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Yadav M, Jain AK, Singhal R, Chadha M, Arora VK, Bhargava A. Incidence and Patterns of Drug Resistance in Patients with Spinal Tuberculosis: a Prospective, Single-Center Study from a Tuberculosis-Endemic Country. Indian J Orthop 2023; 57:1833-1841. [PMID: 37881297 PMCID: PMC10593722 DOI: 10.1007/s43465-023-00986-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 08/20/2023] [Indexed: 10/27/2023]
Abstract
Background There is paucity of data on incidence and pattern of drug resistance in spinal TB. This prospective observational study was conducted to document the incidence and drug-resistance pattern among primary and presumptive resistant cases. Methods 59 consecutive cases diagnosed clinico-radiologically (imaging) were grouped into Group A (n = 51, primary cases) and Group B (n = 8, presumptive resistant cases) based on pre-defined criteria (INDEX-TB guidelines). Tissue samples obtained percutaneously (37.29%, 22/59) and on surgery (62.71%, 37/59) were subjected to genotypic DST (CBNAAT, LPA) and phenotypic DST (BACTEC MGIT 960 culture and sensitivity using fixed critical concentration of drugs). Results Etiological diagnosis was ascertained in all. 13/51 (25.49%) in Group A, while 3/8 (37.5%) in Group B and 16/59 (27.12%) overall demonstrated drug resistance. 12/16 (75%) had no prior history of ATT intake. 4 demonstrated INH (Isoniazid) mono-resistance. 12 polydrug resistance demonstrated: 5MDR, 3pre-XDR, while RIF + FQ (fluoroquinolones), FQ + Lz (linezolid), only SLID (second-line injectable drugs), and only FQ resistance observed in 1 case each. Isolated RIF (Rifampicin) resistance and XDR pattern were not observed. Overall frequency of RIF resistance was 16.4% (9/55) and INH was 25% (12/48) with low-(n-2) and high-level INH resistance (n-10). Among second-line drugs, FQ resistance was more than SLID resistance and within FQ, levofloxacin resistance was more frequent than moxifloxacin. MGIT demonstrated positive growth in 16/59 samples, out of which 1 sample was positive for nontuberculous mycobacteria (M. chelonae) but on genotypic testing demonstrated MTB resistant to RIF and FQ. Conclusion This is the first report on incidence and drug-resistant pattern in culture-positive/negative cases. High (25.49%) primary drug resistance is worrisome. This being the first study in spinal TB cases which document prevalent drug-resistant pattern as evaluated for consecutive culture-positive/negative cases. The tissue obtained must be submitted for AFB culture and molecular tests to ascertain drug resistance in culture-positive/negative cases. However, in the presence of insufficient tissue sample histology and CBNAAT can ascertain etiological diagnosis in 100% cases. INH resistance is more than RIF with isolated RIF resistance unreported.
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Affiliation(s)
- Manish Yadav
- Department of Orthopaedics, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad Garden, Delhi, 110095 India
| | - Anil K. Jain
- Department of Orthopaedics, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad Garden, Delhi, 110095 India
| | - Ritu Singhal
- National Reference Laboratory & Center of Excellence (TB) WHO, Department of Microbiology, National Institute of Tuberculosis & Respiratory Diseases, New Delhi, Delhi 110030 India
| | - Manish Chadha
- Department of Orthopaedics, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad Garden, Delhi, 110095 India
| | - Vinod Kumar Arora
- Department of Pathology, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad Garden, Delhi, 110095 India
| | - Aayush Bhargava
- Department of Orthopaedics, University College of Medical Sciences and Guru Teg Bahadur Hospital, Dilshad Garden, Delhi, 110095 India
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Koleske BN, Jacobs WR, Bishai WR. The Mycobacterium tuberculosis genome at 25 years: lessons and lingering questions. J Clin Invest 2023; 133:e173156. [PMID: 37781921 PMCID: PMC10541200 DOI: 10.1172/jci173156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/03/2023] Open
Abstract
First achieved in 1998 by Cole et al., the complete genome sequence of Mycobacterium tuberculosis continues to provide an invaluable resource to understand tuberculosis (TB), the leading cause of global infectious disease mortality. At the 25-year anniversary of this accomplishment, we describe how insights gleaned from the M. tuberculosis genome have led to vital tools for TB research, epidemiology, and clinical practice. The increasing accessibility of whole-genome sequencing across research and clinical settings has improved our ability to predict antibacterial susceptibility, to track epidemics at the level of individual outbreaks and wider historical trends, to query the efficacy of the bacille Calmette-Guérin (BCG) vaccine, and to uncover targets for novel antitubercular therapeutics. Likewise, we discuss several recent efforts to extract further discoveries from this powerful resource.
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Affiliation(s)
- Benjamin N. Koleske
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - William R. Jacobs
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - William R. Bishai
- Center for Tuberculosis Research, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
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Torane VP, Nataraj G, Kanade S, Deshmukh CT. Comparison of gastric lavage/sputum and stool specimens in the diagnosis of pediatric pulmonary tuberculosis- A pilot study. Indian J Tuberc 2023; 70:445-450. [PMID: 37968050 DOI: 10.1016/j.ijtb.2023.03.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 10/09/2022] [Accepted: 03/29/2023] [Indexed: 11/17/2023]
Abstract
BACKGROUND AND OBJECTIVE Global TB report 2021 mentions 11 % prevalence of pediatric TB, whereas 5.65% of the cases were reported from India in 2020. India features in the list of TB high burden countries, HIV-TB high burden and MDR-TB high burden countries. The diagnosis of pulmonary tuberculosis in children is difficult as they tend to swallow the sputum, invasive techniques of gastric aspirates needs to be followed and the disease itself is paucibacillary. The disease progresses rapidly in young children and hence rapid diagnosis is needed. Obtaining appropriate respiratory samples for diagnosis is difficult especially in primary care settings. Stool sample is easy to obtain and since children swallow sputum, it can be used to diagnose pulmonary tuberculosis. With this background, a pilot study was planned to evaluate the accuracy of the Xpert MTB/RIF assay for the detection of MTB in stool specimens obtained from pediatric pulmonary TB patients confirmed either by gastric lavage(GL) or sputum(SP) Xpert MTB/RIF assay. In addition, the results of microscopy of stool specimen were compared with that of gastric lavage/ sputum (GL/SP) specimen by Ziehl-Neelsen (ZN) and fluorescent light-emitting diode (LED) staining. MATERIAL AND METHODS A prospective study was carried out on 50 GL/SP Xpert MTB/RIF assay positive children (0-14 years). Stool specimens from these children were processed for Xpert MTB/RIF assay. The GL/SP and stool specimens were processed for ZN and Auramine O fluorescent microscopy as well. RESULTS Fluorescent staining detected acid fast bacilli (AFB) in 24 GL/SP and 16 stool specimens as compared to 20 GL/SP and 10 stool specimens by ZN staining. Stool Xpert MTB/ RIF assay was positive in 29 out of 50 children. Rifampicin resistance was detected in 13 of the 50 (26%) GL/SP specimens. Of these 13 children, rifampicin resistance was detected in 7 stool specimens, rifampicin indeterminate resistance was detected in one specimen and in the remaining 5 children, M.tuberculosis was not detected in stool. CONCLUSION Stool is a good non-invasive specimen for the detection of pulmonary TB in children, especially in remote areas, where invasive techniques cannot be performed for sample collection.
