1
|
Asare KK, Azumah DE, Adu-Gyamfi CO, Opoku YK, Adela EM, Afful P, Abotsi GK, Abban EA, Duntu PE, Anyamful A, Moses AB, Botchway E, Mwintige P, Kyei S, Amoah LE, Ekuman EO. Comparison of microscopic and xpert MTB diagnoses of presumptive mycobacteria tuberculosis infection: retrospective analysis of routine diagnosis at Cape Coast Teaching Hospital. BMC Infect Dis 2024; 24:660. [PMID: 38956504 PMCID: PMC11218342 DOI: 10.1186/s12879-024-09566-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 06/25/2024] [Indexed: 07/04/2024] Open
Abstract
INTRODUCTION Tuberculosis is a global health problem that causes 1. 4 million deaths every year. It has been estimated that sputum smear-negative diagnosis but culture-positive pulmonary TB diagnosis contribute to 12.6% of pulmonary TB transmission. TB diagnosis by smear microscopy smear has a minimum detection limit (LOD) of 5,000 to 10,000 bacilli per milliliter (CFU/ml) of sputum result in missed cases and false positives. However, GeneXpert technology, with a LOD of 131-250 CFU/ml in sputum samples and its implementation is believe to facilitate early detection TB and drug-resistant TB case. Since 2013, Ghana health Service (GHS) introduce GeneXpert MTB/RIF diagnostic in all regional hospitals in Ghana, however no assessment of performance between microscopy and GeneXpert TB diagnosis cross the health facilities has been reported. The study compared the results of routine diagnoses of TB by microscopy and Xpert MTB from 2016 to 2020 at the Cape Coast Teaching Hospital (CCTH). METHODS The study compared routine microscopic and GeneXpert TB diagnosis results at the Cape Coast Teaching Hospital (CCTH) from 2016 to 2020 retrospectively. Briefly, sputum specimens were collected into 20 mL sterile screw-capped containers for each case of suspected TB infection and processed within 24 h. The samples were decontaminated using the NALC-NaOH method with the final NaOH concentration of 1%. The supernatants were discarded after the centrifuge and the remaining pellets dissolved in 1-1.5 ml of phosphate buffer saline (PBS) and used for diagnosis. A fixed smears were Ziehl-Neelsen acid-fast stain and observed under microscope and the remainings were used for GeneXpert MTB/RIF diagnosis. The data were analyze using GraphPad Prism. RESULTS 50.11% (48.48-51.38%) were females with an odd ratio (95% CI) of 1.004 (0.944-1.069) more likely to report to the TB clinic for suspected TB diagnosis. The smear-positive cases for the first sputum were 6.6% (5.98-7.25%), and the second sputum was 6.07% (5.45-6.73%). The Xpert MTB-RIF diagnosis detected 2.93% (10/341) (1.42-5.33%) in the first and 5.44% (16/294) (3.14-8.69%) in the second smear-negative TB samples. The prevalence of Xpert MTB-RIF across smear positive showed that males had 56.87% (178/313) and 56.15% (137/244) and females had 43.13% (135/313) and 43.85% (107/244) for the first and second sputum. Also, false negative smears were 0.18% (10/5607) for smear 1 and 0.31% (16/5126) for smear 2. CONCLUSION In conclusion, the study highlights the higher sensitivity of the GeneXpert assay compared to traditional smear microscopy for detecting MTB. The GeneXpert assay identified 10 and 16 positive MTB from smear 1 and smear 2 samples which were microscopic negative.
Collapse
Affiliation(s)
- Kwame Kumi Asare
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana.
- Department of Biomedical Sciences, School of Allied Health Sciences, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana.
| | | | - Czarina Owusua Adu-Gyamfi
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Yeboah Kwaku Opoku
- Department of Biology Education, Faculty of Science Education, University of Education, Winneba, Ghana
| | | | - Philip Afful
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Godwin Kwami Abotsi
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | | | - Paul Ekow Duntu
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
- Department of Medical Laboratory Science, School of Allied Health Sciences, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Akwasi Anyamful
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
- Department of Medical Biochemistry, School of Medical Sciences, College of Health and Allied Sciences, University of Cape Coast, Cape Coast, Ghana
| | | | - Emmanuel Botchway
- Laboratory Departments, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Philimon Mwintige
- Laboratory Departments, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Samuel Kyei
- Biomedical and Clinical Research Centre, College of Allied Health Sciences, University of Cape Coast, Cape Coast, Ghana
- Department of Optometry and Vision Science, University of Cape Coast, Cape Coast, Ghana
| | - Linda Eva Amoah
- Department of Immunology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | | |
Collapse
|
2
|
Liu M, Zhang H, Li L, Mao J, Li R, Yin J, Wu X. The etiological diagnostic value of metagenomic next-generation sequencing in suspected community-acquired pneumonia. BMC Infect Dis 2024; 24:626. [PMID: 38914949 PMCID: PMC11194883 DOI: 10.1186/s12879-024-09507-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/13/2024] [Indexed: 06/26/2024] Open
Abstract
BACKGROUND The emergence of metagenomic next-generation sequencing (mNGS) may provide a promising tool for early and comprehensive identification of the causative pathogen in community-acquired pneumonia (CAP). In this study, we aim to further evaluate the etiological diagnostic value of mNGS in suspected CAP. METHODS A total of 555 bronchoalveolar lavage fluid (BALF) samples were collected for pathogen detection by mNGS from 541 patients with suspected CAP. The clinical value was assessed based on infection diagnosis and treatment guidance. The diagnostic performance for pathogen identification by mNGS and sputum culture and for tuberculosis (TB) by mNGS and X-pert MTB/RIF were compared. To evaluate the potential for treatment guidance, we analyzed the treatment regimen of patients with suspected CAP, including imaging changes of lung after empirical antibacterial therapy, intensified regimen, antifungal treatment, and a 1-year follow up for patients with unconfirmed diagnosis and non-improvement imaging after anti-infective treatment and patients with high suspicion of TB or NTM infection who were transferred to the Wuhan Pulmonary Hospital for further diagnosis and even anti-mycobacterium therapy. RESULTS Of the 516 BALF samples that were analyzed by both mNGS and sputum culture, the positivity rate of mNGS was significantly higher than that of sputum culture (79.1% vs. 11.4%, P = 0.001). A total of 48 samples from patients with confirmed TB were analyzed by both mNGS and X-pert MTB/RIF, and the sensitivity of mNGS for the diagnosis of active TB was significantly lower than that of X-pert MTB/RIF (64.6% vs. 85.4%, P = 0.031). Of the 106 pathogen-negative cases, 48 were ultimately considered non-infectious diseases, with a negative predictive value of 45.3%. Of the 381 pathogen-positive cases, 311 were eventually diagnosed as CAP, with a positive predictive value of 81.6%. A total of 487 patients were included in the evaluation of the therapeutic effect, and 67.1% improved with initial empirical antibiotic treatment. Of the 163 patients in which bacteria were detected, 77.9% improved with antibacterial therapy; of the 85 patients in which fungi were detected, 12.9% achieved remission after antifungal therapy. CONCLUSIONS Overall, mNGS had unique advantages in the detection of suspected CAP pathogens. However, mNGS was not superior to X-pert MTB/RIF for the diagnosis of TB. In addition, mNGS was not necessary as a routine test for all patients admitted with suspected CAP. Furthermore, when fungi are detected by mNGS, antifungal therapy should be cautious.
