sequencing had a sensitivity of 82.9%. Total of 70.1% patients had consistent results in both metagenomic next-generation sequencing and nanopore targeted sequencing. Nanopore targeted sequencing exhibited significantly higher sensitivity in detecting Pneumocystis jiroveci, cytomegalovirus, Mycobacterium tuberculosis, Nontuberculous mycobacteria, Streptococcus pneumoniae, and Mycoplasma pneumoniae compared to conventional microbial testing. However, metagenomic next-generation sequencing demonstrated higher sensitivity than nanopore targeted sequencing for Aspergillus (88.5% vs. 53.8%). Regarding the detection of co-infections, nanopore targeted sequencing displayed significantly higher sensitivity than conventional microbial testing (76.7% vs. 28.7%) and was on par with metagenomic next-generation sequencing (76.7% vs. 82.9%). CONCLUSION Nanopore targeted sequencing performs equally well as metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen diagnosis in pneumonia, both methods showing higher sensitivity than conventional microbial testing. Nanopore targeted sequencing can be considered a reliable method for diagnosing pathogens in pneumonia.
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Affiliation(s)
- Qinqing Lin
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Critical Care Medicine, Affiliated Hospital of Shaoxing University, Shaoxing, China
| | - Yake Yao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xi Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People's Hospital, Affiliated People's Hospital, Hangzhou Medical College, Hangzhou, Zhejiang, China
| | - Shanshan Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
- Department of Respiratory and Critical Care Medicine, Beilun People's Hospital, Ningbo, China
| | - Huimin Guo
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Xiaolong Ma
- Department of Respiratory and Critical Care Medicine, The First Hospital of JiaXing, JiaXing, China
| | - Wenyu Chen
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Chuhui Ru
- Department of Respiratory and Critical Care Medicine, Red Cross Society Hospital of Hangzhou, Hangzhou, China
| | - Limin Wang
- Department of Respiratory and Critical Care Medicine, Affiliated Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bin Wang
- Department of Respiratory and Critical Care Medicine, Huzhou Central Hospital, Huzhou, China
| | - Qiang Ma
- Department of Respiratory and Critical Care Medicine, The Second People's Hospital of Yuhang District, Hangzhou, China
| | - Junfei Zhu
- Department of Respiratory and Critical Care Medicine, Taizhou Central Hospital, Taizhou, China
| | - Xuemei Lin
- Department of Respiratory and Critical Care Medicine, Jiangshan People's Hospital, Quzhou, China
| | - Qi Chen
- Zhejiang Digena Diagnosis Technology CO., Ltd., Hangzhou, Zhejiang, China
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Hui Lou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Qi Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junjun Chen
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Zhu Zeng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jianying Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Chen
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yunsong Yu
- Department of Infectious Disease, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Hua Zhou
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
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Gao J, Zhao L, Chen G, Huang C, Kong W, Feng Y, Zhen G. The value of metagenomic next-generation sequencing for the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid. Lab Med 2024; 55:96-102. [PMID: 37267076 PMCID: PMC10771034 DOI: 10.1093/labmed/lmad041] [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] [Indexed: 06/04/2023] Open
Abstract
OBJECTIVE The aim of this study was to compare metagenomic next-generation sequencing (mNGS) with other methods, including Xpert MTB/RIF, Mycobacterium tuberculosis (MTB) culture, and acid-fast bacillus (AFB) staining in the diagnosis of pulmonary tuberculosis (PTB) using bronchoalveolar lavage fluid (BALF). METHODS The data of 186 patients with suspected PTB were retrospectively collected from January 2020 to May 2021 at Tongji Hospital. BALF samples were collected from all patients and analyzed using AFB staining, MTB culture, Xpert MTB/RIF, and mNGS. RESULTS Of the 186 patients, 38 patients were ultimately diagnosed as PTB. Metagenomic next-generation sequencing exhibited a sensitivity of 78.95%, which was higher than AFB staining (27.59%) and MTB culture (44.12%) but similar to Xpert MTB/RIF (72.73%). Utilization of combined methods demonstrates improvement for PTB diagnosis. In support of this, the area under the receiver operating characteristic curve for the combination of mNGS and MTB culture (0.933, 95% CI: 0.871, 0.995) was larger than those of mNGS, Xpert MTB/RIF, MTB culture, and the combination of Xpert MTB/RIF and MTB culture. CONCLUSION The sensitivity of mNGS in the diagnosis of PTB using BALF specimen is similar to Xpert MTB/RIF. Metagenomic next-generation sequencing in combination with MTB culture may further improve the diagnosis of pulmonary tuberculosis.
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Affiliation(s)
- Jiali Gao
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Lu Zhao
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Gongqi Chen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Chunli Huang
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Weiqiang Kong
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Yuchen Feng
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
| | - Guohua Zhen
- Division of Respiratory and Critical Care Medicine, Department of Internal Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Key Laboratory of Respiratory Diseases, National Health Commission of the People’s Republic of China, and National Clinical Research Center for Respiratory Diseases, Wuhan, China
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Sundararaman B, Sylvester MD, Kozyreva VK, Berrada ZL, Corbett-Detig RB, Green RE. A hybridization target enrichment approach for pathogen genomics. mBio 2023; 14:e0188923. [PMID: 37830873 PMCID: PMC10653935 DOI: 10.1128/mbio.01889-23] [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: 08/10/2023] [Accepted: 09/08/2023] [Indexed: 10/14/2023] Open
Abstract
IMPORTANCE Emerging infectious diseases require continuous pathogen monitoring. Rapid clinical diagnosis by nucleic acid amplification is limited to a small number of targets and may miss target detection due to new mutations in clinical isolates. Whole-genome sequencing (WGS) identifies genome-wide variations that may be used to determine a pathogen's drug resistance patterns and phylogenetically characterize isolates to track disease origin and transmission. WGS is typically performed using DNA isolated from cultured clinical isolates. Culturing clinical specimens increases turn-around time and may not be possible for fastidious bacteria. To overcome some of these limitations, direct sequencing of clinical specimens has been attempted using expensive capture probes to enrich the entire genomes of target pathogens. We present a method to produce a cost-effective, time-efficient, and large-scale synthesis of probes for whole-genome enrichment. We envision that our method can be used for direct clinical sequencing of a wide range of microbial pathogens for genomic epidemiology.
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Affiliation(s)
- Balaji Sundararaman
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
| | - Matthew D. Sylvester
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Varvara K. Kozyreva
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Zenda L. Berrada
- Center for Laboratory Sciences, California Department of Public Health, Microbial Diseases Laboratory Branch, Richmond, California, USA
| | - Russell B. Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
| | - Richard E. Green
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, California, USA
- UCSC Genomics Institute, University of California Santa Cruz, Santa Cruz, California, USA
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8
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An Q, Lin R, Yang Q, Wang C, Wang D. Evaluation of genetic mutations associated with phenotypic resistance to fluoroquinolones, bedaquiline, and linezolid in clinical Mycobacterium tuberculosis: A systematic review and meta-analysis. J Glob Antimicrob Resist 2023; 34:214-226. [PMID: 37172764 DOI: 10.1016/j.jgar.2023.05.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
OBJECTIVES The aim of the study was to update the classification of drugs used in multidrug-resistant tuberculosis (MDR-TB) regimens. Group A drugs (fluoroquinolones, bedaquiline (BDQ), and linezolid (LZD)) are crucial drugs for the control of MDR-TB. Molecular drug resistance assays could facilitate the effective use of Group A drugs. METHODS We summarised the evidence implicating specific genetic mutations in resistance to Group A drugs. We searched PubMed, Embase, MEDLINE, and the Cochrane Library for studies published from the inception of each database until July 1, 2022. Using a random-effects model, we calculated the odds ratios and 95% confidence intervals as our measures of association. RESULTS A total of 5001 clinical isolates were included in 47 studies. Mutations in gyrA A90V, D94G, D94N, and D94Y were significantly associated with an increased risk of a levofloxacin (LFX)-resistant phenotype. In addition, mutations in gyrA G88C, A90V, D94G, D94H, D94N, and D94Y were significantly associated with an increased risk of a moxifloxacin (MFX)-resistant phenotype. In only one study, the majority of gene loci (n = 126, 90.65%) in BDQ-resistant isolates were observed to have unique mutations in atpE, Rv0678, mmpL5, pepQ, and Rv1979c. The most common mutations occurred at four sites in the rrl gene (g2061t, g2270c, g2270t, and g2814t) and at one site in rplC (C154R) in LZD-resistant isolates. Our meta-analysis demonstrated that there were no mutations associated with BDQ- or LZD-resistant phenotypes. CONCLUSION The mutations detected by rapid molecular assay were correlated with phenotypic resistance to LFX and MFX. The absence of mutation-phenotype associations for BDQ and LZD hindered the development of a rapid molecular assay.