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Affiliation(s)
- Vijaya P Torane
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India.
| | - Gita Nataraj
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
| | - Swapna Kanade
- Department of Microbiology, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
| | - Chandrahas T Deshmukh
- Department of Pediatrics, Seth Gordhandas Sunderdas Medical College (GSMC) & King Edward Memorial Hospital (KEMH), Mumbai, Maharashtra, India
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Mishra D, Singh A, Yadav RK, Verma M. Diagnostic Utility of Cartridge-Based Nucleic Acid Amplification Test (CBNAAT) on Induced Sputum Versus Gastric Aspirate Samples for the Diagnosis of Paediatric Pulmonary Tuberculosis. Cureus 2023; 15:e47246. [PMID: 38022348 PMCID: PMC10654686 DOI: 10.7759/cureus.47246] [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] [Accepted: 10/18/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND Tuberculosis (TB) in children is neglected, mainly due to a lack of sensitive diagnostic tools. Paediatric TB is now a global priority. More paediatric TB cases are being recorded as a result of the introduction of Xpert® Mycobacterium tuberculosis (MTB)/rifampicin (RIF) (Cepheid Inc., Sunnyvale, USA). This study was undertaken to evaluate the performance of Xpert MTB/RIF in the diagnosis of pulmonary TB in children. METHODS We recruited 70 paediatric patients with probable pulmonary TB and their gastric aspirate (GA), and induced sputum (IS) samples were collected between January 2021 and June 2022 in Saifai, Etawah, Uttar Pradesh, at the Microbiology Department of the Uttar Pradesh University of Medical Sciences (U.P.U.M.S.). All samples were subjected to smear examination, Bacterial Activation of Continuous Temperature and Environmental Control - Mycobacterial Growth Indicator Tube (BACTEC-MGIT) culture, and Xpert MTB/RIF. RESULTS The specimens included 70 GAs and 70 IS samples. The total number of specimens were 140 and we collected GA as well as IS from each of the patient enrolled in the study. When compared to microscopy, GeneXpert provides a quicker and earlier detection of paediatric TB. The sensitivity of the cartridge-based nucleic acid amplification test (CBNAAT) against mycobacterial growth indicator tube (MGIT) was 75.0% for GA samples and 63.64% for IS samples. CONCLUSION Paediatric TB, owing to its paucibacillary nature and difficulty in the collection of samples, makes the diagnosis difficult by conventional methods. Our study shows that smear and culture yield in GA samples are superior to those of IS samples and the sensitivity of Xpert MTB/RIF assay is also significantly different in GA and IS samples, but a combination of GA and IS yielded the best results.
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Affiliation(s)
- Dipti Mishra
- Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Amit Singh
- Microbiology, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Rajesh K Yadav
- Pediatrics, Uttar Pradesh University of Medical Sciences, Etawah, IND
| | - Mudit Verma
- Community Medicine, Uttar Pradesh University of Medical Sciences, Etawah, IND
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Batista JFC, Santos VSDO, de Jesus CVF, Lima SO. Time series of cases and treatment outcomes from tuberculosis in Sergipe, 2012-2021. REVISTA BRASILEIRA DE EPIDEMIOLOGIA 2023; 26:e230041. [PMID: 37729348 PMCID: PMC10511026 DOI: 10.1590/1980-549720230041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/21/2023] [Accepted: 06/23/2023] [Indexed: 09/22/2023] Open
Abstract
OBJECTIVE The objectives of this study were: (1) to analyze the temporal trend of tuberculosis treatment outcomes in the state of Sergipe; (2) to identify the existence of seasonality of tuberculosis; (3) to verify the influence of the rapid molecular test (MTB-RIF) in the time series of tuberculosis and its treatment outcomes in the state of Sergipe; and (4) to verify treatment outcomes. METHODS Ecological study on tuberculosis and three treatment outcomes (cure, interruption of treatment, and death) extracted from Datasus. Incidence and mortality rates were calculated for the crude occurrences of cases and deaths and the proportions of cure and interruption of treatment (%). The time series was analyzed using Prais-Winsten regression from Jan to Dec/2021. RESULTS The total incidence rate was 36.35 cases per 100,000 inhabitants, with an increase of 0.44% per month (95%CI 0.35; 0.54). The cure rate was 64.0% with a steady trend (p>0.05). The percentage of treatment interruption was 13.3%, with a reduction of -0.73%/month (95%CI -1.11; -0.34). The total mortality rate was 1.92 deaths/100,000 inhabitants with a stationary trend. After the implementation of the MTB-RIF, there was an increase in the incidence rate of 0.65% per month. Seasonality was not identified in any of the analyses performed (p>0.05). CONCLUSION There was an increase in incidence rates, reduction in treatment interruption and mortality in the state of Sergipe. Seasonality was not identified. The rapid molecular test showed a growth effect on the incidence rate.
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Bloom BR. A half-century of research on tuberculosis: Successes and challenges. J Exp Med 2023; 220:e20230859. [PMID: 37552470 PMCID: PMC10407785 DOI: 10.1084/jem.20230859] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 08/09/2023] Open
Abstract
Great progress has been made over the past half-century, but TB remains a formidable global health problem, particularly in low- and middle-income countries. Understanding the mechanisms of pathogenesis and necessary and sufficient conditions for protection are critical. The need for inexpensive and sensitive point-of-care diagnostic tests for earlier detection of infection and disease, shorter and less-toxic drug regimens for drug-sensitive and -resistant TB, and a more effective vaccine than BCG is immense. New and better tools, greater support for international research, collaborations, and training will be required to dramatically reduce the burden of this devastating disease which still kills 1.6 million people annually.
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Affiliation(s)
- Barry R. Bloom
- Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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Li M, Qiu Y, Guo M, Qu R, Tian F, Wang G, Wang Y, Ma J, Liu S, Takiff H, Tang YW, Gao Q. Comparison of Xpert MTB/RIF Ultra with Xpert MTB/RIF for the detection of Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China. Tuberculosis (Edinb) 2023; 142:102397. [PMID: 37597313 DOI: 10.1016/j.tube.2023.102397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/11/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023]
Abstract
The Xpert MTB/RIF Ultra (Ultra) is not yet used for the diagnosis of tuberculosis (TB) in China. We compared the performance of the Xpert and Ultra for detecting Mycobacterium tuberculosis and rifampicin resistance in a primary-level clinic in rural China. Sputum samples from suspected pulmonary TB patients were collected and subjected to smear microscopy, liquid culture, Xpert and Ultra tests. We then compared the sensitivity and specificity of Xpert and Ultra for diagnosing TB against liquid culture. Whole-genome sequencing was performed to predict rifampicin resistance and the results were compared with the Xpert and Ultra tests. The sensitivities of Xpert and Ultra were 88.1% and 95.1%, and the specificities were 91.9% and 84.4%, respectively. Among the 61 smear-negative culture-positive patients, the sensitivities of Xpert and Ultra were 80.3% and 91.8%. All Xpert-positive patients were Ultra-positive. Among culture-negative Xpert or Ultra-positive patients, 69.6% were taking anti-TB drugs or had a previous history of TB. Of the samples that Ultra classified as trace, nearly 25% were probably false-positives. Both Xpert and Ultra accurately detected all rifampicin-resistant patients. In conclusion, Ultra was more sensitive than Xpert, especially for smear-negative patients but had decreased specificity with more false-positives, especially with Ultra trace results.