Collapse
Affiliation(s)
- Mengling Liu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Haiyue Zhang
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Liangyu Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jieyu Mao
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Ruiyun Li
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Jing Yin
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China
| | - Xiaojun Wu
- Department of Pulmonary and Critical Care Medicine, Renmin Hospital of Wuhan University, Wuhan, Hubei, China.
| |
Collapse
|
3
|
Solanki P, Elton L, Honeyborne I, Park M, Satta G, McHugh TD. Improving the diagnosis of tuberculosis: old and new laboratory tools. Expert Rev Mol Diagn 2024:1-10. [PMID: 38832527 DOI: 10.1080/14737159.2024.2362165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 05/28/2024] [Indexed: 06/05/2024]
Abstract
INTRODUCTION Despite recent advances in diagnostic technologies and new drugs becoming available, tuberculosis (TB) remains a major global health burden. If detected early, screened for drug resistance, and fully treated, TB could be easily controlled. AREAS COVERED Here the authors discuss M. tuberculosis culture methods which are considered the definitive confirmation of M. tuberculosis infection, and limited advances made to build on these core elements of TB laboratory diagnosis. Literature searches showed that molecular techniques provide enhanced speed of turnaround, sensitivity, and richness of data. Sequencing of the whole genome, is becoming well established for identification and inference of drug resistance. PubMed® literature searches were conducted (November 2022-March 2024). EXPERT OPINION This section highlights future advances in diagnosis and infection control. Prevention of prolonged hospital admissions and rapid TAT are of the most benefit to the overall patient experience. Host transcriptional blood markers have been used in treatment monitoring studies and, with appropriate evaluation, could be rolled out in a diagnostic setting. Additionally, the MBLA is being incorporated into latest clinical trial designs. Whole genome sequencing has enhanced epidemiological evidence. Artificial intelligence, along with machine learning, have the ability to revolutionize TB diagnosis and susceptibility testing within the next decade.
Collapse
Affiliation(s)
- Priya Solanki
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Linzy Elton
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Isobella Honeyborne
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Mirae Park
- Respiratory Medicine, Imperial Healthcare NHS Trust, London, UK
| | - Giovanni Satta
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| | - Timothy D McHugh
- UCL-TB and Centre for Clinical Microbiology, Division of Infection & Immunity, Royal Free Campus, London, UK
| |
Collapse
|
4
|
Ye J, Huang K, Xu Y, Chen N, Tu Y, Huang J, Shao L, Kong W, Zhao D, Xie Y. Clinical application of nanopore-targeted sequencing technology in bronchoalveolar lavage fluid from patients with pulmonary infections. Microbiol Spectr 2024; 12:e0002624. [PMID: 38687074 DOI: 10.1128/spectrum.00026-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 04/13/2024] [Indexed: 05/02/2024] Open
Abstract
The rapid and effective identification of pathogens in patients with pulmonary infections has posed a persistent challenge in medicine, with conventional microbiological tests (CMTs) proving time-consuming and less sensitive, hindering early diagnosis of respiratory infections. While there has been some research on the clinical performance of targeted sequencing technologies, limited focus has been directed toward bronchoalveolar lavage fluid (BALF). This study primarily evaluates the pathogen detection capabilities of nanopore-targeted sequencing (NTS) in BALF, providing a comprehensive analysis. The retrospective study, spanning from January 2022 to November 2023, includes 223 patients exclusively sourced from a single center. We conducted a detailed comparative analysis among NTS, targeted next-generation sequencing (tNGS), and CMTs. Initially, we compared the detection capabilities of NTS and tNGS and found no significant differences in their sensitivity and specificity. Specifically, we observed that the sensitivity of NTS was significantly higher than that of CMTs (74.83% vs 33.11%, P < 0.001). Furthermore, NTS exhibited a higher positivity rate in common pulmonary infections (62.88% vs. 23.48%) and in clinically suspected tuberculosis patients compared to CMTs (87.18% vs. 48.72%). Additionally, NTS showed less susceptibility to antibiotic interference, indicating a more sensitive detection capability, especially in detecting fastidious organisms. It complements GeneXpert in tuberculosis diagnosis and offers excellent advantages in identifying pathogens challenging for CMTs, such as non-tuberculous mycobacteria and viruses. Moreover, NTS significantly shortens the reporting time and is only a quarter of the cost of metagenomic next-generation sequencing. Clearly, NTS can facilitate faster and more cost-effective early diagnosis of respiratory infections.IMPORTANCEThis study holds paramount significance in advancing the field of respiratory infection diagnostics. By assessing the pathogen detection capabilities in bronchoalveolar lavage fluid (BALF) of patients with pulmonary infections, we illuminate the promising potential of nanopore-targeted sequencing (NTS). The findings underscore NTS as a comparable yet distinct alternative to traditional methods like comprehensive conventional microbiological tests (CMTs). Notably, NTS demonstrates a pivotal edge, expanding the spectrum of identified pathogens, particularly excelling in the detection of challenging entities like non-tuberculous mycobacteria and viruses. The study also highlights the complementary role of NTS alongside GeneXpert in the identification of tuberculosis, providing a comprehensive overview of the diagnostic landscape for respiratory infections. This insight carries significant implications for clinicians seeking rapid, cost-effective, and accurate diagnostic tools in the realm of pulmonary infections.
Collapse
Affiliation(s)
- Jiayuan Ye
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Kai Huang
- Department of General Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Yaojiang Xu
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Nan Chen
- Department of Infectious Diseases, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Yifei Tu
- Department of Radiology, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Jing Huang
- Department of Respiratory, Shangyu People's Hospital Of Shaoxing, Shaoxing, Zhejiang, China
| | - Longfei Shao
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Weiliang Kong
- Department of Respiratory and Critical Care Medicine, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Dongdong Zhao
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Yilian Xie
- Department of Infectious Diseases, The First Affiliated Hospital of Ningbo University, Ningbo, Zhejiang, China
| |
Collapse
|
5
|
Tang Y, Zhu Y, You Z. Mycobacterium tuberculosis sepsis with multiple intermuscular abscesses and respiratory failure as the main manifestations: a case report. BMC Infect Dis 2024; 24:340. [PMID: 38515054 PMCID: PMC10956240 DOI: 10.1186/s12879-024-09187-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 03/01/2024] [Indexed: 03/23/2024] Open
Abstract
BACKGROUND Tuberculous sepsis is uncommon in individuals without human immunodeficiency virus (HIV) infection, and some patients may not exhibit clinical signs and symptoms of suspected sepsis upon admission, leading to delayed diagnosis and treatment. CASE PRESENTATION This report present the case of a 60-year-old female patient who presented with erythema, edema, and pain in her right upper limb accompanied by fever and chills. Further evaluation revealed multiple intermuscular abscesses caused by suspected gram-positive bacteria. Despite receiving anti-infection treatment, the patient rapidly progressed to septic shock and respiratory failure. Metagenomic next-generation sequencing (mNGS) analysis of blood samples detected Mycobacterium tuberculosis complex groups (11 reads). Additionally, mNGS analysis of fluid obtained from puncture of the abscess in the right upper extremity also suggested Mycobacterium tuberculosis complex groups (221 981 reads). Consequently, the patient was diagnosed with tuberculous sepsis resulting from hematogenous dissemination of Mycobacterium tuberculosis. Following the administration of anti-tuberculosis treatment, a gradual recovery was observed during the subsequent follow-up period. CONCLUSION It is noteworthy that atypical hematogenous disseminated tuberculosis can be prone to misdiagnosis or oversight, potentially leading to septic shock. This case illustrates the importance of early diagnosis and treatment of tuberculosis sepsis. Advanced diagnostic techniques such as mNGS can aid clinicians in the early identification of pathogens for definitive diagnosis.