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Affiliation(s)
- Qi An
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Rui Lin
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Qing Yang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Chuan Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
| | - Dongmei Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
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9
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Wang C, Yan D, Huang J, Yang N, Shi J, Pan S, Lin G, Liu Y, Zhang Y, Bian X, Song Q, Qian G. The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China. Front Cell Infect Microbiol 2022; 12:957073. [PMID: 36601307 PMCID: PMC9806342 DOI: 10.3389/fcimb.2022.957073] [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: 05/30/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022] Open
Abstract
Background Compared with traditional diagnostic methods (TDMs), rapid diagnostic methods for infectious diseases (IDs) are urgently needed. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic technology for clinical infections. Methods This retrospective observational study was performed at a tertiary hospital in China between May 2019 and August 2022. The chi-square test was used to compare the sensitivity and specificity of mNGS and TDMs. We also performed a subgroup analysis of the different pathogens and samples. Results A total of 435 patients with clinical suspicion of infection were enrolled and 372 (85.5%) patients were finally categorized as the ID group. The overall sensitivity of mNGS was significantly higher than that of the TDMs (59.7% vs. 30.1%, P < 0.05). However, there was no significant difference in the overall specificity between the two methods (83.3% vs. 89.6%, P = 0.37). In patients with identified pathogens, the positive rates of mNGS for detecting bacteria (88.7%), fungi (87.9%), viruses (96.9%), and Nontuberculous mycobacteria (NTM; 100%) were significantly higher than those of TDMs (P < 0.05). The positive rate of mNGS for detecting Mycobacterium tuberculosis was not superior to that of TDMs (77.3% vs. 54.5%, P = 0.11). The sensitivity rates of mNGS for pathogen identification in bronchoalveolar lavage fluid, blood, cerebrospinal fluid, pleural fluid, and tissue were 72.6%, 39.3%, 37.5%, 35.0% and 80.0%, respectively. Conclusion With the potential for screening multiple clinical samples, mNGS has an overall advantage over TDMs. It can effectively identify pathogens, especially those that are difficult to identify using TDMs, such as NTM, chlamydia, and parasites.
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Affiliation(s)
- Chuwen Wang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Danying Yan
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Jiajia Huang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Naibin Yang
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Jiejun Shi
- Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China
| | - Shou Pan
- Hangzhou DIAN Medical Laboratory, Hangzhou, China
| | - Gaoqiang Lin
- Vision Medicals Center for Infectious Diseases, Guangzhou, Guangdong, China
| | - Ying Liu
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Yingying Zhang
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China
| | - Xueyan Bian
- Department of Nephrology, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
| | - Qifa Song
- Medical Data Center, Ningbo First Hospital, Ningbo University, Ningbo, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
| | - Guoqing Qian
- School of Medicine, Ningbo University, Ningbo, Zhejiang, China,Department of Infectious Diseases, Ningbo First Hospital, Ningbo University, Ningbo, Zhejiang, China,*Correspondence: Guoqing Qian, ; Qifa Song, ; Xueyan Bian,
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Ghosh A, Saha S. Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures. J Med Microbiol 2022; 72. [PMID: 36748565 DOI: 10.1099/jmm.0.001617] [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: 12/23/2022] Open
Abstract
Introduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.Results. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.
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Affiliation(s)
- Abhirupa Ghosh
- Division of Bioinformatics, Bose Institute, Kolkata - 700091, India
| | - Sudipto Saha
- Division of Bioinformatics, Bose Institute, Kolkata - 700091, India
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11
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Kok NA, Peker N, Schuele L, de Beer JL, Rossen JWA, Sinha B, Couto N. Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum. Front Microbiol 2022; 13:949328. [DOI: 10.3389/fmicb.2022.949328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/29/2022] [Indexed: 11/13/2022] Open
Abstract
Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients’ sputum mixture spiked with M. abscessus at three concentrations (final concentrations 108, 107, 106 CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing.While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (108 CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST.In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.
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Ye P, Xie C, Wu C, Yu C, Chen Y, Liang Z, Chen Y, Chen Q, Kong Y. The application of metagenomic next-generation sequencing for detection of pathogens from dialysis effluent in peritoneal dialysis-associated peritonitis . Perit Dial Int 2022; 42:585-590. [PMID: 35993242 DOI: 10.1177/08968608221117315] [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: 11/15/2022] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) can improve pathogen identification in infectious diseases. METHODS A prospective parallel control study was undertaken to evaluate the clinical significance of mNGS in identifying pathogens in dialysis effluent of patients with peritoneal dialysis-associated peritonitis (peritonitis). Dialysis effluent specimens were detected both by peritoneal dialysis effluent culture and mNGS. The positive rates and coincidence rates of the two methods were compared. RESULTS From April 2020 to March 2021, 30 patients presenting with peritonitis were enrolled in this study. The positive pathogen detection rate of mNGS was significantly higher than that of the traditional culture method (86.67% vs. 60.00%; p = 0.039). Fifteen specimens were positive for both of the methods, while 11 specimens were negative for culture but positive for mNGS. Three specimens were positive for culture but negative for mNGS; all of them were streptococcus mitis. One specimen was negative for both methods. The culture method detected one type of pathogen in all specimens; however, two or more types of pathogens were detected in eight specimens by mNGS. In addition to common pathogens, additional pathogens detected by mNGS included Coxiella burnetii, human herpesvirus type 5, human herpesvirus type 6B and Mortierella. CONCLUSION The pathogen detection rate of mNGS in dialysis effluent of peritonitis patients was significantly higher than that of traditional culture. The mNGS is advantageous in diagnosing the pathogens that are difficult to be cultured. However, mNGS did not demonstrate sensitivity to streptococcus mitis. Results from this study show that mNGS, combined with traditional culture, has potential application for detecting pathogens in peritoneal dialysis patients with peritonitis.
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Affiliation(s)
- Peiyi Ye
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Chao Xie
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Cuixia Wu
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Cuiyan Yu
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Yuhe Chen
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Zijie Liang
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Youyuan Chen
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Qiyan Chen
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
| | - Yaozhong Kong
- Department of Nephrology, The First People's hospital of Foshan, Foshan, Guangdong, China
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Fu M, Cao LJ, Xia HL, Ji ZM, Hu NN, Leng ZJ, Xie W, Fang Y, Zhang JQ, Xia DQ. The performance of detecting Mycobacterium tuberculosis complex in lung biopsy tissue by metagenomic next-generation sequencing. BMC Pulm Med 2022; 22:288. [PMID: 35902819 PMCID: PMC9330940 DOI: 10.1186/s12890-022-02079-8] [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: 04/02/2022] [Accepted: 07/18/2022] [Indexed: 11/16/2022] Open
Abstract
Background Tuberculosis (TB) is a chronic infectious disease caused by the Mycobacterium tuberculosis complex (MTBC), which is the leading cause of death from infectious diseases. The rapid and accurate microbiological detection of the MTBC is crucial for the diagnosis and treatment of TB. Metagenomic next-generation sequencing (mNGS) has been shown to be a promising and satisfying application of detection in infectious diseases. However, relevant research about the difference in MTBC detection by mNGS between bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens remains scarce. Methods We used mNGS to detect pathogens in BALF and lung biopsy tissue obtained by CT-guide percutaneous lung puncture (CPLP) or radial endobronchial ultrasound transbronchial lung biopsy (R-EBUS-TBLB) from 443 hospitalized patients in mainland China suspected of pulmonary infections between May 1, 2019 and October 31, 2021. Aim to evaluate the diagnostic performance of mNGS for detecting MTBC and explore differences in the microbial composition in the 2 specimen types. Results Among the 443 patients, 46 patients finally were diagnosed with TB, of which 36 patients were detected as MTBC positive by mNGS (8.93%). Striking differences were noticed in the higher detection efficiency of lung biopsy tissue compared with BALF (P = 0.004). There were no significant differences between the 2 specimen types in the relative abundance among the 27 pathogens detected by mNGS from the 36 patients. Conclusions This study demonstrates that mNGS could offer an effective detection method of MTBC in BALF or lung tissue biopsy samples in patients suspected of TB infections. When it comes to the situations that BALF samples have limited value to catch pathogens for special lesion sites or the patients have contraindications to bronchoalveolar lavage (BAL) procedures, lung biopsy tissue is an optional specimen for MTBC detection by mNGS. However, whether lung tissue-mNGS is superior to BALF-mNGS in patients with MTBC infection requires further prospective multicenter randomized controlled studies with more cases.
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Affiliation(s)
- Meng Fu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.,Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, Anhui, China.,University of Science and Technology of China, Hefei, 230026, Anhui, China
| | - Le-Jie Cao
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Huai-Ling Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Zi-Mei Ji
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Na-Na Hu
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Zai-Jun Leng
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Wang Xie
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Yuan Fang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China
| | - Jun-Qiang Zhang
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.
| | - Da-Qing Xia
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, No. 17 Lujiang Road, Hefei, 230001, Anhui, China.
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Wang D, Fang S, Hu X, Xu Q, Chu X, Mei X, Xie W. Metagenomic Next-Generation Sequencing Is Highly Efficient in Diagnosing Pneumocystis Jirovecii Pneumonia in the Immunocompromised Patients. Front Microbiol 2022; 13:913405. [PMID: 35783441 PMCID: PMC9247511 DOI: 10.3389/fmicb.2022.913405] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/23/2022] [Indexed: 11/13/2022] Open
Abstract
Purposes To explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pneumocystis jiroveciipneumonia (PJP) in the immunocompromised patients. Methods Data of 122 patients with PJP in an immunosuppressed state and 67 non-PJP patients were collected. The diagnostic efficacy of mNGS was compared with the conventional methods, including Gomori methenamine silver (GMS) staining and serum (1,3)-β-D-glucan (BDG). Changes of anti-microbial therapy for patients with PJP based on mNGS results were also reviewed. Results The diagnostic sensitivity of mNGS to PJP was higher than that of GMS and BDG (100% vs. 15 and 74.5%, p < 0.001). The diagnostic specificity (91.%) was lower than that of GMS (100%), and similar with BDG (89.6%). In addition to P. jirovecii, mNGS revealed co-pathogens like human β-herpesvirus 5, human γ-pesvirus 4, and some other opportunistic pathogens. The reads of mNGS were remarkably higher in BALF than in blood samples. Initial antimicrobial treatment was modified in 89.3% patients based on the mNGS results, and 74 cases (60.7%) were treated with anti-P. jirovecii therapy. Conclusion mNGS is highly efficient in diagnosing PJP and good at identifying pathogens in mixed infections.