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Affiliation(s)
- Meng Li
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China
| | - Yong Qiu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Mingcheng Guo
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Rong Qu
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Fajun Tian
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Gengsheng Wang
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Ya Wang
- Wusheng County Center for Disease Control and Prevention, Guang'an, China
| | - Jian Ma
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Siyuan Liu
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Howard Takiff
- Laboratorio de Genética Molecular, CMBC, Instituto Venezolano de Investigaciones Científicas, IVIC, Caracas, Venezuela
| | - Yi-Wei Tang
- Medical Affairs, Danaher Diagnostic Platform/Cepheid, Shanghai, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Science, Shanghai Medical College, Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
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Singh M, Jeyaraman M, Jeyaraman N, Jayakumar T, Iyengar KP, Jain VK. Mycobacterium Tuberculosis infection of the wrist joint: A current concepts review. J Clin Orthop Trauma 2023; 44:102257. [PMID: 37841656 PMCID: PMC10568419 DOI: 10.1016/j.jcot.2023.102257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 07/09/2023] [Accepted: 09/25/2023] [Indexed: 10/17/2023] Open
Abstract
Background Osteoarticular Tuberculosis (TB) of wrist joint is a rare, often misdiagnosed form of site affected by Mycobacterium Tuberculosis infection that can lead to severe disability and morbidity. This review aims to summarize the current literature on the diagnosis and management of Mycobacterium Tuberculosis infection of the wrist joint. Materials and methods A comprehensive search strategy using the PEO (Population, Exposure, Outcome) framework was conducted on PubMed, Google Scholar, and Web of Science databases from 1967 to 2022, excluding single case reports and correspondence articles. The keywords used for the search included 'Mycobacterium tuberculosis' 'osteoarticular' and 'wrist'. Clinical presentation, demographic details, complementary investigations undertaken, trends, and complications of different management interventions were recorded to generate this review. Results Osteoarticular Tuberculosis (TB) of the wrist joint accounts for fewer than 1% of all skeletal TB cases across a spectrum of age ranges. Magnetic Resonance Imaging (MRI) represents an excellent modality to reveal the extent of the disease at an early stage of the condition. Synovial fluid analysis has been recommended for microbiological diagnosis. Treatment options include anti-tubercular therapy (ATT), incision and drainage, debridement, synovectomy, and arthrodesis. Conclusion Early diagnosis and treatment of wrist tuberculosis is crucial for achieving good functional outcomes in patients with this uncommon condition. Polymerase Chain Reaction (PCR) and GeneXpert technology for the detection of Mycobacterium tuberculosis (MTB) have improved diagnostic accuracy in detecting MTB DNA and rifampicin resistance. Anti-Tubercular Therapy (ATT) regime remains a foundation pillar in the overall management of these patients with focused surgical interventions leading to improved clinical outcomes.
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Affiliation(s)
- Mohit Singh
- Department of Orthopaedics, Atal Bihari Vajpayee Institute of Medical Sciences, Dr Ram Manohar Lohia Hospital, New Delhi, 110001, India
| | - Madhan Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai, 600056, Tamil Nadu, India
| | - Naveen Jeyaraman
- Department of Orthopaedics, ACS Medical College and Hospital, Dr MGR Educational and Research Institute, Chennai, 600056, Tamil Nadu, India
| | - Tarun Jayakumar
- Department of Orthopaedics, KIMS-Sunshine Hospital, Hyderabad, 500003, Telangana, India
| | | | - Vijay Kumar Jain
- Department of Orthopaedics, Atal Bihari Vajpayee Institute of Medical Sciences, Dr Ram Manohar Lohia Hospital, New Delhi, 110001, India
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Vocat A, Sturm A, Jóźwiak G, Cathomen G, Świątkowski M, Buga R, Wielgoszewski G, Cichocka D, Greub G, Opota O. Nanomotion technology in combination with machine learning: a new approach for a rapid antibiotic susceptibility test for Mycobacterium tuberculosis. Microbes Infect 2023; 25:105151. [PMID: 37207717 DOI: 10.1016/j.micinf.2023.105151] [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: 10/04/2022] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 05/21/2023]
Abstract
Nanomotion technology is a growth-independent approach that can be used to detect and record the vibrations of bacteria attached to cantilevers. We have developed a nanomotion-based antibiotic susceptibility test (AST) protocol for Mycobacterium tuberculosis (MTB). The protocol was used to predict strain phenotype towards isoniazid (INH) and rifampicin (RIF) using a leave-one-out cross-validation (LOOCV) and machine learning techniques. This MTB-nanomotion protocol takes 21 h, including cell suspension preparation, optimized bacterial attachment to functionalized cantilever, and nanomotion recording before and after antibiotic exposure. We applied this protocol to MTB isolates (n = 40) and were able to discriminate between susceptible and resistant strains for INH and RIF with a maximum sensitivity of 97.4% and 100%, respectively, and a maximum specificity of 100% for both antibiotics when considering each nanomotion recording to be a distinct experiment. Grouping recordings as triplicates based on source isolate improved sensitivity and specificity to 100% for both antibiotics. Nanomotion technology can potentially reduce time-to-result significantly compared to the days and weeks currently needed for current phenotypic ASTs for MTB. It can further be extended to other anti-TB drugs to help guide more effective TB treatment.
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Affiliation(s)
- Anthony Vocat
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland; Resistell AG, Muttenz, 4132, Switzerland
| | | | | | | | | | | | | | | | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland; Service of Infectious Diseases, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, 1011, Switzerland.
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Dewi DNSS, Mertaniasih NM, Soedarsono, Hagino K, Yamazaki T, Ozeki Y, Artama WT, Kobayashi H, Inouchi E, Yoshida Y, Ishikawa S, Shaban AK, Tateishi Y, Nishiyama A, Ato M, Matsumoto S. Antibodies against native proteins of Mycobacterium tuberculosis can detect pulmonary tuberculosis patients. Sci Rep 2023; 13:12685. [PMID: 37542102 PMCID: PMC10403504 DOI: 10.1038/s41598-023-39436-4] [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: 03/01/2023] [Accepted: 07/25/2023] [Indexed: 08/06/2023] Open
Abstract
Accurate point-of-care testing (POCT) is critical for managing tuberculosis (TB). However, current antibody-based diagnosis shows low specificity and sensitivity. To find proper antigen candidates for TB diagnosis by antibodies, we assessed IgGs responsiveness to Mycobacterium tuberculosis proteins in pulmonary TB (PTB) patients. We employed major secreted proteins, such as Rv1860, Ag85C, PstS1, Rv2878c, Ag85B, and Rv1926c that were directly purified from M. tuberculosis. In the first screening, we found that IgG levels were significantly elevated in PTB patients only against Rv1860, PstS1, and Ag85B among tested antigens. However, recombinant PstS1 and Ag85B from Escherichia coli (E. coli) couldn't distinguish PTB patients and healthy controls (HC). Recombinant Rv1860 was not checked due to its little expression. Then, the 59 confirmed PTB patients from Soetomo General Academic Hospital, Surabaya, Indonesia, and 102 HC were tested to Rv1860 and Ag85B only due to the low yield of the PstS1 from M. tuberculosis. The ROC analysis using native Ag85B and Rv1860 showed an acceptable area under curve for diagnosis, which is 0.812 (95% CI 0.734-0.890, p < 0.0001) and 0.821 (95% CI 0.752-0.890, p < 0.0001). This study indicates that taking consideration of native protein structure is key in developing TB's POCT by antibody-based diagnosis.
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Affiliation(s)
- Desak Nyoman Surya Suameitria Dewi
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan.
- Department of Microbiology, Faculty of Medicine, Universitas Ciputra, CitraLand CBD Boulevard, Made, Kec. Sambikerep, Surabaya, 60219, Indonesia.
| | - Ni Made Mertaniasih
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, Surabaya, 60131, Indonesia.