Collapse
Affiliation(s)
- Yingzi Tang
- Department of Infectious Diseases, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Ying Zhu
- Department of Infectious Diseases, First Affiliated Hospital, Army Medical University, Chongqing, China
| | - Zhonglan You
- Department of Infectious Diseases, First Affiliated Hospital, Army Medical University, Chongqing, China.
| |
Collapse
|
6
|
Zhou L, Zou X, Hu Q, Hua H, Qi Q. Determination of the diagnostic accuracy of nanopore sequencing using bronchoalveolar lavage fluid samples from patients with sputum-scarce pulmonary tuberculosis. J Infect Chemother 2024; 30:98-103. [PMID: 37714266 DOI: 10.1016/j.jiac.2023.09.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 08/22/2023] [Accepted: 09/13/2023] [Indexed: 09/17/2023]
Abstract
PURPOSE The early and efficient diagnosis of patients suspected of having pulmonary tuberculosis (PTB) remains challenging. This study aimed to evaluate the accuracy of nanopore sequencing for PTB diagnosis using bronchoalveolar lavage fluid (BALF) samples and compared it with other techniques such as acid-fast bacilli smear, culture, Xpert MTB/RIF, and CapitalBio Mycobacterium reverse transcription-polymerase chain reaction (MTB RT-PCR). METHODS We retrospectively analyzed the clinical data of 195 patients with suspected PTB who were admitted to our hospital. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the receiver operating characteristic curve (AUC) of these assays were calculated and compared. RESULTS The overall sensitivity, specificity, PPV, NPV, and AUC of nanopore sequencing were 90.70%, 84.85%, 92.13%, 82.35%, and 0.88; those of acid-fast bacilli smear were 12.40%, 98.48%, 94.12%, 36.52%, and 0.55; those of culture were 36.43%, 100%, 100%, 44.59%, and 0.68; those of Xpert MTB/RIF were 41.09%, 100%, 100%, 46.48%, and 0.71; and those of CapitalBio MTB RT-PCR were 34.88%, 98.48%, 97.83%, 43.62%, and 0.67, respectively. CONCLUSION The nanopore sequencing assay using BALF samples showed the best diagnostic accuracy for sputum-scarce PTB. Moreover, it can improve the clinical diagnosis of PTB.
Collapse
Affiliation(s)
- Lihong Zhou
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Xingwu Zou
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Qin Hu
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Haibo Hua
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| | - Qi Qi
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, No. 208 Huancheng East Road, Gongshu District, Hangzhou, Zhejiang, China.
| |
Collapse
|
7
|
Gota BVA, Shenoy VP, Kamath A. Correlation of Cyclic Threshold Values Generated by GeneXpert Ultra MTB/RIF and Fluorescence Microscopy to Predict Mycobacterial Burden in Suspected Cases of Pulmonary Tuberculosis. Int J Mycobacteriol 2024; 13:47-52. [PMID: 38771279 DOI: 10.4103/ijmy.ijmy_199_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 02/26/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Smear microscopy for acid-fast bacilli visualization is important to assess the infectivity rate in patients with pulmonary tuberculosis (PTB), but it has limited sensitivity; hence, it is important to find an alternative strategy. The aim of our study was to compare the fluorescence microscopy grading by Auramine O phenol staining technique of respiratory samples with the cyclic threshold (Ct) values of GeneXpert Ultra (Mycobacterium tuberculosis/rifampicin [MTB/RIF]) and assess the diagnostic efficacy of GeneXpert Ultra (MTB/RIF) compared to microscopy in suspected cases of PTB. METHODS The study was conducted in the Mycobacteriology Laboratory, Department of Microbiology, in Kasturba Hospital, Manipal. The study was a prospective, single-centered, cross-sectional study. Four hundred and fifty-two respiratory samples were included in the study. An optimal Ct cutoff value for ruling smear-positivity and smear-negativity and the mean Ct cutoff value were calculated. Clinical and radiological data from the requisition forms were assessed. IBM SPSS statistics software version 22 was used. The correlation between GeneXpert Ultra (MTB/RIF) Ct values and smear status was calculated by polychoric correlation. The extended McNemar's test was used to find the association between the variables. RESULTS GeneXpert Ultra (MTB/RIF) yielded a higher positivity rate of 22.2% compared to smear microscopy 17.2%. Ct value and smear grading yielded a positive correlation (P = 0.8681; P < 0.05). GeneXpert Ultra (MTB/RIF) yielded nontuberculous mycobacteria in five undetected cases and speciated as Mycobacterium abscessus complex. CONCLUSIONS Our study confirms the GeneXpert Ultra (MTB/RIF) Ct value levels as a predictor of smear positivity.
Collapse
Affiliation(s)
- B V Apoorva Gota
- Department of Microbiology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vishnu Prasad Shenoy
- Department of Microbiology, Kasturba Medical College Manipal, Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Asha Kamath
- Department of Data Science, Prasanna School of Public Health, Manipal Academy of Higher Education, Manipal, Karnataka, India
| |
Collapse
|
8
|
Huang F, Wang H, Qiao R, Peng Q, Zhao C, Miao L. Diagnostic accuracy and microbial profiles of tuberculous pleurisy: a comparative study of metagenomic next generation sequencing and GeneXpert Mycobacterium tuberculosis. Front Cell Infect Microbiol 2023; 13:1243441. [PMID: 38089819 PMCID: PMC10711093 DOI: 10.3389/fcimb.2023.1243441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/10/2023] [Indexed: 12/18/2023] Open
Abstract
Introduction There is a clinical challenge in diagnosing tuberculous pleurisy accurately and promptly, highlighting the urgent need for a rapid and sensitive diagnostic method. This study aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) and GeneXpert Mycobacterium tuberculosis (MTB) for identifying tuberculous pleurisy and analyzing the microbial profiles of both tuberculous and non-tuberculous pleural effusions. Methods The study enrolled 31 patients with suspected tuberculous pleurisy, of which 15 were confirmed to have tuberculous pleurisy and subsequently allocated to the tuberculous pleurisy group (TP group), while the remaining 16 individuals were assigned to the non-tuberculous pleurisy group (NTP group). mNGS and GeneXpert MTB were performed on pleural effusion samples, and the diagnostic accuracy of both tests was compared. We employed established formulas to compute crucial indicators, including sensitivity, specificity, missed diagnosis rate, misdiagnosed rate, positive predictive value (PPV), and negative predictive value (NPV). Results The results showed that both tests had high specificity (100%) and positive predictive value (100%) for detecting tuberculous pleurisy, along with comparable sensitivity (46.67% for mNGS and 40.0% for GeneXpert MTB). Further analysis of the combined efficacy of mNGS and GeneXpert MTB showed that the combined test had a sensitivity of 66.67% and a specificity of 100%. mNGS analysis revealed that MTB was detected in 7 out of 15 patients with tuberculous pleural effusions, while non-tuberculous pleural effusions were associated with a diverse range of microbial genera and species. The most frequently detected genera at the microbial genus level in the NTP group were Microbacterium spp. (6/16), Prevotella spp. (5/16), and Campylobacter spp. (5/16). Discussion These findings suggest that mNGS and GeneXpert MTB are useful diagnostic tools for identifying patients with tuberculous pleurisy, and mNGS can provide valuable insights into the microbial profiles of both tuberculous and non-tuberculous pleural effusions.