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Affiliation(s)
- Dongsheng Wang
- Department of Pulmonary and Critical Care Medicine, Anhui Provincial Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Shihua Fang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Wannan Medical College, Wuhu, China
| | - Xiaowen Hu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Qixia Xu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xinmin Chu
- Department of Clinical Laboratory, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
| | - Xiaodong Mei
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- *Correspondence: Xiaodong Mei,
| | - Wang Xie
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China
- Wang Xie,
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Risk Factors and Outcome of Sepsis in Traumatic Patients and Pathogen Detection Using Metagenomic Next-Generation Sequencing. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:2549413. [PMID: 35509518 PMCID: PMC9061056 DOI: 10.1155/2022/2549413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 04/06/2022] [Indexed: 11/18/2022]
Abstract
Objective Sepsis, a life-threatening clinical syndrome, is a leading cause of mortality after experiencing multiple traumas. Once diagnosed with sepsis, patients should be given an appropriate empiric antimicrobial treatment followed by the specific antibiotic therapy based on blood culture due to its rapid progression to tissue damage and organ failure. In this study, we aimed to analyze the risk factors and outcome of sepsis in traumatic patients and to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in post-traumatic sepsis. Methods The study included 528 patients with multiple traumas among which there were 142 cases with post-traumatic sepsis. Patients' demographic and clinical data were recorded. The outcome measures included mortality during the emergency intensive care unit (EICU), EICU length of stay (LOS), all-cause 28-day mortality, and total ventilator days in 28 days after admission. A total of 89 blood samples from 89 septic patients underwent standard microbiological blood cultures and 89 samples of peripheral blood (n = 21), wound secretion (n = 41), bronchoalveolar lavage fluid (BALF) (19), ascites (n = 5), and sputum (n = 3) underwent mNGS. Pathogen detection was compared between standard microbiological blood cultures and mNGS. Results The sepsis group and non-sepsis group exhibited significant differences regarding shock on admission, blood transfusion, mechanical ventilation, body temperature, heart rate, WBC count, neutrophil count, hematocrit, urea nitrogen, creatinine, CRP, D-D dimer, PCT, scores of APACHE II, sequential organ failure assessment (SOFA), and Injury Severity Score (ISS) on admission to the EICU, and Multiple Organ Dysfunction Syndromes (MODS) (P < 0.05). Multivariate logistic regression analysis showed that scores of APACHE II, SOFA, and ISS on admission, and MODS were independent risk factors for the occurrence of sepsis in patients with multiple traumas. The 28-day mortality was higher in the sepsis group than in the non-sepsis group (45.07% vs. 19.17%, P < 0.001). The mortality during the EICU was higher in the sepsis group than in the non-sepsis group (P=0.002). The LOS in the EICU in the sepsis group was increased compared with the non-sepsis group (P=0.004). The total ventilator days in 28 days after admission in the sepsis group was increased compared with the non-sepsis group (P < 0.001). Multivariate logistic regression analysis showed that septic shock, APACHE II score on admission, SOFA score, and MODS were independent risk factors of death for patients with post-traumatic sepsis. The positive detection rate of mNGS was 91.01% (81/89), which was significantly higher than that of standard microbiological blood cultures (39.33% (35/89)). Standard microbiological blood cultures and mNGS methods demonstrated double positive results in 33 (37.08%) specimens and double-negative results in 8 (8.99%) specimens, while 46 (51.69%) samples and 2 (2.25%) samples had positive results only with mNGS or culture alone, respectively. Conclusion Our study identifies risk factors for the incidence and death of sepsis in traumatic patients and shows that mNGS may serve as a better diagnostic tool for the identification of pathogens in post-traumatic sepsis than standard microbiological blood cultures.
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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Cade A, Turnbull PR. Clinical testing of mild traumatic brain injury using computerised eye-tracking tests. Clin Exp Optom 2022; 105:680-686. [PMID: 35021960 DOI: 10.1080/08164622.2021.2018915] [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: 10/19/2022] Open
Abstract
Traumatic brain injury (TBI) refers to the alteration of typical brain function that occurs following a blow to the head. Even a mild case of traumatic brain injury (mTBI) can lead to long-term impairment, so accurate and timely detection is vital. Visual symptoms are common following mTBI, so while it may seem to fall outside their typical scope of practice, optometrists are ideally qualified to assess the visual impacts and help with the diagnosis of mTBI. Given that mTBI is challenging to objectively diagnose and has no universally accepted diagnostic criteria, clinicians can lack confidence in diagnosing mTBI, and be hesitant in becoming involved in the management of such patients. The development of easily quantifiable techniques using eye tracking as an objective diagnostic tool provides practitioners with an easier pathway into the field, assigning numerical values to parameters which are difficult to assess using conventional optometric tests. As this evolving technology becomes increasingly integrated into optometric clinical settings, the potential for it to identify deficits accurately and reliably in patients following mTBI, and to monitor both their recovery and the effectiveness of potential treatments will increase. This paper provides an overview of clinical tests, relevant to optometrists, that can uncover oculomotor, attentional, and exteroceptive deficits following a mTBI, so that an optometrist with an interest in eye tracking can play a role in the detection and monitoring of mTBI symptoms.
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Affiliation(s)
- Alice Cade
- School of Optometry and Vision Science, University of Auckland, Auckland, New Zealand
| | - Philip Rk Turnbull
- School of Optometry and Vision Science, University of Auckland, Auckland, New Zealand
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Dippenaar A, Ismail N, Grobbelaar M, Oostvogels S, de Vos M, Streicher EM, Heupink TH, van Rie A, Warren RM. Optimizing liquefaction and decontamination of sputum for DNA extraction from Mycobacterium tuberculosis. Tuberculosis (Edinb) 2022; 132:102159. [PMID: 34906896 DOI: 10.1016/j.tube.2021.102159] [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: 08/27/2021] [Revised: 11/21/2021] [Accepted: 12/02/2021] [Indexed: 10/19/2022]
Abstract
Whole genome sequencing (WGS) can investigate the entire Mycobacterium tuberculosis (Mtb) genome but currently requires large amounts of mycobacterial DNA, necessitating culture. Culture-free Mtb WGS could revolutionize the clinical use of WGS but is hampered by the high viscosity, low mycobacterial load, and high contamination with bacterial and human DNA in sputum samples. To improve the sputum liquefaction and decontamination step prior to DNA extraction, we assessed the efficiency of Myco-TB, MycoPrep, and Sputolysin with/without TiKa-Kic in liquefying and decontaminating sputum and aimed to evaluate the effect of these approaches on mycobacterial viability, and Mtb DNA quality and quantity. Experiments using spiked sputum samples showed that Myco-TB and BD MycoPrep with standard (15 min) or increased (30 min) incubation time, but not reduced (7,5 min) incubation time performed well in liquefying and decontaminating sputum. No difference in DNA quality or quantity, contamination, or the amount of human DNA present was observed. In comparison, Sputolysin with/without TiKa-Kic was less effective for liquefaction and decontamination of sputum. PCR amplification of the human GAPDH gene after sputum treatment, showed the presence of human DNA in all samples, regardless of sputum treatment. Focused efforts are needed to deplete contaminating DNA for culture-free Mtb WGS.
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Affiliation(s)
- Anzaan Dippenaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa; Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium.
| | - Nabila Ismail
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Melanie Grobbelaar
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Selien Oostvogels
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Margaretha de Vos
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Elizabeth M Streicher
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tim H Heupink
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Annelies van Rie
- Tuberculosis Omics Research Consortium, Department of Family Medicine and Population Health, Faculty of Medicine and Health Sciences, University of Antwerp, Antwerp, Belgium
| | - Robin M Warren
- Department of Science and Innovation-National Research Foundation Centre for Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
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Guo F, Kang L, Zhang L. mNGS for identifying pathogens in febrile neutropenic children with hematological diseases. Int J Infect Dis 2021; 116:85-90. [PMID: 34929357 DOI: 10.1016/j.ijid.2021.12.335] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/24/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVE To investigate the application value of metagenomic next-generation sequencing (mNGS) in children with hematological diseases presenting with Febrile Neutropenic (FN). METHODS We retrospectively analyzed the clinical data of 49 hematological children with FN, and compared the results of mNGS with those of traditional pathogen detection (TPD) and the prognoses of mNGS positive group and negative group. RESULTS A total of 77 pathogenic strains were identified, of which 70 strains were detected by mNGS, 19 strains by TPD , and Aspergillus and G- bacterias were the predominant strains in FN children who developed bloodstream infections. 42 cases were in the mNGS-positive group, of which 17 were simple infections, 25 were mixed infections, and 7 were in the negative group; the TPD-positive group contained 19 cases, all of which were simple infections. The detection rate of total and mixed pathogens was higher than that of TPD, and the difference was statistically significant (P<0.05). mNGS positive group was detected earlier than the negative group, and with lower mortality and drug-related adverse events (DRAE) , and the difference was statistically significant (P<0.05). CONCLUSION For FN children with hematological diseases, early mNGS can effectively improve the efficacy of pathogen detection, and precise treatment after clarifying the pathogens can reduce mortality and avoid antibiotic abuse.
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Affiliation(s)
- Fang Guo
- Department of Infections, Hebei Children's Hospital, affiliated to Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Lei Kang
- Department of Pediatric Intensive Care Unit, Hebei Children's Hospital, affiliated to Hebei Medical University, Shijiazhuang, Hebei, China.
| | - Lin Zhang
- Department of Pediatrics, Hebei Medical University Third Hospital, Shijiazhuang, Hebei, China.