- Laboratory of Tuberculosis, Institute of Tropical Disease, Universitas Airlangga, Kampus C Jl. Mulyorejo, Surabaya, 60115, Indonesia.
| | - Soedarsono
- Sub-Pulmonology Department of Internal Medicine, Faculty of Medicine, Hang Tuah University, Komplek Barat RSAL Dr. Ramelan, Jl. Gadung No.1, Jagir, Surabaya, 60111, Indonesia
| | - Kimika Hagino
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Tomoya Yamazaki
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Yuriko Ozeki
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Wayan Tunas Artama
- Department of Biochemistry, Faculty of Veterinary Medicine, Universitas Gadjah Mada, Jl. Fauna 2 Karangmalang, Yogyakarta, 55281, Indonesia
- One Health/Eco-Health Resource Center, Universitas Gadjah Mada, Jl. Teknika Utara, Barek, Sleman, Yogyakarta, 55281, Indonesia
| | - Haruka Kobayashi
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Erina Inouchi
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Yutaka Yoshida
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Satoshi Ishikawa
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
- Fukuyama Zoo, 276‑1, Fukuda, Ashida‑cho, Fukuyama, Hiroshima, 720‑1264, Japan
| | - Amina Kaboso Shaban
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Yoshitaka Tateishi
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Akihito Nishiyama
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan
| | - Manabu Ato
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Aoba-cho 4-2-1, Higashimurayama-shi, Tokyo, 189-0002, Japan
| | - Sohkichi Matsumoto
- Department of Bacteriology, School of Medicine, Niigata University, Asahimachi-Dori 1-757, Chuo-ku, Niigata, 951-8510, Japan.
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Jl. Mayjen Prof. Dr. Moestopo 47, Surabaya, 60131, Indonesia.
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Wang Y, Chan YS, Chae M, Shi D, Lee CY, Diao J. Programmable Digital-Microfluidic Biochips for SARS-CoV-2 Detection. Bioengineering (Basel) 2023; 10:923. [PMID: 37627808 PMCID: PMC10451662 DOI: 10.3390/bioengineering10080923] [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: 06/29/2023] [Revised: 07/20/2023] [Accepted: 08/01/2023] [Indexed: 08/27/2023] Open
Abstract
Biochips, a novel technology in the field of biomolecular analysis, offer a promising alternative to conventional testing equipment. These chips integrate multiple functions within a single system, providing a compact and efficient solution for various testing needs. For biochips, a pattern-control micro-electrode-dot-array (MEDA) is a new, universally viable design that can replace microchannels and other micro-components. In a Micro Electrode Dot Array (MEDA), each electrode can be programmatically controlled or dynamically grouped, allowing a single chip to fulfill the diverse requirements of different tests. This capability not only enhances flexibility, but also contributes to cost reduction by eliminating the need for multiple specialized chips. In this paper, we present a visible biochip testing system for tracking the entire testing process in real time, and describe our application of the system to detect SARS-CoV-2.
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Affiliation(s)
- Yuxin Wang
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- The Materials Science and Engineering Program, Department of Mechanical and Materials Engineering, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
- Advanced Sensing Lab, Digital Futures, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Yun-Sheng Chan
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Institute of Electronics, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Matthew Chae
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Donglu Shi
- The Materials Science and Engineering Program, Department of Mechanical and Materials Engineering, College of Engineering and Applied Science, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Chen-Yi Lee
- Institute of Electronics, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
- Advanced Sensing Lab, Digital Futures, University of Cincinnati, Cincinnati, OH 45221, USA
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Büyükbayraktar HK, Pelit Arayıcı P, Ihlamur M, Gökkaya D, Karahan M, Abamor EŞ, Topuzoğulları M. Effect of polycation coating on the long-term pulsatile release of antigenic ESAT-6 1-20 peptide from PLGA nanoparticles. Colloids Surf B Biointerfaces 2023; 228:113421. [PMID: 37356137 DOI: 10.1016/j.colsurfb.2023.113421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 06/12/2023] [Accepted: 06/18/2023] [Indexed: 06/27/2023]
Abstract
The development of novel vaccine formulations against tuberculosis is necessary to reduce the number of new cases worldwide. Polymeric nanoparticles offer great potential as antigen delivery and immunostimulant systems for such purposes. In the study, we have encapsulated the antigenic peptide epitope of ESAT-6 protein of M. tuberculosis into PLGA nanoparticles and coated these nanoparticles with the cationic polymer of quaternized poly(4-vinylpyridine) (QPVP) to obtain a positively charged system as a potential nasal vaccine prototype. The produced spherical nanoparticles had hydrodynamic diameters between 180 and 240 nm with a narrow size distribution. The non-coated nanoparticle exhibited a 3-phase in vitro release profile that was completed in more than 4 months. In this release study, 5% of the peptide was released in the first 6 h and the nanoparticle remained silent until the 70th day. Then, an additional 5% of the peptide was released in 45 days. After coating the nanoparticle with QPVP, the release periods and peptide amounts dramatically changed. The antigenic peptide-loaded nanoparticles coated with the polycation stimulated the macrophages in vitro to release more nitric oxide (NO) compared to the free peptide and non-coated nanoparticle, which reveals the immunostimulant activity of the produced nanoparticle systems. The produced non-coated nanoparticles with the prolonged pulsatile release of the antigenic peptide can be used in the development of single injection self-boosting vaccine formulations. By coating these nanoparticles, both the release profile and immunogenicity can be changed.
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Affiliation(s)
- Hatice Kübra Büyükbayraktar
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye
| | - Pelin Pelit Arayıcı
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye
| | - Murat Ihlamur
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye
| | - Damla Gökkaya
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye
| | - Mesut Karahan
- Vocational School of Health Sciences Services, Üsküdar University, İstanbul, Turkiye
| | - Emrah Şefik Abamor
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye
| | - Murat Topuzoğulları
- Department of Bioengineering, Faculty of Chemical and Metallurgical Engineering, Yildiz Technical University, İstanbul, Turkiye.
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Hassanin ESA, Mohamed Hussein AA, Abdelrheem SS, Dongol E, Mhsb AHA, Zahran AM, Zein M, G Sayed I. Frequency of rifampicin-resistant mycobacterium tuberculosis by GeneXpert MTB/RIF assay and its correlates among 2605 probable tuberculosis patients in upper Egypt. Indian J Tuberc 2023; 70:345-355. [PMID: 37562911 DOI: 10.1016/j.ijtb.2022.09.004] [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: 04/22/2022] [Revised: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 08/12/2023]
Abstract
RATIONALE GeneXpert MTB/RIF (Mycobacterium tuberculosis/rifampicin) assay is a method for detecting rifampicin resistance (RR-MTB) in suspected samples in less than 2 hours with high sensitivity and specificity yield. This study aimed to use the GeneXpert MTB/RIF assay to determine the frequency of RR-MTB and to study the possible influencing correlates associated with positive results. SUBJECTS AND METHODS This is a retrospective cross-sectional study of patients who visited TB clinic in 5 years (2016-2021). According to the data sheet of the patients, all the collected specimens were divided into 2 parts one for diagnosis by Ziehl-Neelsen stain and the other part for GeneXpert analysis. GeneXpert was also used to look for evidence of RR. RESULTS Out of the 2605 total samples screened, 718 (27.6%) tested positive for MTB on GeneXpert assay; of them 633 (88.4%) were sensitive to Rifampicin, 83 (11.6%) were resistant to Rifampicin and 2 cases were undetermined. Factors contributing to RR-MTB were: smoker/ex-smoker, with 2.5 times more risk (p = 0.013.0, p = 0.001); recurrence cases had a 4-fold increased risk (p < 0.001); patients with very low M. tuberculosis detected on the GeneXpert MTB/RIF test were 8 times more likely to have RR-TB (P = 0.004). CONCLUSION This study disclosed a high-rate MTB in Egyptian probable TB cases. Smoking, recurrence and cases with a very low M. tuberculosis burden noticed on the GeneXpert MTB/RIF test had augmented risk of RR-TB.