Collapse
Affiliation(s)
- Fengxiang Huang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Haoran Wang
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ruiping Qiao
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Qiang Peng
- Department of Respiratory and Critical Care Medicine, Chest Hospital of Henan Province, Zhengzhou, China
| | - Chang Zhao
- Department of Respiratory and Critical Care Medicine, Chest Hospital of Henan Province, Zhengzhou, China
| | - Lijun Miao
- Department of Respiratory and Critical Care Medicine, First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| |
Collapse
|
9
|
Zhang K, Bai YZ, Liu C, Liu SS, Lu XX, Yang RG. Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis. BMC Microbiol 2023; 23:313. [PMID: 37891467 PMCID: PMC10612345 DOI: 10.1186/s12866-023-03046-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
BACKGROUND Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, complicating the precise guidance of infection treatment. This study employed metagenomic next-generation sequencing (mNGS) to detect these microorganisms in chronic osteomyelitis with three main objectives: 1). Gain a deeper understanding of the composition of pathogenic microorganisms in chronic osteomyelitis. 2). Compare the microbial detection rates between mNGS and the standard culture methods used in laboratories to enhance the effectiveness of the traditional culture methods. 3). Explore the potential of mNGS in etiological diagnosis. METHODS Fifty clinically confirmed intraoperative bone tissue samples of chronic osteomyelitis from January 2021 to December 2021 were collected and subjected to mNGS and microbiological testing, respectively. The orthopaedic surgeon combined clinical manifestations and related examinations to determine the causative pathogens. RESULTS The culture method obtained 29 aerobic and parthenogenic anaerobic bacteria, 3 specific anaerobic bacteria, and 1 yeast-like fungus. Thirty-six aerobic and parthenogenic anaerobic bacteria, 11 specific anaerobic bacteria, and 1 yeast-like fungus were obtained by mNGS, and 2 Mycobacterium tuberculosis(MTB) strains were detected. However, there was no significant difference in the overall positive detection rate between mNGS and the culture method (P = 0.07), and the two were not statistically significant in detecting aerobic and partly anaerobic bacteria (P = 0.625). But, mNGS was significantly superior to culture in detecting anaerobic bacteria and Mycobacterium tuberculosis (P<0.05). CONCLUSIONS The mNGS method has enhanced our understanding of the distribution of pathogenic microorganisms in chronic osteomyelitis. Traditional culture methods help isolate and cultivate aerobic and facultative anaerobic bacteria, and fungi, and are also utilized for antibacterial drug sensitivity tests. However, mNGS has shown superior capabilities in detecting anaerobic bacteria, MTB, and mixed infection bacteria. This finding offers invaluable guidance for improving laboratory microbial culture and detection conditions. Hence, mNGS should be judiciously used for chronic osteomyelitis, and PCR can be implemented for certain difficult-to-culture microorganisms, such as MTB.
Collapse
Affiliation(s)
- Kang Zhang
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Yu-Zhe Bai
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, China
| | - Chang Liu
- Clinical Laboratory of Tsinghua University Hospital, Beijing, China
| | - Shan-Shan Liu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China
| | - Xin-Xin Lu
- Laboratory Medicine of Beijing Tongren Hospital affiliated to Capital Medical University, Beijing, China.
| | - Run-Gong Yang
- Department of Tissue Repair and Regeneration, The First Medical Center of PLA General Hospital, Beijing, China
| |
Collapse
|
10
|
Li Y, Bian W, Wu S, Zhang J, Li D. Metagenomic next-generation sequencing for Mycobacterium tuberculosis complex detection: a meta-analysis. Front Public Health 2023; 11:1224993. [PMID: 37637815 PMCID: PMC10450767 DOI: 10.3389/fpubh.2023.1224993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 07/24/2023] [Indexed: 08/29/2023] Open
Abstract
Objective Metagenomic next-generation sequencing (mNGS) has been gradually applied to the diagnosis of tuberculosis (TB) due to its rapid and highly sensitive characteristics. Despite numerous studies on this subject, their results vary significantly. Thus, the current meta-analysis was performed to assess the performance of the mNGS on tuberculosis. Methods PubMed, Embase, Web of Science, and The Cochrane Library were searched up to June 21, 2023. Studies utilizing the mNGS for tuberculosis detection were included. The risk of bias was assessed by QUADAS-2, and a meta-analysis was performed with STATA14.0 software. Results Seventeen studies comprising 3,205 specimens were included. The combined sensitivity and specificity of mNGS for clinical specimens were 0.69[0.58-0.79] and 1.00[0.99-1.00], respectively. Subgroup analysis identified sequencing platform, diagnostic criteria, study type, sample size, and sample types as potential sources of heterogeneity. Cerebrospinal Fluid (CSF) has a lower sensitivity of 0.58 (0.39-0.75). In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%. Conclusion Metagenomic next-generation sequencing technology exhibits high sensitivity and speed in diagnosing Mycobacterium tuberculosis. Its application in mono and mixed infections peoples shows promise, and mNGS is likely to be increasingly used to address challenges posed by Mycobacterium tuberculosis complexes in the future.
Collapse
Affiliation(s)
- Yulian Li
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Wentao Bian
- College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Shiping Wu
- Affiliated Hospital of North Sichuan Medical College, Nanchong, China
| | - Jie Zhang
- Department of Laboratory Medicine, Sichuan Provincial People's Hospital, University of Electronic Science and Technology of China, Chengdu, China
| | - Dan Li
- School of Medicine, University of Electronic Science and Technology of China, Chengdu, China
| |
Collapse
|
11
|
He S, Wei J, Feng J, Liu D, Wang N, Chen L, Xiong Y. The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science. Front Cell Infect Microbiol 2023; 13:1112229. [PMID: 37600953 PMCID: PMC10434771 DOI: 10.3389/fcimb.2023.1112229] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
Background Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis. Methods The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3). Results In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections. Conclusion This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.
Collapse
Affiliation(s)
- Sike He
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jingwen Wei
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Jiaming Feng
- West China School of Medicine, Sichuan University, Chengdu, China
| | - Dan Liu
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
| | - Neng Wang
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Liyu Chen
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Ying Xiong
- Department of Periodical Press, West China Hospital, Sichuan University, Chengdu, China
| |
Collapse
|
12
|
Batool M, Galloway-Peña J. Clinical metagenomics-challenges and future prospects. Front Microbiol 2023; 14:1186424. [PMID: 37448579 PMCID: PMC10337830 DOI: 10.3389/fmicb.2023.1186424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 06/12/2023] [Indexed: 07/15/2023] Open
Abstract
Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.