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Zheng Y, Qiu X, Wang T, Zhang J. The Diagnostic Value of Metagenomic Next-Generation Sequencing in Lower Respiratory Tract Infection. Front Cell Infect Microbiol 2021; 11:694756. [PMID: 34568089 PMCID: PMC8458627 DOI: 10.3389/fcimb.2021.694756] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023] Open
Abstract
Lower respiratory tract infections are associated with high morbidity and mortality and significant clinical harm. Due to the limited ability of traditional pathogen detection methods, anti-infective therapy is mostly empirical. Therefore, it is difficult to adopt targeted drug therapy. In recent years, metagenomic next-generation sequencing (mNGS) technology has provided a promising means for pathogen-specific diagnosis and updated the diagnostic strategy for lower respiratory tract infections. This article reviews the diagnostic value of mNGS for lower respiratory tract infections, the impact of different sampling methods on the detection efficiency of mNGS, and current technical difficulties in the clinical application of mNGS.
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Affiliation(s)
- Yan Zheng
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Xiaojian Qiu
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Ting Wang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
| | - Jie Zhang
- Department of Respiratory and Critical Care, Beijing Tian Tan Hospital, Capital Medical University, Beijing, China
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21
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Tuberculosis Diagnosis by Metagenomic Next-generation Sequencing on Bronchoalveolar Lavage Fluid: a cross-sectional analysis. Int J Infect Dis 2020; 104:50-57. [PMID: 33359946 DOI: 10.1016/j.ijid.2020.12.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 12/20/2020] [Accepted: 12/21/2020] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Metagenomic next-generation sequencing (mNGS) is an effective diagnostic method for infectious diseases, however, its clinical utility for tuberculosis (TB) diagnosis remains to be demonstrated. METHODS A total of 322 bronchoalveolar lavage fluid (BALF) samples were collected from 311 suspected and confirmed pulmonary TB patients and tested by mNGS, acid-fast bacillus (AFB) smear by microscopy, Xpert® MTB/RIF (Xpert), mycobacterium culture and bacterial/fungal culture. Diagnostic performance of mNGS was compared with conventional methods for detection of Mycobacterium tuberculosis complex (MTBC) and other pathogens in BALF. Underlying factors associated with positive detection in pulmonary TB patients were investigated. RESULTS mNGS, Xpert and culture presented a high proportion of complete matching for MTBC detection (244/322, 75.8%). In pulmonary TB patients pre-treatment the sensitivity of MTBC detection by mNGS, Xpert, culture and smear was 59.9% (85/142), 69.0% (98/142), 59.9% (85/142) and 24.6% (35/142), respectively, and 79.6% overall; MTBC was detected by mNGS in 33.2% (5/34) Xpert and culture negative samples. Positive MTBC detection by mNGS was affected by Vitamin D, erythrocyte sedimentation rate, TB initial treatment/retreatment, and cavity in chest imaging (χ2 = 37.42, P < 0.001), but not by prior anti-TB therapy within 3 months. mNGS was able to detect new potential pathogens in 8.7% (28/322) of samples. CONCLUSIONS Combining mNGS with conventional detection methods could increase the detection rate for MTBC. Additionally, mNGS could identify pathogens in a non-targeted approach for better diagnosis of coinfection.
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Wang Q, Feng J, Zhang J, Shi L, Jin Z, Liu D, Wu B, Chen J. Diagnosis of complication in lung transplantation by TBLB + ROSE + mNGS. Open Med (Wars) 2020; 15:968-980. [PMID: 33313416 PMCID: PMC7706120 DOI: 10.1515/med-2020-0232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 07/26/2020] [Accepted: 09/02/2020] [Indexed: 11/18/2022] Open
Abstract
Lung transplantation is a potentially life-saving therapy for patients with terminal respiratory illnesses. Long-term survival is limited by the development of a variety of opportunistic infections and rejection. Optimal means of differential diagnosis of infection and rejection have not been established. With these challenges in mind, we tried to use transbronchial lung biopsy (TBLB) rapid on-site cytological evaluation (ROSE), metagenomic next-generation sequencing (mNGS), and routine histologic examination to timely distinguish infection and rejection, and accurately detect etiologic pathogens. We reviewed the medical records of all patients diagnosed with infection or rejection by these means from December 2017 to September 2018 in our center. We identified seven recipients whose clinical course was complicated by infection or rejection. Three patients were diagnosed with acute rejection, organizing pneumonia, and acute fibrinoid organizing pneumonia, respectively. Four of the seven patients were diagnosed with infections, including Pneumocystis carinii pneumonia, cytomegalovirus, Aspergillus, and bacterial pneumonia. These patients recovered after proper treatment. TBLB + ROSE + mNGS might be a good method to accurately detect etiologic pathogens, which may help us to facilitate the use of targeted and precision medicine therapy in postoperative complications and avoid unnecessary potential adverse effects of drugs.
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Affiliation(s)
- Qing Wang
- Respiratory Department of Kunming Municipal First People’s Hospital, Kunming 650000, China
- Graduate School, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Jing Feng
- Respiratory Department of Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Ji Zhang
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Lingzhi Shi
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Zhixian Jin
- Respiratory Department of Kunming Municipal First People’s Hospital, Kunming 650000, China
| | - Dong Liu
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Bo Wu
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
| | - Jingyu Chen
- Respiratory Department of Lung Transplant Center, The Affiliated Wuxi People’s Hospital of Nanjing Medical University, Wuxi 214023, China
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Sensitive Identification of Bacterial DNA in Clinical Specimens by Broad-Range 16S rRNA Gene Enrichment. J Clin Microbiol 2020; 58:JCM.01605-20. [PMID: 33028602 DOI: 10.1128/jcm.01605-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/30/2020] [Indexed: 12/30/2022] Open
Abstract
The broad-range detection and identification of bacterial DNA from clinical specimens are a foundational approach in the practice of molecular microbiology. However, there are circumstances under which conventional testing may yield false-negative or otherwise uninterpretable results, including the presence of multiple bacterial templates or degraded nucleic acids. Here, we describe an alternative, next-generation sequencing approach for the broad range detection of bacterial DNA using broad-range 16S rRNA gene hybrid capture ("16S Capture"). The method is able to deconvolute multiple bacterial species present in a specimen, is compatible with highly fragmented templates, and can be readily implemented when the overwhelming majority of nucleic acids in a specimen derive from the human host. We find that this approach is sensitive to detecting as few as 17 Staphylococcus aureus genomes from a background of 100 ng of human DNA, providing 19- to 189-fold greater sensitivity for identifying bacterial sequences than standard shotgun metagenomic sequencing, and is able to successfully recover organisms from across the eubacterial tree of life. Application of 16S Capture to a proof-of-principle case series demonstrated its ability to identify bacterial species that were consistent with histological evidence of infection, even when diagnosis could not be established using conventional broad range bacterial detection assays. 16S Capture provides a novel means for the efficient and sensitive detection of bacteria embedded in human tissues and for specimens containing highly fragmented template DNA.
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Ransom EM, Potter RF, Dantas G, Burnham CAD. Genomic Prediction of Antimicrobial Resistance: Ready or Not, Here It Comes! Clin Chem 2020; 66:1278-1289. [PMID: 32918462 DOI: 10.1093/clinchem/hvaa172] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 07/01/2020] [Indexed: 12/17/2022]
Abstract
BACKGROUND Next-generation sequencing (NGS) technologies are being used to predict antimicrobial resistance. The field is evolving rapidly and transitioning out of the research setting into clinical use. Clinical laboratories are evaluating the accuracy and utility of genomic resistance prediction, including methods for NGS, downstream bioinformatic pipeline components, and the clinical settings in which this type of testing should be offered. CONTENT We describe genomic sequencing as it pertains to predicting antimicrobial resistance in clinical isolates and samples. We elaborate on current methodologies and workflows to perform this testing and summarize the current state of genomic resistance prediction in clinical settings. To highlight this aspect, we include 3 medically relevant microorganism exemplars: Mycobacterium tuberculosis, Staphylococcus aureus, and Neisseria gonorrhoeae. Last, we discuss the future of genomic-based resistance detection in clinical microbiology laboratories. SUMMARY Antimicrobial resistance prediction by genomic approaches is in its infancy for routine patient care. Genomic approaches have already added value to the current diagnostic testing landscape in specific circumstances and will play an increasingly important role in diagnostic microbiology. Future advancements will shorten turnaround time, reduce costs, and improve our analysis and interpretation of clinically actionable results.