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Affiliation(s)
| | | | - Shaimaa S Abdelrheem
- Department of Public Health and Community Medicine, Faculty of Medicine, Aswan University, Egypt and Armed Forces College of Medicine (AFCM), Cairo, Egypt
| | | | | | - Asmaa M Zahran
- Clinical Pathology Department, South Egypt Cancer Institute Assiut University, Egypt
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Li R, Li Y, Chen X, Jia L, Yu H, Huang Y, Wu Q, Xiao M, Ge S, Zhang Y, Feng Z, Li Q, Xu Y, Shi W, Sun F, Zhang W. Ability of the MeltPro MTB/PZA Assay to Detect Susceptibility to Pyrazinamide in Rifampin-Resistant Tuberculosis Patients. Microbiol Spectr 2023; 11:e0483622. [PMID: 37162355 PMCID: PMC10269598 DOI: 10.1128/spectrum.04836-22] [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: 11/24/2022] [Accepted: 04/12/2023] [Indexed: 05/11/2023] Open
Abstract
Prediction of susceptibility to pyrazinamide (PZA) directly from sputum has been challenging. The MeltPro MTB/PZA assay, based on melting curve analysis, can simultaneously detect Mycobacterium tuberculosis and the resistance to PZA from sputum. We aimed to evaluate the MeltPro MTB/PZA assay to predict PZA resistance among rifampin-resistant tuberculosis (RR-TB) patients. We prospectively enrolled RR-TB patients in the registered trials, and their baseline sputum samples were obtained to perform the assay and culture. DNA sequencing of culture isolates was analyzed and used as the reference standard. Sanger sequencing was performed for samples with discrepant results between next-generation sequencing (NGS) and the investigational assay. The main analysis was conducted in the population of patients with interpretable results by both NGS and the assay. A total of 239 patients with RR-TB were screened, and 220 underwent the MeltPro MTB/PZA assay. The assay provided no information for 25 of 220 patients (11.4%). Among the remaining 195 patients, 13 had negative culture or insufficient raw NGS sequencing data, and 15 had indeterminate assay results. A total of 167 patients were included in the main analysis. Against DNA sequencing, the sensitivity, specificity, and negative predictive value of the assay for detecting resistance to PZA were 91.4% (95% confidence interval [CI], 87.1% to 95.6%), 89.9% (95% CI, 85.3% to 94.5%), and 95.2% (95% CI, 91.9% to 98.4%), respectively. In conclusion, the MeltPro MTB/PZA assay is a fast semiautomatic molecular platform to rapidly predict resistance to PZA from sputum and holds promise as a screening tool with satisfactory sensitivity. IMPORTANCE This study evaluated the accuracy of the MeltPro MTB/PZA assay at detecting the presence of PZA resistance through registered clinical trials. Compared to DNA sequencing, the assay had high sensitivity and negative predictive value, suggesting its potential utility as a screening tool in clinical practice. The assay could serve as an ideal primary screening tool in low PZA-resistant M. tuberculosis prevalence settings and could be used as an additional test to identify PZA resistance rapidly and initially in the RR-TB population.
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Affiliation(s)
- Rong Li
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yang Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinchang Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Lina Jia
- Department of Tuberculosis, Guiyang Public Health Clinical Center, Guiyang, China
| | - Hongying Yu
- Center for Infectious Diseases, The First People’s Hospital of Huaihua, Huaihua, Hunan, China
| | - Ya Huang
- Department of Tuberculosis, Ge Jiu Infectious Disease Hospital, Gejiu, China
| | - Qianhong Wu
- Department of Tuberculosis, Shaanxi Provincial Tuberculosis Prevention and Control Hospital, Xi’an, Shannxi, China
| | - Mingying Xiao
- Department of Tuberculosis, Baoshan People’s Hospital, Baoshan, China
| | - Shijia Ge
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Yilin Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhen Feng
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Qingge Li
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Ye Xu
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Wenzhi Shi
- Engineering Research Centre of Molecular Diagnostics of the Ministry of Education, State Key Laboratory of Cellular Stress Biology, State Key Laboratory of Molecular Vaccinology and Molecular Diagnostics, School of Life Sciences, Faculty of Medicine and Life Sciences, Xiamen University, Xiamen, China
| | - Feng Sun
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Jing’an District Central Hospital, Fudan University, Shanghai, China
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Medical Molecular Virology (MOE/MOH), Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Huashen Institute of Microbes and Infections, Shanghai, China
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Xiong Y, Zeng X, Yan L, Wang Y, Lin Y, Ao K, Feng P, Xie Y, Chen P. Target Enzyme-Triggered Click Chemistry and Hybridization Chain Reaction for Fluorescence Nonculture Homogeneous Analysis of E. coli in Bloodstream Infections. ACS APPLIED MATERIALS & INTERFACES 2023. [PMID: 37262009 DOI: 10.1021/acsami.3c04065] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Escherichia coli is the major pathogen that causes bloodstream infections (BSI). It is critical to develop nonculture identification methods which can meet the urgent need of clinical diagnosis and treatment. In this study, we reported a homogeneous fluorescence E. coli analysis system using β-galactosidase (β-Gal) as the biomarker and double-stranded DNA-templated copper nanoparticles (dsDNA-Cu NPs) as the signal output. The product of the enzymatic hydrolysis reaction, p-aminophenol (PAP), could reduce Cu2+ to Cu+, triggering the alkyne-azido cycloaddition reaction (CuAAC). Subsequently, the hybrid chain reaction (HCR) was initiated, producing the dsDNA template used to generate Cu NPs in situ. The system achieved a wide linear range for β-Gal and E. coli 1-104 mU/L and 10-2-10 colony-forming unit (CFU)/mL, and a detection limit of 0.3 mU/L and 0.003 CFU/mL, respectively. 65 samples (45 blood and 20 urine) were collected to evaluate the clinical practicality. The results demonstrated remarkable area under the curve (AUC) values of 0.95 and 0.916 from uncultured urine and blood, respectively. It had 100% specificity and 83.3% sensitivity. The whole duration of the strategy was 3.5 h, which significantly reduced the turnaround time (TAT) and facilitated early BSI diagnosis to improve patients' prognosis. Our work had the potential to be an alternative to culture-based methods in clinics.
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Affiliation(s)
- Ying Xiong
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Xianghu Zeng
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Li Yan
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yue Wang
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yuling Lin
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Keping Ao
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Pan Feng
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yi Xie
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Piaopiao Chen
- Department of Laboratory Medicine, Med+X Center for Manufacturing, Out-Patient Department, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
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Cao B, Mijiti X, Deng LL, Wang Q, Yu JJ, Anwaierjiang A, Qian C, Li M, Fang DA, Jiang Y, Zhao LL, Zhao X, Wan K, Liu H, Li G, Yuan X. Genetic Characterization Conferred Co-Resistance to Isoniazid and Ethionamide in Mycobacterium tuberculosis Isolates from Southern Xinjiang, China. Infect Drug Resist 2023; 16:3117-3135. [PMID: 37228658 PMCID: PMC10204763 DOI: 10.2147/idr.s407525] [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: 02/23/2023] [Accepted: 05/02/2023] [Indexed: 05/27/2023] Open
Abstract
Background Ethionamide (ETH), a structural analogue of isoniazid (INH), is used for treating multidrug-resistant tuberculosis (MDR-TB). Due to the common target InhA, INH and ETH showed cross-resistance in M. tuberculosis. This study aimed to explore the INH and ETH resistant profiles and genetic mutations conferring independent INH- or ETH-resistance and INH-ETH cross-resistance in M. tuberculosis circulating in south of Xinjiang, China. Methods From Sep 2017 to Dec 2018, 312 isolates were included using drug susceptibility testing (DST), spoligotyping, and whole genome sequencing (WGS) to analyze the resistance characteristics for INH and/or ETH. Results Among the 312 isolates, 185 (58.3%) and 127 (40.7%) belonged to the Beijing family and non-Beijing family, respectively; 90 (28.9%) were INH-resistant (INHR) with mutation rates of 74.4% in katG, 13.3% in inhA and its promoter, 11.1% in ahpC and its upstream region, 2.2% in ndh, 0.0% in mshA, whilst 34 (10.9%) were ETH-resistant (ETHR) with mutation rates of 38.2% in ethA, 26.2% in inhA and its promoter, and 5.9% in ndh, 0.0% in ethR or mshA; and 25 (8.0%) were INH-ETH co-resistant (INHRETHR) with mutation rates of 40.0% in inhA and its promoter, and 8% in ndh. katG mutants tended to display high-level resistant to INH; and more inhA and its promoter mutants showed low-level of INH and ETH resistance. The optimal gene combinations by WGS for the prediction of INHR, ETHR, and INHRETHR were, respectively, katG+inhA and its promoter (sensitivity: 81.11%, specificity: 90.54%), ethA+inhA and its promoter+ndh (sensitivity: 61.76%, specificity: 76.62%), and inhA and its promoter+ndh (sensitivity: 48.00%, specificity: 97.65%). Conclusion This study revealed the high diversity of genetic mutations conferring INH and/or ETH resistance among M. tuberculosis isolates, which would facilitate the study on INHR and/or ETHR mechanisms and provide clues for choosing ETH for MDR treatment and molecular DST methods in south of Xinjiang, China.