Collapse
|
13
|
Zhang X, Chen H, Lin Y, Yang M, Zhao H, Hu J, Han D. Diagnosis of Non-Tuberculous Mycobacterial Pulmonary Disease by Metagenomic Next-Generation Sequencing on Bronchoalveolar Lavage Fluid. Infect Drug Resist 2023; 16:4137-4145. [PMID: 37396070 PMCID: PMC10312351 DOI: 10.2147/idr.s417088] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 06/15/2023] [Indexed: 07/04/2023] Open
Abstract
Purpose Metagenomic next-generation sequencing (mNGS) has been extensively used in the diagnosis of infectious diseases but has rarely been applied in non-tuberculous mycobacterial pulmonary disease (NTMPD). This study analyzed the diagnostic performance of mNGS in bronchoalveolar lavage fluid (BALF) samples to identify non-tuberculous mycobacteria (NTM). Patients and Methods A total of 231 patients with suspected NTMPD were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, from March 2021 to October 2022. A total of 118 cases were ultimately included. Of these patients, 61 cases were enrolled in the NTMPD group, 23 cases were enrolled in the suspected-NTMPD group, and 34 cases were enrolled in the non-NTMPD group. The diagnostic performance of traditional culture, acid-fast staining (AFS), and mNGS for NTMPD was assessed. Results Patients in the NTMPD group had a higher proportion of bronchiectasis (P=0.007). Among mNGS-positive samples in the NTMPD group, a significantly higher reads number of NTM was observed in AFS-positive patients [61.50 (22.00, 395.00) vs 15.50 (6.00, 36.25), P=0.008]. Meanwhile, mNGS demonstrated a sensitivity of 90.2%, which was far superior to AFS (42.0%) and culture (77.0%) (P<0.001). The specificity of mNGS in detecting NTM was 100%, which was the same as that of traditional culture. The area under the receiver operating characteristic curve of mNGS was 0.951 (95% CI 0.906-0.996), which was higher than that of culture (0.885 [95% CI 0.818-0.953]) and AFS (0.686 [95% CI 0.562-0.810]). In addition to NTM, other pulmonary pathogens were also found by mNGS. Conclusion mNGS using BALF samples is a rapid and effective diagnostic tool for NTMPD, and mNGS is recommended for patients with suspected NMTPD or NTM coinfected pneumonia.
Collapse
Affiliation(s)
- Xuan Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Huixin Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Yaqing Lin
- Shulan (Hangzhou) Hospital Affiliated to Zhejiang Shuren University Shulan International Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Meifang Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Hong Zhao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Jianhua Hu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
| | - Dongsheng Han
- Department of Laboratory Medicine, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, People’s Republic of China
- Key Laboratory of Clinical in vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, Zhejiang, People’s Republic of China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, Zhejiang, People’s Republic of China
| |
Collapse
|
14
|
Han S, Zhao Z, Yang L, Huang J, Wang Y, Feng J. The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform. Front Pharmacol 2023; 14:1164633. [PMID: 37138853 PMCID: PMC10149716 DOI: 10.3389/fphar.2023.1164633] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 04/03/2023] [Indexed: 05/05/2023] Open
Abstract
Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories. Presently, mNGS platforms mainly include those from Illumina and the Beijing Genomics Institute (BGI). Previous studies have reported that various sequencing platforms have similar sensitivity in detecting the reference panel that mimics clinical specimens. However, whether the Illumina and BGI platforms provide the same diagnostic performance using authentic clinical samples remains unclear. Methods: In this prospective study, we compared the performance of the Illumina and BGI platforms in detecting pulmonary pathogens. Forty-six patients with suspected pulmonary infection were enrolled in the final analysis. All patients received bronchoscopy, and the specimens collected were sent for mNGS on the two different sequencing platforms. Results: The diagnostic sensitivity of the Illumina and BGI platforms was notably higher than that of conventional examination (76.9% vs. 38.5%, p < 0.001; 82.1% vs. 38.5%, p < 0.001; respectively). The sensitivity and specificity for pulmonary infection diagnosis were not significantly different between the Illumina and BGI platforms. Furthermore, the pathogenic detection rate of the two platforms were not significantly different. Conclusion: The Illumina and BGI platforms exhibited similar diagnostic performance for pulmonary infectious diseases using clinical specimens, and both are superior to conventional examinations.
Collapse
Affiliation(s)
| | | | | | | | - Yubao Wang
- *Correspondence: Yubao Wang, , Jing Feng,
| | - Jing Feng
- *Correspondence: Yubao Wang, , Jing Feng,
| |
Collapse
|
15
|
Song P, Li X. Diagnostic value of metagenomics next-generation sequencing technology in disseminated strongyloidiasis. World J Clin Cases 2022; 10:12455-12457. [PMID: 36483821 PMCID: PMC9724536 DOI: 10.12998/wjcc.v10.i33.12455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 10/04/2022] [Accepted: 10/31/2022] [Indexed: 11/22/2022] Open
Abstract
The symptoms of disseminated strongyloidiasis are not typical, and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas. We report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient’s gastric fluid, and metagenomic next generation sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden. In recent years, mNGS has been increasingly used in clinical practice, and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas. Especially during the corona virus disease 2019 pandemic, mNGS technology has irreplaceable value in identifying the source of infection.
Collapse
Affiliation(s)
- Peng Song
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250000, Shandong Province, China
| | - Xia Li
- Department of Thoracic Surgery, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan 250021, Shandong Province, China
| |
Collapse
|
16
|
Song P, Li H, Liu T, Liu Y, Ma X, Su L. Disseminated Strongyloidiasis Misdiagnosed as Guillain-Barré Syndrome: The Value of High-Throughput Genetic Sequencing of Pathogenic Microorganisms in Parasitic Infections. Infect Drug Resist 2022; 15:5601-5607. [PMID: 36172625 PMCID: PMC9512064 DOI: 10.2147/idr.s381298] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 12/20/2022] Open
Abstract
Background With the widespread use of steroids and immunosuppressants in mainland China, disseminated strongyloidiasis is becoming a severely underestimated tropical disease due to the lack of disease-specific manifestations and well-established diagnostic methods. Case Presentation Here, we report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient’s gastric fluid, and metagenomic Next Generation Sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the ICU due to the excessive strongyloidiasis burden. Conclusion This case highlights the combined application of mNGS and traditional testing in the clinical diagnosis of difficult and critical parasitic infections in immunocompromised patients. mNGS is a new, adjunct diagnostic method to rapidly screen for possible parasitic etiologies.
Collapse
Affiliation(s)
- Peng Song
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Huaichen Li
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Tingting Liu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Yao Liu
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Xiaobin Ma
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| | - Lili Su
- Department of Respiratory Medicine, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, People's Republic of China
| |
Collapse
|
17
|
Kong M, Li W, Kong Q, Dong H, Han A, Jiang L. Application of metagenomic next-generation sequencing in cutaneous tuberculosis. Front Cell Infect Microbiol 2022; 12:942073. [PMID: 36211955 PMCID: PMC9539668 DOI: 10.3389/fcimb.2022.942073] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Tuberculous infection in a skin wound is a rare but well-known condition. This study describes a child infected with tuberculosis after being wounded. Because of swelling and pain in his wrist tissue, he was admitted to the Affiliated Hospital of Jining Medical University of Shandong Province on 16 October 2021. His medical history only included a wound. He was discharged after debridement. The laboratory data were normal. Two months after surgery, his wound was still swollen and painful. Secretions from the wound were sent for metagenomic next-generation sequencing (mNGS), which revealed three reads related to the Mycobacterium tuberculosis complex group (MTBC). A diagnosis of cutaneous tuberculosis (TB) was made. The wound disappeared after anti-TB drugs were administered. This case demonstrates that, while TB presenting as a severe cutaneous wound is rare, it should be considered in the clinical diagnosis. Clinicians should also pay attention to extrapulmonary infection with MTBC in patients, particularly in some long-suffering patients, and identify the specific pathogen as soon as possible. mNGS could help to identify pathogens and facilitate early treatment, thereby improving the prognosis.