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Affiliation(s)
- Eric M Ransom
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
| | - Robert F Potter
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
| | - Gautam Dantas
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO
- Departments of Pediatrics and Medicine, Washington University School of Medicine, St. Louis, MO
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DNA Thermo-Protection Facilitates Whole-Genome Sequencing of Mycobacteria Direct from Clinical Samples. J Clin Microbiol 2020; 58:JCM.00670-20. [PMID: 32719032 PMCID: PMC7512152 DOI: 10.1128/jcm.00670-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Accepted: 07/15/2020] [Indexed: 02/03/2023] Open
Abstract
Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0. Mycobacterium tuberculosis is the leading cause of death from bacterial infection. Improved rapid diagnosis and antimicrobial resistance determination, such as by whole-genome sequencing, are required. Our aim was to develop a simple, low-cost method of preparing DNA for sequencing direct from M. tuberculosis-positive clinical samples (without culture). Simultaneous sputum liquefaction, bacteria heat inactivation (99°C/30 min), and enrichment for mycobacteria DNA were achieved using an equal volume of thermo-protection buffer (4 M KCl, 0.05 M HEPES buffer, pH 7.5, 0.1% dithiothreitol [DTT]). The buffer emulated intracellular conditions found in hyperthermophiles, thus protecting DNA from rapid thermodegradation, which renders it a poor template for sequencing. Initial validation experiments employed mycobacteria DNA, either extracted or intracellular. Next, mock clinical samples (infection-negative human sputum spiked with 0 to 105Mycobacterium bovis BCG cells/ml) underwent liquefaction in thermo-protection buffer and heat inactivation. DNA was extracted and sequenced. Human DNA degraded faster than mycobacteria DNA, resulting in target enrichment. Four replicate experiments achieved M. tuberculosis detection at 101 BCG cells/ml, with 31 to 59 M. tuberculosis complex reads. Maximal genome coverage (>97% at 5× depth) occurred at 104 BCG cells/ml; >91% coverage (1× depth) occurred at 103 BCG cells/ml. Final validation employed M. tuberculosis-positive clinical samples (n = 20), revealing that initial sample volumes of ≥1 ml typically yielded higher mean depths of M. tuberculosis genome coverage, with an overall range of 0.55 to 81.02. A mean depth of 3 gave >96% 1-fold tuberculosis (TB) genome coverage (in 15/20 clinical samples). A mean depth of 15 achieved >99% 5-fold genome coverage (in 9/20 clinical samples). In summary, direct-from-sample sequencing of M. tuberculosis genomes was facilitated by a low-cost thermo-protection buffer.
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Lepuschitz S, Weinmaier T, Mrazek K, Beisken S, Weinberger J, Posch AE. Analytical Performance Validation of Next-Generation Sequencing Based Clinical Microbiology Assays Using a K-mer Analysis Workflow. Front Microbiol 2020; 11:1883. [PMID: 32849463 PMCID: PMC7422695 DOI: 10.3389/fmicb.2020.01883] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Accepted: 07/17/2020] [Indexed: 12/13/2022] Open
Abstract
Next-generation sequencing (NGS) enables clinical microbiology assays such as molecular typing of bacterial isolates which is now routinely applied for infection control and epidemiology. Additionally, feasibility for NGS-based identification of antimicrobial resistance (AMR) markers as well as genetic prediction of antibiotic susceptibility testing results has been demonstrated. Various bioinformatics approaches enabling NGS-based clinical microbiology assays exist, but standardized, computationally efficient and scalable sample-to-results workflows including validated quality control parameters are still lacking. Bioinformatics analysis workflows based on k-mers have been shown to allow for fast and efficient analysis of large genomics data sets as obtained from microbial sequencing applications. We here demonstrate applicability of k-mer based clinical microbiology assays for whole-genome sequencing (WGS) including variant calling, taxonomic identification, bacterial typing as well as AMR marker detection. The wet-lab and dry-lab workflows were developed and validated in line with Clinical Laboratory Improvement Act (CLIA) guidelines for laboratory-developed tests (LDTs) on multi-drug resistant ESKAPE pathogens. The developed k-mer based workflow demonstrated ≥99.39% repeatability, ≥99.09% reproducibility and ≥99.76% accuracy for variant calling and applied assays as determined by intra-day and inter-day triplicate measurements. The limit of detection (LOD) across assays was found to be at 20× sequencing depth and 15× for AMR marker detection. Thorough benchmarking of the k-mer based workflow revealed analytical performance criteria are comparable to state-of-the-art alignment based workflows across clinical microbiology assays. Diagnostic sensitivity and specificity for multilocus sequence typing (MLST) and phylogenetic analysis were 100% for both approaches. For AMR marker detection, sensitivity and specificity were 95.29 and 99.78% for the k-mer based workflow as compared to 95.17 and 99.77% for the alignment-based approach. Summarizing, results illustrate that k-mer based analysis workflows enable a broad range of clinical microbiology assays, potentially not only for WGS-based typing and AMR gene detection but also genetic prediction of antibiotic susceptibility testing results.
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Shi CL, Han P, Tang PJ, Chen MM, Ye ZJ, Wu MY, Shen J, Wu HY, Tan ZQ, Yu X, Rao GH, Zhang JP. Clinical metagenomic sequencing for diagnosis of pulmonary tuberculosis. J Infect 2020; 81:567-574. [PMID: 32768450 DOI: 10.1016/j.jinf.2020.08.004] [Citation(s) in RCA: 60] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2020] [Revised: 07/29/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVES The aim of this study is to investigate the clinical usefulness of metagenomic Next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples to discriminate pulmonary tuberculosis (PTB) from Non-TB community-acquired pneumonia (CAP) in PTB suspects. METHODS We investigate the performance of mNGS on BALF samples from 110 PTB suspects, in comparison with conventional microbiological testing (solid media culture, acid-fast bacilli staining (AFS), Xpert) of BALF or sputum samples and final clinical diagnosis. RESULTS We finally clinically diagnosed 48 cases of pulmonary tuberculosis patients and 62 cases of non-tuberculosis patients. Comparing to the final clinical diagnosis, mNGS produced a sensitivity of 47.92%, which was similar to that of Xpert (45.83%) and culture (46.81%), but much higher than that of AFS (29.17%) for TB diagnosis in BALF samples. Apart from detecting Mycobacterium tuberculosis, mNGS also identified mixed infections in PTB patients, including 3 fungal cases and 1 bacteria case. Meanwhile, mNGS efficiently identified 14 of 22 (63.63%) cases of non-tuberculous mycobacteria (NTM), 7 cases of fungi, 1 case of viral infection, and other common bacterial pathogens in Non-PTB group. Finally, mNGS identified 67.23% infection cases within 3 days, while the conventional methods identified 49.58% infection cases for over 90 days. CONCLUSION Our data show that mNGS of BALF represents a potentially effective tool for the rapid diagnosis of PTB suspects.
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Affiliation(s)
- Cui-Lin Shi
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Peng Han
- Genskey Medical Technology Co., Ltd, Beijing, China
| | - Pei-Jun Tang
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | | | - Zhi-Jian Ye
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Mei-Ying Wu
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Jie Shen
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Hai-Yan Wu
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Zhu-Qing Tan
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Xin Yu
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China.
| | - Guan-Hua Rao
- Genskey Medical Technology Co., Ltd, Beijing, China.
| | - Jian-Ping Zhang
- The Affiliated Infectious Hospital of Soochow University, 10 Guangqian Road, Suzhou, Suzhou, Jiangsu 215131, China; The Fifth People's Hospital of Suzhou, Suzhou, China.
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Goig GA, Cancino-Muñoz I, Torres-Puente M, Villamayor LM, Navarro D, Borrás R, Comas I. Whole-genome sequencing of Mycobacterium tuberculosis directly from clinical samples for high-resolution genomic epidemiology and drug resistance surveillance: an observational study. THE LANCET MICROBE 2020; 1:e175-e183. [DOI: 10.1016/s2666-5247(20)30060-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Revised: 04/21/2020] [Accepted: 05/20/2020] [Indexed: 12/17/2022] Open
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Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Shanghai, China. Int J Infect Dis 2020; 96:48-53. [DOI: 10.1016/j.ijid.2020.04.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Revised: 04/14/2020] [Accepted: 04/17/2020] [Indexed: 11/19/2022] Open
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Dohál M, Porvazník I, Pršo K, Rasmussen EM, Solovič I, Mokrý J. Whole-genome sequencing and Mycobacterium tuberculosis: Challenges in sample preparation and sequencing data analysis. Tuberculosis (Edinb) 2020; 123:101946. [PMID: 32741530 DOI: 10.1016/j.tube.2020.101946] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 04/29/2020] [Accepted: 04/30/2020] [Indexed: 12/26/2022]
Abstract
The numbers of patients with tuberculosis (TB) caused by resistant strains are still alarming. Therefore, it is necessary to determine resistance more quickly and precisely, than it is with the currently used phenotypic and genotypic methods. In recent years, technological advances have been made and the whole-genome sequencing (WGS) method has been introduced as a part of routine diagnostics in clinical laboratories. Comparing a wide range of mycobacterial genomic variations with a reference genome leads to a consistent evaluation of molecular-epidemiology and resistance of Mycobacterium tuberculosis (M. tuberculosis) to a wide range of anti-TB drugs. The quality of the obtained sequencing data is closely related to the type of sample and the method used for DNA extraction and sequencing library preparation. Moreover, the correct interpretation of results is also influenced by a bioinformatic data processing. A large number of bioinformatics pipelines are currently available, the sensitivity of which varies due to the different sizes of databases containing relevant mutations. This review focuses on the individual steps included in the sequencing workflow and factors that may affect the interpretation of final results.