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Affiliation(s)
- Bin Cao
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiaokaiti Mijiti
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Le-Le Deng
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Quan Wang
- The Eighth Affiliated Hospital of Xinjiang Medical University, Urumqi, 830000, People’s Republic of China
| | - Jin-Jie Yu
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | | | - Chengyu Qian
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Machao Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Dan-Ang Fang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
- Wenzhou Key Laboratory of Sanitary Microbiology, Key Laboratory of Laboratory Medicine, Ministry of Education, China, School of Laboratory Medicine and Life Sciences, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, People’s Republic of China
| | - Yi Jiang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Li-Li Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Zhao
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Kanglin Wan
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Guilian Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, People’s Republic of China
| | - Xiuqin Yuan
- School of Public Health, University of South China, Hengyang, 421001, People’s Republic of China
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Valeyre D, Brauner M, Bernaudin JF, Carbonnelle E, Duchemann B, Rotenberg C, Berger I, Martin A, Nunes H, Naccache JM, Jeny F. Differential diagnosis of pulmonary sarcoidosis: a review. Front Med (Lausanne) 2023; 10:1150751. [PMID: 37250639 PMCID: PMC10213276 DOI: 10.3389/fmed.2023.1150751] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/24/2023] [Indexed: 05/31/2023] Open
Abstract
Diagnosing pulmonary sarcoidosis raises challenges due to both the absence of a specific diagnostic criterion and the varied presentations capable of mimicking many other conditions. The aim of this review is to help non-sarcoidosis experts establish optimal differential-diagnosis strategies tailored to each situation. Alternative granulomatous diseases that must be ruled out include infections (notably tuberculosis, nontuberculous mycobacterial infections, and histoplasmosis), chronic beryllium disease, hypersensitivity pneumonitis, granulomatous talcosis, drug-induced granulomatosis (notably due to TNF-a antagonists, immune checkpoint inhibitors, targeted therapies, and interferons), immune deficiencies, genetic disorders (Blau syndrome), Crohn's disease, granulomatosis with polyangiitis, eosinophilic granulomatosis with polyangiitis, and malignancy-associated granulomatosis. Ruling out lymphoproliferative disorders may also be very challenging before obtaining typical biopsy specimen. The first step is an assessment of epidemiological factors, notably the incidence of sarcoidosis and of alternative diagnoses; exposure to risk factors (e.g., infectious, occupational, and environmental agents); and exposure to drugs taken for therapeutic or recreational purposes. The clinical history, physical examination and, above all, chest computed tomography indicate which differential diagnoses are most likely, thereby guiding the choice of subsequent investigations (e.g., microbiological investigations, lymphocyte proliferation tests with metals, autoantibody assays, and genetic tests). The goal is to rule out all diagnoses other than sarcoidosis that are consistent with the clinical situation. Chest computed tomography findings, from common to rare and from typical to atypical, are described for sarcoidosis and the alternatives. The pathology of granulomas and associated lesions is discussed and diagnostically helpful stains specified. In some patients, the definite diagnosis may require the continuous gathering of information during follow-up. Diseases that often closely mimic sarcoidosis include chronic beryllium disease and drug-induced granulomatosis. Tuberculosis rarely resembles sarcoidosis but is a leading differential diagnosis in regions of high tuberculosis endemicity.
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Affiliation(s)
- Dominique Valeyre
- Pulmonology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
| | - Michel Brauner
- Radiology Department, Avicenne University Hospital, Bobigny, France
| | - Jean-François Bernaudin
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
- Faculté de Médecine, Sorbonne University Paris, Paris, France
| | | | - Boris Duchemann
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
- Thoracic and Oncology Department, Avicenne University Hospital, Bobigny, France
| | - Cécile Rotenberg
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
- Pulmonology Department, Avicenne University Hospital, Bobigny, France
| | - Ingrid Berger
- Pulmonology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | - Antoine Martin
- Pathology Department, Avicenne University Hospital, Bobigny, France
| | - Hilario Nunes
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
- Pulmonology Department, Avicenne University Hospital, Bobigny, France
| | - Jean-Marc Naccache
- Pulmonology Department, Groupe Hospitalier Paris Saint Joseph, Paris, France
| | - Florence Jeny
- INSERM UMR 1272, Sorbonne University Paris-Nord, Paris, France
- Pulmonology Department, Avicenne University Hospital, Bobigny, France
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Fan D, Yue Y, Li H, Shang X, Li H, Xiao R, Cai L. Evaluation of the performances of InnowaveDx MTB-RIF assay in the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid. Tuberculosis (Edinb) 2023; 140:102349. [PMID: 37187053 DOI: 10.1016/j.tube.2023.102349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 03/27/2023] [Accepted: 05/02/2023] [Indexed: 05/17/2023]
Abstract
OBJECTIVE To evaluate the tuberculosis diagnostic performance of the InnowaveDx MTB-RIF assay (InnowaveDx test) in bronchoalveolar lavage fluid (BALF). METHODS A total of 213 BALF samples from suspected PTB patients were analyzed. AFB smear, culture, Xpert, Innowavedx test, CapitalBio test and simultaneous amplification and testing (SAT) were performed. RESULTS Of the 213 patients included in the study, 163 were diagnosed with PTB, and 50 were TB negative. Using the final clinical diagnosis as the reference, the sensitivity of InnowaveDx assay was 70.6%, which was significantly higher than the values achieved using the other methods (P < 0.05), and the specificity was 88.0%, which was comparable with other methods (P > 0.05). Among the 83 PTB cases with negative culture results, the detection rate of InnowaveDx assay was significantly higher than those of AFB smear, Xpert, CapitalBio test and SAT (P < 0.05). Kappa analysis was used to compare the agreement of InnowaveDx and Xpert in detecting RIF sensitivity, and the result showed the Kappa value was 0.78. CONCLUSIONS The InnowaveDx test is a sensitive, rapid and cost-effective tool for PTB diagnosis. In addition, the sensitivity of InnowaveDx to RIF in samples with low TB load should be interpreted with caution in light of other clinical data.
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Affiliation(s)
- Dapeng Fan
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Yongning Yue
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Hao Li
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Xuechai Shang
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Huanyu Li
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China
| | - Rong Xiao
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China.
| | - Long Cai
- Zhejiang Tuberculosis Diagnosis and Treatment Center, Affiliated Hangzhou Chest Hospital, Zhejiang University School of Medicine, PR China.