Collapse
Affiliation(s)
- Min Kong
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Wei Li
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Qingsheng Kong
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Haixin Dong
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
| | - Aizhong Han
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
| | - Liqing Jiang
- Affiliated Hospital of Jining Medical University, Jining Medical University, Jining, China
- Medical Laboratory of Jining Medical University, Jining Medical University, Jining, China
- *Correspondence: Liqing Jiang,
| |
Collapse
|
18
|
Chen S, Kang Y, Li D, Li Z. Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis. Int J Infect Dis 2022; 122:867-873. [PMID: 35907477 DOI: 10.1016/j.ijid.2022.07.054] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/04/2022] [Accepted: 07/21/2022] [Indexed: 10/16/2022] Open
Abstract
BACKGROUND The identification of pathogens in patients with pulmonary infection has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state in the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with pulmonary infections. METHODS Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated by using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures. RESULTS The pooled sensitivity was 78% (95% confidence interval: 67-87%; I2 = 92%) and the pooled specificity was 77% (95% confidence interval: 64-94%; I2 = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with pulmonary infections who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% confidence interval: 78-100%). CONCLUSION mNGS has high diagnostic performance for BALF pathogens in patients with pulmonary infections, especially in critically ill or immunocompromised patients.
Collapse
Affiliation(s)
- Shenglin Chen
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China
| | - Yutong Kang
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Dan Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China
| | - Zhenjun Li
- State Key Laboratory for Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155 Changbai Road, Changping, Beijing 102206, China; School of Public Health, Shanxi Medical University, 56 Xinjiannanlu Street, Taiyuan 030001, Shanxi, People's Republic of China.
| |
Collapse
|
19
|
Performance Comparison of GeneXpert MTB/RIF, Gene Chip Technology, and Modified Roche Culture Method in Detecting Mycobacterium tuberculosis and Drug Susceptibility in Sputum. CONTRAST MEDIA & MOLECULAR IMAGING 2022; 2022:2995464. [PMID: 35935306 PMCID: PMC9314178 DOI: 10.1155/2022/2995464] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 07/04/2022] [Accepted: 07/05/2022] [Indexed: 11/29/2022]
Abstract
Our aim of this study was to observe and analyze the performance of the real-time fluorescence quantitative nucleic acid amplification detection of Mycobacterium tuberculosis/rifampicin resistance (GeneXpert MTB/RIF), gene chip technology, and modified Roche culture method in detecting MTB in sputum submitted for inspection and drug susceptibility. Patients with smear-negative suspected pulmonary TB (n = 120) in our hospital were enrolled in this study using a random number table, and sputum samples submitted for inspection were tested by the GeneXpert MTB/RIF, gene chip technology, and modified Roche culture method. With clinical diagnosis as the gold standard, the performance (mainly sensitivity and specificity) of the above three detection methods in the diagnosis of MTB was compared. Next, the drug susceptibility test (DST) was carried out on sputum samples, tested positive by the three methods. With the solid culture results as the evaluation criteria, the performance of the three detection methods in the diagnosis MTB and DST was compared. When compared with the modified Roche culture method, the GeneXpert MTB/RIF had the highest positive rate and a shorter overall test duration (P < 0.05). In contrast with the gene chip technology, the GeneXpert MTB/RIF exhibited higher sensitivity and negative predictive value (NPV) and lower specificity, accuracy, positive predictive value (PPV), and Kappa value (P < 0.05). According to analysis of the diagnostic performance of the three detection methods, GeneXpert MTB/RIF displayed the highest diagnostic sensitivity, ideal predictive values, and the highest similarity with clinical diagnosis in results (P < 0.05). The detection of susceptibility to isoniazid (INH) and RIF showed that the GeneXpert MTB/RIF and gene chip technology performed ideally in DST of MTB. In comparison with the modified Roche culture method, the GeneXpert MTB/RIF and gene chip technology have more prominent performance in detecting MTB and drug susceptibility. Besides, to further improve the accuracy of clinical diagnosis, various molecular biology detection methods can be combined to avoid delaying of the best time for the diagnosis and treatment of the disease.
Collapse
|
20
|
Aggarwal AN, Agarwal R, Dhooria S, Prasad KT, Sehgal IS, Muthu V. Xpert MTB/RIF Ultra versus Xpert MTB/RIF for diagnosis of tuberculous pleural effusion: A systematic review and comparative meta-analysis. PLoS One 2022; 17:e0268483. [PMID: 35816471 PMCID: PMC9273090 DOI: 10.1371/journal.pone.0268483] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 04/29/2022] [Indexed: 12/03/2022] Open
Abstract
Objective We compared diagnostic accuracy of pleural fluid Xpert MTB/RIF (Xpert) and Xpert MTB/RIF Ultra (Ultra) assays for diagnosing tuberculous pleural effusion (TPE), through systematic review and comparative meta-analysis. Methods We searched PubMed and Embase databases for publications reporting diagnostic accuracy of Xpert or Ultra for TPE. We used bivariate random-effects modeling to summarize diagnostic accuracy information from individual studies using either mycobacterial culture or composite criteria as reference standard. We performed meta-regression through hierarchical summary receiver operating characteristic (HSROC) modeling to evaluate comparative performance of the two tests from studies reporting diagnostic accuracy of both in the same study population. Results We retrieved 1097 publications, and included 74 for review. Summary estimates for sensitivity and specificity for Xpert were 0.52 (95% CI 0.43–0.60, I2 82.1%) and 0.99 (95% CI 0.97–0.99, I2 85.1%), respectively, using culture-based reference standard; and 0.21 (95% CI 0.17–0.26, I2 81.5%) and 1.00 (95% CI 0.99–1.00, I2 37.6%), respectively, using composite reference standard. Summary estimates for sensitivity and specificity for Ultra were 0.68 (95% CI 0.55–0.79, I2 80.0%) and 0.97 (95% CI 0.97–0.99, I2 92.1%), respectively, using culture-based reference standard; and 0.47 (95% CI 0.40–0.55, I2 64.1%) and 0.98 (95% CI 0.95–0.99, I2 54.8%), respectively, using composite reference standard. HSROC meta-regression yielded relative diagnostic odds ratio of 1.28 (95% CI 0.65–2.50) and 1.80 (95% CI 0.41–7.84) respectively in favor of Ultra, using culture and composite criteria as reference standard. Conclusion Ultra provides superior diagnostic accuracy over Xpert for diagnosing TPE, mainly because of its higher sensitivity.
Collapse
Affiliation(s)
- Ashutosh Nath Aggarwal
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
- * E-mail:
| | - Ritesh Agarwal
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Sahajal Dhooria
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Kuruswamy Thurai Prasad
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Inderpaul Singh Sehgal
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Valliappan Muthu
- Department of Pulmonary Medicine, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| |
Collapse
|
21
|
Qu J, Zong Z. Strongyloidiasis in a Patient Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report. Front Med (Lausanne) 2022; 9:835252. [PMID: 35463003 PMCID: PMC9022660 DOI: 10.3389/fmed.2022.835252] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 02/28/2022] [Indexed: 12/11/2022] Open
Abstract
Background Strongylodiasis may be asymptomatic or cause mild gastrointestinal symptoms, and may be a fatal disseminated disease or Strongyloides hyperinfection syndrome. Non-specific clinical manifestations, such as pneumonia and gastroenteritis, pose a diagnostic dilemma. Case Presentation We report a case of a 67-year-old Chinese male who presented with abdominal pain, fever, headache, vomiting, constipation, and slight cough with sputum for nearly 2 months. He had been in good health and had no history of glucocorticoid use. He was diagnosed with enterococcal meningitis and intestinal obstruction at a local hospital and improved after treatment with vancomycin, but symptoms of headache and abdominal pain soon recurred. The metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid using Illumina X10 sequencer revealed seven sequence reads matching Strongyloides stercoralis. Strongyloidiasis was suspected. Microscopic examination of gastric fluid revealed the presence of S. stercoralis larvae, which was confirmed by PCR to amplify both S. stercoralis ribosomal DNA gene and mitochondrial cytochrome c oxidase subunit 1 gene and sequencing amplicons. Strongyloidiasis was diagnosed. Albendazole (400 mg, twice daily) was used, and the patient recovered gradually. Conclusion mNGS may be a useful tool for detecting uncommon infectious disease. The case would help clinicians to raise awareness of strongyloidiasis in non-endemic areas and reduce fatality.