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Affiliation(s)
- Matúš Dohál
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia.
| | - Igor Porvazník
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia; Faculty of Health, Catholic University, Ružomberok, Slovakia
| | - Kristián Pršo
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Ivan Solovič
- National Institute of Tuberculosis, Lung Diseases and Thoracic Surgery, Vyšné Hágy, Slovakia
| | - Juraj Mokrý
- Department of Pharmacology and Biomedical Center Martin, Jessenius Faculty of Medicine, Comenius University, Martin, Slovakia
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Acharya B, Acharya A, Gautam S, Ghimire SP, Mishra G, Parajuli N, Sapkota B. Advances in diagnosis of Tuberculosis: an update into molecular diagnosis of Mycobacterium tuberculosis. Mol Biol Rep 2020; 47:4065-4075. [DOI: 10.1007/s11033-020-05413-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Accepted: 03/28/2020] [Indexed: 01/02/2023]
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Whole genome enrichment approach for rapid detection of Mycobacterium tuberculosis and drug resistance-associated mutations from direct sputum sequencing. Tuberculosis (Edinb) 2020; 121:101915. [PMID: 32279871 DOI: 10.1016/j.tube.2020.101915] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Revised: 02/12/2020] [Accepted: 02/17/2020] [Indexed: 11/24/2022]
Abstract
Tuberculosis is the leading cause of death among infectious diseases worldwide. Detection of Mycobacterium tuberculosis (Mtb), using routine culture-based methods is time consuming resulting in delayed diagnosis and poor treatment outcomes. Currently available molecular tests provide faster diagnosis but are able to screen only limited hot-spot mutations. Whole genome sequencing from direct sputum offers a potential solution, however, due to the presence of other microbes and host DNA its use in diagnostic testing remains challenging. In this study, we present a targeted Mtb-enrichment assay for lineage-4 coupled with an improved analysis pipeline that uses 1657 bacterial taxa as background for reducing non-Mtb genome from sputum DNA. This method drastically improved the recovery of Mtb DNA from sputum (Mtb alignment increased from 3% to >65%) as compared to non-enrichment-based sequencing. We obtained >99% Mtb genome coverage as compared to 49% in non-enriched sputum sequencing. We were able to identify Mtb positive samples from controls with 100% accuracy using Mpt64 gene coverage. Our method not only achieved 100% sensitivity to resistance variants profiled by line probe assay (LPA), but also outperformed LPA in determining drug resistance based on phenotypic drug susceptibility tests for 6 anti-tuberculosis drugs (accuracy of 97.7% and 92.8% by enriched WGS and LPA, respectively).
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Matsumoto Y, Kinjo T, Motooka D, Nabeya D, Jung N, Uechi K, Horii T, Iida T, Fujita J, Nakamura S. Comprehensive subspecies identification of 175 nontuberculous mycobacteria species based on 7547 genomic profiles. Emerg Microbes Infect 2019; 8:1043-1053. [PMID: 31287781 PMCID: PMC6691804 DOI: 10.1080/22221751.2019.1637702] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The prevalence of nontuberculous mycobacteria (NTM) pulmonary diseases has been increasing worldwide. NTM consist of approximately 200 species and distinguishing between them at the subspecies level is critical to treatment. In this study, we sequenced 63 NTM genomes, 27 of which were newly determined, by hybrid assembly using sequencers from Illumina and Oxford Nanopore Technologies (ONT). This analysis expanded the available genomic data to 175 NTM species and redefined their subgenus classification. We also developed a novel multi-locus sequence typing (MLST) database based on 184 genes from 7547 assemblies and an identification software, mlstverse, which can also be used for detecting other bacteria given a suitable MLST database. This method showed the highest sensitivity and specificity amongst conventional methods and demonstrated the capacity for rapid detection of NTM, 10 min of sequencing of the ONT MinION being sufficient. Application of this methodology could improve disease epidemiology and increase the cure rates of NTM diseases.
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Affiliation(s)
- Yuki Matsumoto
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Takeshi Kinjo
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Daisuke Motooka
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Daijiro Nabeya
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Nicolas Jung
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Kohei Uechi
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan.,d Division of Clinical Laboratory and Blood Transfusion , University of the Ryukyus Hospital , Nakagami-gun , Japan
| | - Toshihiro Horii
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Tetsuya Iida
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan
| | - Jiro Fujita
- b Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine , University of the Ryukyus , Nakagami-gun , Japan
| | - Shota Nakamura
- a Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,c Laboratory of Pathogen Detection and Identification, International Research Center for Infectious Diseases, Research Institute for Microbial Diseases , Osaka University , Suita , Japan.,e Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives , Osaka University , Suita , Japan
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Dara M, Ehsani S, Mozalevskis A, Vovc E, Simões D, Avellon Calvo A, Casabona I Barbarà J, Chokoshvili O, Felker I, Hoffner S, Kalmambetova G, Noroc E, Shubladze N, Skrahina A, Tahirli R, Tsertsvadze T, Drobniewski F. Tuberculosis, HIV, and viral hepatitis diagnostics in eastern Europe and central Asia: high time for integrated and people-centred services. THE LANCET. INFECTIOUS DISEASES 2019; 20:e47-e53. [PMID: 31740252 DOI: 10.1016/s1473-3099(19)30524-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 08/12/2019] [Accepted: 08/20/2019] [Indexed: 12/21/2022]
Abstract
Globally, high rates (and in the WHO European region an increasing prevalence) of co-infection with tuberculosis and HIV and HIV and hepatitis C virus exist. In eastern European and central Asian countries, the tuberculosis, HIV, and viral hepatitis programmes, including diagnostic services, are separate vertical structures. In this Personal View, we consider underlying reasons for the poor integration for these diseases, particularly in the WHO European region, and how to address this with an initial focus on diagnostic services. In part, this low integration has reflected different diagnostic development histories, global funding sources, and sample types used for diagnosis (eg, typically sputum for tuberculosis and blood for HIV and hepatitis C). Cooperation between services improved as patients with tuberculosis needed routine testing for HIV and vice versa, but financial, infection control, and logistical barriers remain. Multidisease diagnostic platforms exist, but to be used optimally, appropriate staff training and sensible understanding of different laboratory and infection control risks needs rapid implementation. Technically these ideas are all feasible. Poor coordination between these vertical systems remains unhelpful. There is a need to increase political and operational integration of diagnostic and treatment services and bring them closer to patients.
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Affiliation(s)
- Masoud Dara
- Communicable Diseases Department, Division of Health Emergencies and Communicable Diseases, Regional Office for Europe, World Health Organization, Copenhagen, Denmark.
| | - Soudeh Ehsani
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Antons Mozalevskis
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Elena Vovc
- Joint Tuberculosis, HIV and Viral Hepatitis Programme, Regional Office for Europe, World Health Organization, Copenhagen, Denmark
| | - Daniel Simões
- EPI Unit, Institute of Public Health, University of Porto, Porto, Portugal
| | - Ana Avellon Calvo
- Hepatitis Unit, National Center of Microbiology, Carlos III Institute of Health, Majadahonda, Madrid, Spain
| | - Jordi Casabona I Barbarà
- Center for Epidemiological Studies on STI and AIDS in Catalonia and Research Network on Biomedical Research, Epidemiology and Public Health, Catalan Agency of Public Health, Badalona, Spain
| | - Otar Chokoshvili
- Infectious diseases and Clinical Immunology Research Center, Tbilisi, Georgia
| | - Irina Felker
- Scientific department, Novosibirsk Tuberculosis Research Institute, Novosibirsk, Russia
| | - Sven Hoffner
- Department of Public Health Sciences, Karolinska Institute, Stockholm, Sweden
| | | | - Ecatarina Noroc
- National AIDS Programme, Dermatology and Communicable Diseases Hospital, Chisinau, Moldova
| | - Natalia Shubladze
- National Reference Laboratory, National Center for Tuberculosis and Lung Diseases, Tbilisi, Georgia
| | - Alena Skrahina
- Clinical department, Republican Scientific and Practical Centre for Pulmonology and Tuberculosis, Minsk, Belarus
| | - Rasim Tahirli
- Laboratory for Medical Service, Specialized Treatment Institution, Main Medical Department, Ministry of Justice, Baku, Azerbaijan
| | - Tengiz Tsertsvadze
- Infectious Diseases and Clinical Immunology Research Center, Tbilisi State University, Tbilisi, Georgia
| | - Francis Drobniewski
- Global Health and Tuberculosis, Imperial College London, London, UK; WHO European Laboratory Initiative on Tuberculosis, HIV and Viral hepatitis, WHO Regional Office of Europe, Copenhagen, Denmark
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Miao Q, Ma Y, Wang Q, Pan J, Zhang Y, Jin W, Yao Y, Su Y, Huang Y, Wang M, Li B, Li H, Zhou C, Li C, Ye M, Xu X, Li Y, Hu B. Microbiological Diagnostic Performance of Metagenomic Next-generation Sequencing When Applied to Clinical Practice. Clin Infect Dis 2019; 67:S231-S240. [PMID: 30423048 DOI: 10.1093/cid/ciy693] [Citation(s) in RCA: 462] [Impact Index Per Article: 92.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Background Metagenomic next-generation sequencing (mNGS) was suggested to potentially replace traditional microbiological methodology because of its comprehensiveness. However, clinical experience with application of the test is relatively limited. Methods From April 2017 to December 2017, 511 specimens were collected, and their retrospective diagnoses were classified into infectious disease (347 [67.9%]), noninfectious disease (119 [23.3%]), and unknown cases (45 [8.8%]). The diagnostic performance of pathogens was compared between mNGS and culture. The effect of antibiotic exposure on detection rate was also assessed. Results The sensitivity and specificity of mNGS for diagnosing infectious disease were 50.7% and 85.7%, respectively, and these values outperformed those of culture, especially for Mycobacterium tuberculosis (odds ratio [OR], 4 [95% confidence interval {CI}, 1.7-10.8]; P < .01), viruses (mNGS only; P < .01), anaerobes (OR, ∞ [95% CI, 1.71-∞]; P < .01) and fungi (OR, 4.0 [95% CI, 1.6-10.3]; P < .01). Importantly, for mNGS-positive cases where the conventional method was inconclusive, 43 (61%) cases led to diagnosis modification, and 41 (58%) cases were not covered by empirical antibiotics. For cases where viruses were identified, broad-spectrum antibiotics were commonly administered (14/27), and 10 of 27 of these cases were suspected to be inappropriate. Interestingly, the sensitivity of mNGS was superior to that of culture (52.5% vs 34.2%; P < .01) in cases with, but not without, antibiotic exposure. Conclusions mNGS could yield a higher sensitivity for pathogen identification and is less affected by prior antibiotic exposure, thereby emerging as a promising technology for detecting infectious diseases.