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Ho MM, Dagg B, Govind S, Hockley J. The development and establishment of a heat inactivated preparation of Mycobacterium tuberculosis (H37Rv) as the first international standard for nucleic acid amplification techniques. Biologicals 2023; 82:101667. [PMID: 37004276 DOI: 10.1016/j.biologicals.2023.101667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 12/13/2022] [Accepted: 03/06/2023] [Indexed: 04/03/2023] Open
Abstract
A need to develop an inactivated Mycobacterium tuberculosis (Mtb) preparation, to be used as a DNA standard, as an important and urgent requirement for Tuberculosis (TB) diagnostics standardization was identified in 2018. A candidate material was generated using a heat inactivated culture of Mtb strain H37Rv. A lyophilised preparation was evaluated for its suitability as an International Standard for molecular detection of Mtb DNA in an international collaborative study. Together with the use of quantitative PCR assays and rapid diagnostic tests, this candidate standard was demonstrated to be fit-for-purpose. Based on the results from this collaborative study, it is proposed this lyophilised heat inactivated Mtb preparation (NIBSC code: 20/152) to be established by the World Health Organization Expert Committee on Biological Standardization, as the First WHO International Standard for Mycobacterium tuberculosis (H37Rv) for nucleic acid amplification techniques with an assigned unitage of 6.3 log10 or 2 × 106 International Units per vial. The intended uses of this IS are for calibration of secondary or in-house reference preparations used in the assays for the molecular detection of Mtb DNA. It may also be used for assay validation and monitoring the performance in terms of limit of detection of rapid diagnostic tests.
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Uddin MKM, Ather MF, Kabir S, Rahman A, Choudhury S, Nasrin R, Rahman T, Rahman SMM, Ahmed S, Banu S. Diagnostic Performance of Different Laboratory Methods for the Detection of Extrapulmonary Tuberculosis. Microorganisms 2023; 11:microorganisms11041066. [PMID: 37110489 PMCID: PMC10142428 DOI: 10.3390/microorganisms11041066] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/06/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
Accurate and appropriate extrapulmonary tuberculosis (EPTB) diagnosis remains challenging due to its paucibacillary nature, requirement of invasive collection procedures, and lack of sensitive tests. This study investigated the diagnostic performance of different methods for the diagnosis of EPTB. A total of 1340 EPTB specimens were collected from presumptive EPTB patients from four different hospitals between November 2015 and March 2017. The collected specimens were tested with AFB microscopy, culture, Xpert MTB/RIF assay (Xpert), and MTBDRplus assay. Among the 1340 EPTB specimens, 49 (3.66%), 141 (10.52%), 166 (12.39%), and 154 (11.49%) were positive in AFB microscopy, culture, Xpert MTB/RIF, and MTBDRplus assay, respectively. A total of 194 (14.9%) cases were found positive in at least one of these methods. Using culture as a reference standard, the sensitivity and specificity of AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay were: 27.0%/99.1%, 83.7%/96.0%, and 79.4%/96.5%, respectively. Compared to the composite reference standard, the sensitivity of culture, AFB microscopy, Xpert MTB/RIF, and MTBDRplus assay was 72.7%, 25.3%, 85.6%, and 79.4%, respectively, with a specificity of 100% for all the methods. The Xpert MTB/RIF assay showed the highest sensitivity compared to other methods. Considering the short turnaround time and promising findings, Xpert MTB/RIF assay should be integrated into national TB guidelines as a routine diagnostic test.
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Affiliation(s)
- Mohammad Khaja Mafij Uddin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Md Fahim Ather
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Senjuti Kabir
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Arfatur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
- Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Sabrina Choudhury
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Rumana Nasrin
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Tanjina Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - S M Mazidur Rahman
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Shahriar Ahmed
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
| | - Sayera Banu
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka 1212, Bangladesh
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Stanley S, Spaulding CN, Liu Q, Chase MR, Ha DTM, Thai PVK, Lan NH, Thu DDA, Quang NL, Brown J, Hicks ND, Wang X, Marin M, Howard NC, Vickers AJ, Karpinski WM, Chao MC, Farhat MR, Caws M, Dunstan SJ, Thuong NTT, Fortune SM. High-throughput phenogenotyping of Mycobacteria tuberculosis clinical strains reveals bacterial determinants of treatment outcomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.09.536166. [PMID: 37090677 PMCID: PMC10120664 DOI: 10.1101/2023.04.09.536166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Background Combatting the tuberculosis (TB) epidemic caused by Mycobacterium tuberculosis ( Mtb ) necessitates a better understanding of the factors contributing to patient clinical outcomes and transmission. While host and environmental factors have been evaluated, the impact of Mtb genetic background and phenotypic diversity is underexplored. Previous work has made associations between Mtb genetic lineages and some clinical and epidemiological features, but the bacterial traits underlying these connections are largely unknown. Methods We developed a high-throughput functional genomics platform for defining genotype-phenotype relationships across a panel of Mtb clinical isolates. These phenotypic fitness profiles function as intermediate traits which can be linked to Mtb genetic variants and associated with clinical and epidemiological outcomes. We applied this approach to a collection of 158 Mtb strains from a study of Mtb transmission in Ho Chi Minh City, Vietnam. Mtb strains were genetically tagged in multiplicate, which allowed us to pool the strains and assess in vitro competitive fitness using deep sequencing across a set of 14 host-relevant antibiotic and metabolic conditions. Phylogenetic and monogenic associations with these intermediate traits were identified and then associated with clinical outcomes. Findings Mtb clinical strains have a broad range of growth and drug response dynamics that can be clustered by their phylogenetic relationships. We identified novel monogenic associations with Mtb fitness in various metabolic and antibiotic conditions. Among these, we find that mutations in Rv1339 , a phosphodiesterase, which were identified through their association with slow growth in glycerol, are further associated with treatment failure. We also identify a previously uncharacterized subclade of Lineage 1 strains (L1.1.1.1) that is phenotypically distinguished by slow growth under most antibiotic and metabolic stress conditions in vitro . This clade is associated with cavitary disease, treatment failure, and demonstrates increased transmission potential. Interpretation High-throughput phenogenotyping of Mtb clinical strains enabled bacterial intermediate trait identification that can provide a mechanistic link between Mtb genetic variation and patient clinical outcomes. Mtb strains associated with cavitary disease, treatment failure, and transmission potential display intermediate phenotypes distinguished by slow growth under various antibiotic and metabolic conditions. These data suggest that Mtb growth regulation is an adaptive advantage for host bacterial success in human populations, in at least some circumstances. These data further suggest markers for the underlying bacterial processes that govern these clinical outcomes. Funding National Institutes of Allergy and Infectious Diseases: P01 AI132130 (SS, SMF); P01 AI143575 (XW, SMF); U19 AI142793 (QL, SMF); 5T32AI132120-03 (SS); 5T32AI132120-04 (SS); 5T32AI049928-17 (SS) Wellcome Trust Fellowship in Public Health and Tropical Medicine: 097124/Z/11/Z (NTTT) National Health and Medical Research Council (NHMRC)/A*STAR joint call: APP1056689 (SJD) The funding sources had no involvement in study methodology, data collection, analysis, and interpretation nor in the writing or submission of the manuscript. Research in context Evidence before this study: We used different combinations of the words mycobacterium tuberculosis, tuberculosis, clinical strains, intermediate phenotypes, genetic barcoding, phenogenomics, cavitary disease, treatment failure, and transmission to search the PubMed database for all studies published up until January 20 th , 2022. We only considered English language publications, which biases our search. Previous work linking Mtb determinants to clinical or epidemiological data has made associations between bacterial lineage, or less frequently, genetic polymorphisms to in vitro or in vivo models of pathogenesis, transmission, and clinical outcomes such as cavitary disease, treatment failure, delayed culture conversion, and severity. Many of these studies focus on the global pandemic Lineage 2 and Lineage 4 Mtb strains due in part to a deletion in a