Collapse
Affiliation(s)
- Junyan Qu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
- *Correspondence: Zhiyong Zong,
| |
Collapse
|
22
|
Li Y, Jiao M, Liu Y, Ren Z, Li A. Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection. Front Med (Lausanne) 2022; 9:802719. [PMID: 35433724 PMCID: PMC9010669 DOI: 10.3389/fmed.2022.802719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 02/22/2022] [Indexed: 11/13/2022] Open
Abstract
The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.
Collapse
Affiliation(s)
- Yaoguang Li
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Mengfan Jiao
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Ying Liu
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Zhigang Ren
- Department of Infectious Diseases, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- *Correspondence: Zhigang Ren,
| | - Ang Li
- Gene Hospital of Henan Province, Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Ang Li,
| |
Collapse
|
23
|
Sun W, Dong Z, Zhou Y, Xiong K, Liu H, Zhang Z, Fan L. Early Identification of Fungal and Mycobacterium Infections in Pulmonary Granulomas Using Metagenomic Next-Generation Sequencing on Formalin fixation and paraffin embedding tissue. Expert Rev Mol Diagn 2022; 22:461-468. [PMID: 35261303 DOI: 10.1080/14737159.2022.2052046] [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: 11/04/2022]
Abstract
BACKGROUND The purpose of the study is to assess the etiology detection ability of Metagenomic Next-Generation Sequencing (mNGS) on formalin fixation and paraffin embedding (FFPE) tissue from postoperative biopsy specimen. METHODS We prospectively enrolled specimens from patients undergone surgery biopsy due to undefinite diagnosis and pathologically indicated granulomatous lesions. FFPE tissues were tested by mNGS and histopathology. The etiology detection rate of mNGS was calculated and compared with histopathology, using the clinical diagnosis as the reference criteria. RESULTS Among the 69 cases eventually included, 41 (59.42%) were diagnosed as infectious granuloma. The overall fungi and mycobacteria etiology detection rate of mNGS in granuloma lesions was 87.80 % (36/41) . The mNGS increased detection rate by 68.29 % (28/41) compared with histopathology, the difference was statistically significant (χ2= 28.97, P 0.00).The detection rates of mNGS in fungal infections (12/12,100%) and in mycobacterium infections (22/27, 81.48%) were significant higher than those of histopathology (8/12, 66.67% and 0/27,0.00 %;both P 0.00). 2 (2/2.100%) cases of co-infection were detected at one time by mNGS. All mNGS-based clinical decisions were made within 2 days. CONCLUSIONS The mNGS could accurately and quickly detect fungi and mycobacteria on FFPE specimens from postoperative granuloma specimens and identify the pathogens to the species level. CLINICAL TRIALS REGISTRATION China Clinical Trial Registry ChiCTR2000035464.
Collapse
Affiliation(s)
- Wenwen Sun
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Zhengwei Dong
- Department of Pathology, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Yiming Zhou
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | - Kunlong Xiong
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| | - Hongcheng Liu
- Department of Thoracic Surgery, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai, China
| | | | - Lin Fan
- Department of Tuberculosis and Shanghai Key Lab of Tuberculosis, Shanghai Pulmonary Hospital Affiliated to School of Medicine, Tongji University, Shanghai 200092, China
| |
Collapse
|
24
|
Guo Y, Li H, Chen H, Li Z, Ding W, Wang J, Yin Y, Jin L, Sun S, Jing C, Wang H. Metagenomic next-generation sequencing to identify pathogens and cancer in lung biopsy tissue. EBioMedicine 2021; 73:103639. [PMID: 34700283 PMCID: PMC8554462 DOI: 10.1016/j.ebiom.2021.103639] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/25/2021] [Accepted: 10/06/2021] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Lung biopsy tissue samples can be used for infection detection and cancer diagnosis. Metagenomic next-generation sequencing (mNGS) has the potential to further improve diagnosis. METHODS From July 2018 to May 2020, lung biopsy samples of 133 patients with suspected pulmonary infection or abnormal imaging findings were collected and subjected to clinical microbiological testing, Illumina and Nanopore sequencing to identify pathogens. The neural networks were pretrained by extracting features of human reads from 2,095 metagenomic next-generation sequencing results, and the human reads of lung biopsy samples were entered into the validated pipeline to predict the risk of cancer. FINDINGS Based on the pathogen-cancer detection pipeline, the Illumina platform showed 77·6% sensitivity and 97·6% specificity compared to the composite reference standard for infection diagnosis. However, the Nanopore platform showed 34·7% sensitivity and 98·7% specificity. mNGS identified more fungi, which was confirmed by subsequent pathological examination. M. tuberculosis complex was weakly detected. For cancer detection, compared with histology, the Illumina platform showed 83·7% sensitivity and 97·6% specificity, diagnosing an additional 36 cancer patients, of whom half had abnormal imaging findings (pulmonary shadow, space-occupying lesions, or nodules). INTERPRETATION For the first time, we have established a pipeline to simultaneously detect pathogens and cancer based on Illumina sequencing of lung biopsy tissue. This pipeline efficiently diagnosed cancer in patients with abnormal imaging findings. FUNDING This work was supported by the National Key Research and Development Program of China and National Natural Science Foundation of China.
Collapse
Affiliation(s)
- Yifan Guo
- Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China; Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Henan Li
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hongbin Chen
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Zhenzhong Li
- State Key Laboratory of Translational Medicine and Innovative Drug Development, Jiangsu Simcere Diagnostics Co., Ltd., Nanjing 210000, China
| | - Wenchao Ding
- MatriDx Biotechnology Co., Ltd., Hangzhou 310000, China
| | - Jun Wang
- MatriDx Biotechnology Co., Ltd., Hangzhou 310000, China
| | - Yuyao Yin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Longyang Jin
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Shijun Sun
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Chendi Jing
- Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China
| | - Hui Wang
- Institute of Medical Technology, Peking University Health Science Center, Beijing 100191, China; Department of Clinical Laboratory, Peking University People's Hospital, Beijing 100044, China.