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Affiliation(s)
- Qing Miao
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yuyan Ma
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Qingqing Wang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Jue Pan
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yao Zhang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Wenting Jin
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yumeng Yao
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yi Su
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Yingnan Huang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Mengran Wang
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Bing Li
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
| | - Huaying Li
- Department of Microbiology, Zhongshan Hospital of Fudan University
| | - Chunmei Zhou
- Department of Microbiology, Zhongshan Hospital of Fudan University
| | - Chun Li
- Department of Respiratory, Zhongshan Hospital of Fudan University
| | - Maosong Ye
- Department of Respiratory, Zhongshan Hospital of Fudan University
| | - Xiaoling Xu
- BGI China, Shanghai, People's Republic of China
| | - Yongjun Li
- BGI China, Shanghai, People's Republic of China
| | - Bijie Hu
- Department of Infectious Diseases, Zhongshan Hospital of Fudan University
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36
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Saad J, Loukil A, Drancourt M. Bead-captured Mycobacterium tuberculosis for next-generation sequencing diagnosis of uncultured tuberculosis. Eur J Clin Microbiol Infect Dis 2019; 39:205-207. [PMID: 31612370 DOI: 10.1007/s10096-019-03700-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 10/25/2022]
Affiliation(s)
- Jamal Saad
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ., 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Ahmed Loukil
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ., 19-21 Boulevard Jean Moulin, 13005, Marseille, France
| | - Michel Drancourt
- IRD, MEPHI, IHU Méditerranée Infection, Aix-Marseille-Univ., 19-21 Boulevard Jean Moulin, 13005, Marseille, France.
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37
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Abstract
Mycobacterium tilburgii
is a fastidious mycobacterium which has previously been reported to cause severe disseminated infections. Genome sequencing of the
M. tilburgii
MEPHI clinical isolate yielded 3.14 Mb, with 66.3% GC content, and confirmed phylogenetic placement within the
Mycobacterium simiae
complex.
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38
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Wang S, Chen Y, Wang D, Wu Y, Zhao D, Zhang J, Xie H, Gong Y, Sun R, Nie X, Jiang H, Zhang J, Li W, Liu G, Li X, Huang K, Huang Y, Li Y, Guan H, Pan S, Hu Y. The Feasibility of Metagenomic Next-Generation Sequencing to Identify Pathogens Causing Tuberculous Meningitis in Cerebrospinal Fluid. Front Microbiol 2019; 10:1993. [PMID: 31551954 PMCID: PMC6733977 DOI: 10.3389/fmicb.2019.01993] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Accepted: 08/14/2019] [Indexed: 01/22/2023] Open
Abstract
Purpose The application of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains poorly characterized. Here, we retrospectively analyzed data from patients with TBM who had taken both mNGS and conventional tests including culture of Mycobacterium tuberculosis (MTB), polymerase chain reaction (PCR) and acid-fast bacillus (AFB) stain, and the sensitivity and specificity of these methods were compared. Methods We retrospectively recruited TBM patients admitted to the hospital between December 2015 and October 2018. The first collection of cerebrospinal fluid (CSF) samples underwent both mNGS and conventional tests. In addition, patients with bacterial/cryptococcal meningitis or viral meningoencephalitis were mNGS positive controls, and a patient with auto-immune encephalitis was an mNGS negative control. Results Twenty three TBM patients were classified as 12 definite and 11 clinical diagnoses, which were based on clinical manifestations, pathogen evidence, CSF parameters, brain imaging, and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MBTC) from 18 samples (18/23, 78.26%). In patients with definite TBM, the sensitivity of mNGS, AFB, PCR, and culture to detect MTB in the first CSF samples were 66.67, 33.33, 25, and 8.33%, respectively. The specificity of each method was 100%. Among the four negative mNGS cases (4/23, 17.39%), three turned out positive by repeated AFB stain. The agreement of mNGS with the total of conventional methods was 44.44% (8/18). Combination of mNGS and conventional methods increased the detection rate to 95.65%. One patient was diagnosed as complex of TBM and cryptococcal meningitis, in which AFB stain and cryptococcal antigen enzyme immunoassay were positive and the DNA of Cryptococcus neoformans was detected by mNGS. Conclusion Our study indicates that mNGS is an alternative method to detect the presence of mycobacterial DNA in CSF samples from patients with TBM and deserves to be applied as a front-line CSF test.
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Affiliation(s)
- Shengnan Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingli Chen
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Dongmei Wang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongming Wu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Deqiang Zhao
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jianzhao Zhang
- Department of Neurology, Beijing Children's Hospital, Capital Medical University, Beijing, China
| | - Huifang Xie
- Department of Neurology, Zhujiang Hospital, Southern Medical University, Guangzhou, China
| | - Yanping Gong
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Ruixue Sun
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Xifang Nie
- Tianjin Medical Laboratory, BGI-Tianjin, BGI-Shenzhen, Tianjin, China
| | - Haishan Jiang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jian Zhang
- Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Wei Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Guanghui Liu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Xuan Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Kaibin Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yingwei Huang
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yongjun Li
- BGI Genomics, BGI-Shenzhen, Shenzhen, China
| | - Hongzhi Guan
- Department of Neurology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Suyue Pan
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Yafang Hu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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García de Viedma D. Pathways and strategies followed in the genomic epidemiology of Mycobacterium tuberculosis. INFECTION GENETICS AND EVOLUTION 2019; 72:4-9. [DOI: 10.1016/j.meegid.2019.01.027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 10/27/2022]
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Cohen KA, Manson AL, Desjardins CA, Abeel T, Earl AM. Deciphering drug resistance in Mycobacterium tuberculosis using whole-genome sequencing: progress, promise, and challenges. Genome Med 2019; 11:45. [PMID: 31345251 PMCID: PMC6657377 DOI: 10.1186/s13073-019-0660-8] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Tuberculosis (TB) is a global infectious threat that is intensified by an increasing incidence of highly drug-resistant disease. Whole-genome sequencing (WGS) studies of Mycobacterium tuberculosis, the causative agent of TB, have greatly increased our understanding of this pathogen. Since the first M. tuberculosis genome was published in 1998, WGS has provided a more complete account of the genomic features that cause resistance in populations of M. tuberculosis, has helped to fill gaps in our knowledge of how both classical and new antitubercular drugs work, and has identified specific mutations that allow M. tuberculosis to escape the effects of these drugs. WGS studies have also revealed how resistance evolves both within an individual patient and within patient populations, including the important roles of de novo acquisition of resistance and clonal spread. These findings have informed decisions about which drug-resistance mutations should be included on extended diagnostic panels. From its origins as a basic science technique, WGS of M. tuberculosis is becoming part of the modern clinical microbiology laboratory, promising rapid and improved detection of drug resistance, and detailed and real-time epidemiology of TB outbreaks. We review the successes and highlight the challenges that remain in applying WGS to improve the control of drug-resistant TB through monitoring its evolution and spread, and to inform more rapid and effective diagnostic and therapeutic strategies.
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Affiliation(s)
- Keira A Cohen
- Division of Pulmonary and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, 21205, USA.
| | - Abigail L Manson
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Christopher A Desjardins
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA
- Delft Bioinformatics Lab, Delft University of Technology, 2628, XE, Delft, The Netherlands
| | - Ashlee M Earl
- Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA, 02142, USA.
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41
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues. Nat Rev Microbiol 2019; 17:533-545. [DOI: 10.1038/s41579-019-0214-5] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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42
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Miller IJ, Rees ER, Ross J, Miller I, Baxa J, Lopera J, Kerby RL, Rey FE, Kwan JC. Autometa: automated extraction of microbial genomes from individual shotgun metagenomes. Nucleic Acids Res 2019; 47:e57. [PMID: 30838416 PMCID: PMC6547426 DOI: 10.1093/nar/gkz148] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 02/15/2019] [Accepted: 02/21/2019] [Indexed: 12/28/2022] Open
Abstract
Shotgun metagenomics is a powerful, high-resolution technique enabling the study of microbial communities in situ. However, species-level resolution is only achieved after a process of 'binning' where contigs predicted to originate from the same genome are clustered. Such culture-independent sequencing frequently unearths novel microbes, and so various methods have been devised for reference-free binning. As novel microbiomes of increasing complexity are explored, sometimes associated with non-model hosts, robust automated binning methods are required. Existing methods struggle with eukaryotic contamination and cannot handle highly complex single metagenomes. We therefore developed an automated binning pipeline, termed 'Autometa', to address these issues. This command-line application integrates sequence homology, nucleotide composition, coverage and the presence of single-copy marker genes to separate microbial genomes from non-model host genomes and other eukaryotic contaminants, before deconvoluting individual genomes from single metagenomes. The method is able to effectively separate over 1000 genomes from a metagenome, allowing the study of previously intractably complex environments at the level of single species. Autometa is freely available at https://bitbucket.org/jason_c_kwan/autometa and as a docker image at https://hub.docker.com/r/jasonkwan/autometa under the GNU Affero General Public License 3 (AGPL 3).
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Affiliation(s)
- Ian J Miller
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Evan R Rees
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Jennifer Ross
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Izaak Miller
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Jared Baxa
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Juan Lopera
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
| | - Robert L Kerby
- Department of Bacteriology, University of Wisconsin–Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Federico E Rey
- Department of Bacteriology, University of Wisconsin–Madison, 1550 Linden Drive, Madison, WI 53706, USA
| | - Jason C Kwan
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin–Madison, 777 Highland Avenue, Madison, WI 53705, USA
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Nimmo C, Shaw LP, Doyle R, Williams R, Brien K, Burgess C, Breuer J, Balloux F, Pym AS. Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture. BMC Genomics 2019; 20:389. [PMID: 31109296 PMCID: PMC6528373 DOI: 10.1186/s12864-019-5782-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 05/07/2019] [Indexed: 12/28/2022] Open
Abstract
Background Repeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture. Results DNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p = 0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance. Conclusions Culture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating. Electronic supplementary material The online version of this article (10.1186/s12864-019-5782-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK. .,Africa Health Research Institute, Durban, South Africa.
| | - Liam P Shaw
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK.,Nuffield Department of Clinical Medicine, Oxford University, Oxford, OX3 7BN, UK
| | - Ronan Doyle
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK.,Clinical Research Department, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Rachel Williams
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | - Carrie Burgess
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, WC1E 6BT, UK
| | - Francois Balloux
- UCL Genetics Institute, University College London, London, WC1E 6BT, UK
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Trotter AJ, Aydin A, Strinden MJ, O'Grady J. Recent and emerging technologies for the rapid diagnosis of infection and antimicrobial resistance. Curr Opin Microbiol 2019; 51:39-45. [PMID: 31077935 DOI: 10.1016/j.mib.2019.03.001] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2018] [Revised: 02/04/2019] [Accepted: 03/08/2019] [Indexed: 10/26/2022]
Abstract
The rise in antimicrobial resistance (AMR) is predicted to cause 10 million deaths per year by 2050 unless steps are taken to prevent this looming crisis. Microbiological culture is the gold standard for the diagnosis of bacterial/fungal pathogens and antimicrobial resistance and takes 48 hours or longer. Hence, antibiotic prescriptions are rarely based on a definitive diagnosis and patients often receive inappropriate treatment. Rapid diagnostic tools are urgently required to guide appropriate antimicrobial therapy, thereby improving patient outcomes and slowing AMR development. We discuss new technologies for rapid infection diagnosis including: sample-in-answer-out PCR-based tests, BioFire FilmArray and Curetis Unyvero; rapid susceptibility tests, Accelerate Pheno and microfluidic tests; and sequencing-based approaches, focusing on targeted and clinical metagenomic nanopore sequencing.
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Affiliation(s)
- Alexander J Trotter
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Alp Aydin
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Michael J Strinden
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK
| | - Justin O'Grady
- University of East Anglia, Norwich Research Park, Norwich, Norfolk, NR4 7TJ, UK; Quadram Institute Bioscience, Norwich Research Park, Norwich, Norfolk, NR4 7UQ, UK.
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45
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Whole-Genome Sequencing in Relation to Resistance of Mycobacterium Tuberculosis. ACTA MEDICA MARTINIANA 2019. [DOI: 10.2478/acm-2019-0002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
Abstract
Tuberculosis, a disease caused by Mycobacterium tuberculosis, represents one of the deadliest infections worldwide. The incidence of resistant forms is increasing year by year; therefore, it is necessary to involve new methods for rapid diagnostics and treatment. One of the possible solutions is the use of whole-genome sequencing (WGS).
The WGS provides an identification of complete genome of the microorganism, including all genes responsible for resistance, in comparison with other genotypic methods (eg. Xpert MTB / RIF or Hain line-probes) that are capable to detect only basic genes. WGS data are available in 1-9 days and several online software tools (TBProfiler, CASTB, Mykrobe PredictorTB) are used for their interpretation and analysis, compared to 3-8 weeks in the case of classic phenotypic evaluation.
Furthermore, WGS predicts resistance to the first-line antituberculotics with a sensitivity of 85-100% and a specificity of 85-100%.
This review elucidates the importance and summarizes the current knowledge about the possible use of WGS in diagnosis and treatment of resistant forms of tuberculosis elucidates.
WGS of M. tuberculosis brings new possibilities for rapid and accurate diagnostics of resistant forms of tuberculosis. Introducing WGS into routine practice can help to reduce the spread of resistant forms of tuberculosis as well as to increase the success rate of the treatment, especially through an appropriate combination of antituberculotics ATs. Introduction of WGS into routine diagnostics can, in spite of the financial difficulty, significantly improve patient care.
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46
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Jacob JJ, Veeraraghavan B, Vasudevan K. Metagenomic next-generation sequencing in clinical microbiology. Indian J Med Microbiol 2019; 37:133-140. [PMID: 31745012 DOI: 10.4103/ijmm.ijmm_19_401] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore - 632 004, Tamil Nadu, India
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Bachmann NL, Rockett RJ, Timms VJ, Sintchenko V. Advances in Clinical Sample Preparation for Identification and Characterization of Bacterial Pathogens Using Metagenomics. Front Public Health 2018; 6:363. [PMID: 30619804 PMCID: PMC6299010 DOI: 10.3389/fpubh.2018.00363] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/28/2018] [Indexed: 12/12/2022] Open
Abstract
Whole genome sequencing (WGS) plays an increasing role in communicable disease control through high-resolution outbreak tracing, laboratory surveillance and diagnostics. However, WGS has traditionally relied on microbial culture in order to obtain pathogen specific DNA for sequencing. This has severely limited the application of whole genome sequencing on pathogens with fastidious culturing requirements. In addition, the widespread adoption of culture-independent diagnostic tests has reduced availability of cultured isolates for confirmatory testing and surveillance. These recent developments have created demand for the implementation of techniques enabling direct sequencing of microbial genomes in clinical samples without having to culture an isolate. However, sequencing of specific organisms from clinical samples can be affected by high levels of contaminating DNA from the host and other commensal microorganisms. Several methods have been introduced for selective lysis of host cells and/or separate specific organisms from a clinical sample. This review examines the different approaches for sample preparation that have been used in diagnostic and public health laboratories for metagenomic sequencing.
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Affiliation(s)
- Nathan L. Bachmann
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centenary Institute, University of Sydney, Camperdown, NSW, Australia
| | - Rebecca J. Rockett
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Verlaine Joy Timms
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
| | - Vitali Sintchenko
- Sydney Medical School, University of Sydney, Camperdown, NSW, Australia
- Centre for Infectious Diseases and Microbiology–Public Health, Westmead Hospital, Sydney, NSW, Australia
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Mycobacterium tuberculosis Next-Generation Whole Genome Sequencing: Opportunities and Challenges. Tuberc Res Treat 2018; 2018:1298542. [PMID: 30631597 PMCID: PMC6304523 DOI: 10.1155/2018/1298542] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 10/29/2018] [Accepted: 11/25/2018] [Indexed: 11/29/2022] Open
Abstract
Mycobacterium tuberculosis drug resistance is a threat to global tuberculosis (TB) control. Comprehensive and timely drug susceptibility determination is critical to inform appropriate treatment of drug-resistant tuberculosis (DR-TB). Phenotypic drug susceptibility testing (DST) is the gold standard for M. tuberculosis drug resistance determination. M. tuberculosis whole genome sequencing (WGS) has the potential to be a one-stop method for both comprehensive DST and epidemiological investigations. We discuss in this review the tremendous opportunities that next-generation WGS presents in terms of understanding the molecular epidemiology of tuberculosis and mechanisms of drug resistance. The potential clinical value and public health impact in the areas of DST for patient management and tracing of transmission chains for timely public health intervention are also discussed. We present the current challenges for the implementation of WGS in low and middle-income settings. WGS analysis has already been adapted routinely in laboratories to inform patient management and public health interventions in low burden high-income settings such as the United Kingdom. We predict that the technology will be adapted similarly in high burden settings where the impact on the epidemic will be greatest.
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Tagliani E, Nikolayevskyy V, Tortoli E, Cirillo DM. Laboratory diagnosis of tuberculosis. Tuberculosis (Edinb) 2018. [DOI: 10.1183/2312508x.10021318] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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50
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Jeanes C, O'Grady J. Diagnosing tuberculosis in the 21st century - Dawn of a genomics revolution? Int J Mycobacteriol 2018; 5:384-391. [PMID: 27931678 DOI: 10.1016/j.ijmyco.2016.11.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
Abstract
Tuberculosis (TB) ranks alongside HIV as the leading cause of death worldwide, killing 1.5million people in 2014. Traditional laboratory techniques do not provide sufficiently rapid results to inform clinicians on appropriate treatment, especially in the face of increasingly prevalent drug-resistant TB. Rapid molecular methods such as PCR and LAMP are vital tools in the fight against TB, however, rapid advances in next generation sequencing (NGS) technology are allowing increasingly rapid and accurate sequencing of entire bacterial genomes at ever decreasing cost, providing unprecedented depth of information. These advances mean NGS stands to revolutionise the diagnosis and epidemiological study of Mycobacterium tuberculosis infection. This review focuses on current applications of NGS for TB diagnosis including sequencing cultured isolates to predict drug resistance and, more desirably, direct diagnostic metagenomic sequencing of clinical samples. Also discussed is the potential impact of NGS on the epidemiological study of TB and some of the key challenges that need to be overcome to enable this promising technology to be translated into routine use.
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Affiliation(s)
- Christopher Jeanes
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
| | - Justin O'Grady
- Norwich Medical School, University of East Anglia, Norwich Research Park, Norfolk NR4 7TJ, United Kingdom.
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