| |
Collapse
|
25
|
Zhu L, Jiang M, Wang H, Sun H, Zhu J, Zhao W, Fang Q, Yu J, Chen P, Wu S, Zheng Z, He Y. A narrative review of tumor heterogeneity and challenges to tumor drug therapy. ANNALS OF TRANSLATIONAL MEDICINE 2021; 9:1351. [PMID: 34532488 PMCID: PMC8422119 DOI: 10.21037/atm-21-1948] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 06/17/2021] [Indexed: 12/31/2022]
Abstract
Objective To accurately evaluate tumor heterogeneity, make multidimensional diagnosis according to the causes and phenotypes of tumor heterogeneity, and assist in the individualized treatment of tumors. Background Tumor heterogeneity is one of the most essential characteristics of malignant tumors. In tumor recurrence, development, and evolution, tumor heterogeneity can lead to the formation of different cell groups with other molecular characteristics. Tumor heterogeneity can be characterized by the uneven distribution of tumor cell subsets of other genes between and within the disease site (spatial heterogeneity) or the time change of cancer cell molecular composition (temporal heterogeneity). The discovery of tumor targeting drugs has dramatically promoted tumor therapy. However, the existence of heterogeneity seriously affects the effect of tumor treatment and the prognosis of patients. Methods The literature discussing tumor heterogeneity and its resistance to tumor therapy was broadly searched to analyze tumor heterogeneity as well as the challenges and solutions for gene detection and tumor drug therapy. Conclusions Tumor heterogeneity is affected by many factors consist of internal cell factors and cell microenvironment. Tumor heterogeneity greatly hinders effective and individualized tumor treatment. Understanding the fickle of tumors in multiple dimensions and flexibly using a variety of detection methods to capture the changes of tumors can help to improve the design of diagnosis and treatment plans for cancer and benefit millions of patients.
Collapse
Affiliation(s)
- Liang Zhu
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Minlin Jiang
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Hao Wang
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Hui Sun
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Jun Zhu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Wencheng Zhao
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Qiyu Fang
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Jia Yu
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Peixin Chen
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Shengyu Wu
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Zixuan Zheng
- Tongji University, Shanghai, China.,Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| | - Yayi He
- Department of Medical Oncology, Shanghai Pulmonary Hospital, Tongji University Medical School Cancer Institute, Tongji University School of Medicine, Shanghai, China
| |
Collapse
|
26
|
Ye Y, Yang N, Zhou J, Qian G, Chu J. Case Report: Metagenomic Next-Generation Sequencing in Diagnosis of Disseminated Tuberculosis of an Immunocompetent Patient. Front Med (Lausanne) 2021; 8:687984. [PMID: 34322503 PMCID: PMC8310911 DOI: 10.3389/fmed.2021.687984] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/14/2021] [Indexed: 01/05/2023] Open
Abstract
Disseminated tuberculosis (TB) is a rare disease and mainly occurs in immunodeficient patients. It is marked by hematogenous or lymphatic dissemination of Mycobacterium tuberculosis, causing tuberculous infection involving any organ system. Here, we report a case of disseminated TB involving lung, liver, spine, mediastinum, and prostate in an immunocompetent man. The present patient found a hepatic mass without any symptom during health examination. In the next 2 years, further examinations revealed multiple lesions in the lung, mediastinum, spine, and prostate. Imaging examinations, such as contrast-enhanced abdominal CT, F-18 FDG-PET/CT, and radionuclide bone scan, suggested the diagnosis of malignancy or metastatic tumor. Furthermore, histopathological results of the biopsies of the hepatic mass, mediastinal mass, and prostatic mass demonstrated granulomatous inflammation. Therefore, metagenomic next-generation sequencing (mNGS) was utilized to confirm the diagnosis. Mycobacterium tuberculosis complex was simultaneously detected in the spinal surgical resection specimens and bronchoalveolar lavage fluid (BALF), indicating the diagnosis of disseminated TB. mNGS is an emerging molecular diagnostic technology, and its application in disseminated TB has been rarely reported. We highlight that disseminated TB should be considered even in an immunocompetent patient, and mNGS can be performed when the diagnosis is difficult.
Collapse
Affiliation(s)
- Yuanting Ye
- School of Medicine, Ningbo University, Ningbo, China.,Department of General Practice, Ningbo First Hospital, Ningbo, China
| | - Naibin Yang
- Department of Infectious Disease, Ningbo First Hospital, Ningbo, China
| | - Jingying Zhou
- Department of Hematology, The Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University, Wenzhou, China
| | - Guoqing Qian
- Department of Infectious Disease, Ningbo First Hospital, Ningbo, China
| | - Jinguo Chu
- Department of General Practice, Ningbo First Hospital, Ningbo, China
| |
Collapse
|
27
|
Li N, Cai Q, Miao Q, Song Z, Fang Y, Hu B. High-Throughput Metagenomics for Identification of Pathogens in the Clinical Settings. SMALL METHODS 2021; 5:2000792. [PMID: 33614906 PMCID: PMC7883231 DOI: 10.1002/smtd.202000792] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/24/2020] [Indexed: 05/25/2023]
Abstract
The application of sequencing technology is shifting from research to clinical laboratories owing to rapid technological developments and substantially reduced costs. However, although thousands of microorganisms are known to infect humans, identification of the etiological agents for many diseases remains challenging as only a small proportion of pathogens are identifiable by the current diagnostic methods. These challenges are compounded by the emergence of new pathogens. Hence, metagenomic next-generation sequencing (mNGS), an agnostic, unbiased, and comprehensive method for detection, and taxonomic characterization of microorganisms, has become an attractive strategy. Although many studies, and cases reports, have confirmed the success of mNGS in improving the diagnosis, treatment, and tracking of infectious diseases, several hurdles must still be overcome. It is, therefore, imperative that practitioners and clinicians understand both the benefits and limitations of mNGS when applying it to clinical practice. Interestingly, the emerging third-generation sequencing technologies may partially offset the disadvantages of mNGS. In this review, mainly: a) the history of sequencing technology; b) various NGS technologies, common platforms, and workflows for clinical applications; c) the application of NGS in pathogen identification; d) the global expert consensus on NGS-related methods in clinical applications; and e) challenges associated with diagnostic metagenomics are described.
Collapse
Affiliation(s)
- Na Li
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Qingqing Cai
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Qing Miao
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| | - Zeshi Song
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Yuan Fang
- Genoxor Medical Science and Technology Inc.Zhejiang317317China
| | - Bijie Hu
- Department of Infectious DiseasesZhongshan HospitalFudan UniversityShanghai200032China
| |
Collapse
|
28
|
Clinical efficacy of metagenomic next-generation sequencing for rapid detection of Mycobacterium tuberculosis in smear-negative extrapulmonary specimens in a high tuberculosis burden area. Int J Infect Dis 2020; 103:91-96. [PMID: 33227518 DOI: 10.1016/j.ijid.2020.11.165] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 11/10/2020] [Accepted: 11/15/2020] [Indexed: 01/27/2023] Open
Abstract
OBJECTIVE The aim of this study was to assess the clinical utility of metagenomic next-generation sequencing (mNGS) on smear-negative extrapulmonary specimens collected in China. METHODS Specimens were tested by mNGS and other routine tests for tuberculosis (TB). The diagnostic accuracy of mNGS was calculated and compared with the final clinical diagnosis. RESULTS The sensitivity of mNGS was found to be significantly higher than the sensitivities of the other routine TB tests. Receiver operating characteristic curve analysis showed that mNGS achieved the highest area under the curve (AUC) value of 0.79. The mNGS positive rate was highest for tuberculous meningitis. All non-tuberculous extrapulmonary pathogens were directly and simultaneously detected. CONCLUSIONS mNGS appeared to be superior to all previous etiological tests for TB on smear-negative extrapulmonary specimens and could identify all possible pathogens at once within 48 h.
Collapse
|