polyketide synthase implicated in host-pathogen interactions. There are a number of Mtb GWAS studies that have led to novel genetic determinants of in vitro drug resistance and tolerance. Previous Mtb GWAS analyses with clinical outcomes did not experimentally test any predicted phenotypes of the clinical strains. Published laboratory-based studies of Mtb clinical strains involve relatively small numbers of strains, do not identify the genetic basis of relevant phenotypes, or link findings to the corresponding clinical outcomes. There are two recent studies of other pathogens that describe phenogenomic analyses. One study of 331 M. abscessus clinical strains performed one-by-one phenotyping to identify bacterial features associated with clearance of infection and another details a competition experiment utilizing three barcoded Plasmodium falciparum clinical isolates to assay antimalarial fitness and resistance. Added value of this study: We developed a functional genomics platform to perform high-throughput phenotyping of Mtb clinical strains. We then used these phenotypes as intermediate traits to identify novel bacterial genetic features associated with clinical outcomes. We leveraged this platform with a sample of 158 Mtb clinical strains from a cross sectional study of Mtb transmission in Ho Chi Minh City, Vietnam. To enable high-throughput phenotyping of large numbers of Mtb clinical isolates, we applied a DNA barcoding approach that has not been previously utilized for the high-throughput analysis of Mtb clinical strains. This approach allowed us to perform pooled competitive fitness assays, tracking strain fitness using deep sequencing. We measured the replicative fitness of the clinical strains in multiplicate under 14 metabolic and antibiotic stress condition. To our knowledge, this is the largest phenotypic screen of Mtb clinical isolates to date. We performed bacterial GWAS to delineate the Mtb genetic variants associated with each fitness phenotype, identifying monogenic associations with several conditions. We then defined Mtb phenotypic and genetic features associated with clinical outcomes. We find that a subclade of Mtb strains, defined by variants largely involved in fatty acid metabolic pathways, share a universal slow growth phenotype that is associated with cavitary disease, treatment failure and increased transmission potential in Vietnam. We also find that mutations in Rv1339 , a poorly characterized phosphodiesterase, also associate with slow growth in vitro and with treatment failure in patients. Implications of all the available evidence: Phenogenomic profiling demonstrates that Mtb strains exhibit distinct growth characteristics under metabolic and antibiotic stress conditions. These fitness profiles can serve as intermediate traits for GWAS and association with clinical outcomes. Intermediate phenotyping allows us to examine potential processes by which bacterial strain differences contribute to clinical outcomes. Our study identifies clinical strains with slow growth phenotypes under in vitro models of antibiotic and host-like metabolic conditions that are associated with adverse clinical outcomes. It is possible that the bacterial intermediate phenotypes we identified are directly related to the mechanisms of these outcomes, or they may serve as markers for the causal yet unidentified bacterial determinants. Via the intermediate phenotyping, we also discovered a surprising diversity in Mtb responses to the new anti-mycobacterial drugs that target central metabolic processes, which will be important in considering roll-out of these new agents. Our study and others that have identified Mtb determinants of TB clinical and epidemiological phenotypes should inform efforts to improve diagnostics and drug regimen design.
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Wang J, Zhang X, Huo F, Qin L, Liu R, Shang Y, Yao C, Ma L, Pang Y. Analysis of Xpert MTB/RIF results in retested patients with very low initial bacterial loads: A retrospective study in China. J Infect Public Health 2023; 16:911-916. [PMID: 37068397 DOI: 10.1016/j.jiph.2023.04.004] [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: 09/03/2022] [Revised: 02/18/2023] [Accepted: 04/04/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The Xpert MTB/RIF (Xpert) assay has been widely used to diagnose suspected active tuberculosis (TB) and rifampicin-resistant TB cases. Despite its excellent performance record, false-positive Xpert rifampicin (RIF) resistance results are obtained for specimens with extremely low bacterial loads. OBJECTIVE We aimed to study the feasibility of repeat Xpert testing as a strategy for reducing the odds of obtaining false-positive results when testing paucibacillary TB patients. METHODS We enrolled previously tested TB patients with very low initial bacterial loads from May 2016 to February 2022 for Xpert retesting. A total of 251 TB patients were retested using the Xpert assay. RESULTS RIF resistance was noted in 65 (25.9 %) patients when tested by Xpert at initial diagnosis. Only 107 (42.6 %) of 251 patients tested positive for MTB when retested via Xpert. The majority (98.6 %) of RIF-susceptible cases were still susceptible to RIF when retested. Initial Xpert testing yielded 35 positive results for MTB in the RIF-resistant group, of whom 25 (71.4 %) still exhibited RIF resistance when retested. All culture-positive MTB isolates in the RIF-susceptible group were also RIF-susceptible by phenotypic DST. In the RIF-resistant group, 10 of 14 culture-positive MTB isolates exhibited RIF resistance, of which 4 isolates were deemed RIF-susceptible by phenotypic DST. The proportion of double mutations within the MTB rpoB RRDR sequence, as detected by hybridization of Xpert D and E probes, was significantly higher in the RIF-susceptible group than in the RIF-susceptible group. CONCLUSIONS Our results demonstrated that initial RIF-susceptible results were more accurate than RIF-resistant results. Additionally, patients with double mutations that delayed probe D/E hybridization were more likely to have false-positive Xpert results. Our findings emphasize that repeat Xpert MTB/RIF testing is necessary for TB patients with extremely low bacterial loads who are at high risk for RIF-resistant TB.
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Affiliation(s)
- Jun Wang
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Xuxia Zhang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Fengmin Huo
- National Clinical Laboratory on Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Lin Qin
- Department of Endoscopic Diagnosis & Treatment, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Rongmei Liu
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Cong Yao
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China
| | - Liping Ma
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing 101149, People's Republic of China.
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Domínguez J, Boeree MJ, Cambau E, Chesov D, Conradie F, Cox V, Dheda K, Dudnyk A, Farhat MR, Gagneux S, Grobusch MP, Gröschel MI, Guglielmetti L, Kontsevaya I, Lange B, van Leth F, Lienhardt C, Mandalakas AM, Maurer FP, Merker M, Miotto P, Molina-Moya B, Morel F, Niemann S, Veziris N, Whitelaw A, Horsburgh CR, Lange C. Clinical implications of molecular drug resistance testing for Mycobacterium tuberculosis: a 2023 TBnet/RESIST-TB consensus statement. THE LANCET. INFECTIOUS DISEASES 2023; 23:e122-e137. [PMID: 36868253 PMCID: PMC11460057 DOI: 10.1016/s1473-3099(22)00875-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/16/2022] [Accepted: 12/16/2022] [Indexed: 03/05/2023]
Abstract
Drug-resistant tuberculosis is a substantial health-care concern worldwide. Despite culture-based methods being considered the gold standard for drug susceptibility testing, molecular methods provide rapid information about the Mycobacterium tuberculosis mutations associated with resistance to anti-tuberculosis drugs. This consensus document was developed on the basis of a comprehensive literature search, by the TBnet and RESIST-TB networks, about reporting standards for the clinical use of molecular drug susceptibility testing. Review and the search for evidence included hand-searching journals and searching electronic databases. The panel identified studies that linked mutations in genomic regions of M tuberculosis with treatment outcome data. Implementation of molecular testing for the prediction of drug resistance in M tuberculosis is key. Detection of mutations in clinical isolates has implications for the clinical management of patients with multidrug-resistant or rifampicin-resistant tuberculosis, especially in situations when phenotypic drug susceptibility testing is not available. A multidisciplinary team including clinicians, microbiologists, and laboratory scientists reached a consensus on key questions relevant to molecular prediction of drug susceptibility or resistance to M tuberculosis, and their implications for clinical practice. This consensus document should help clinicians in the management of patients with tuberculosis, providing guidance for the design of treatment regimens and optimising outcomes.
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Affiliation(s)
- José Domínguez
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain.
| | - Martin J Boeree
- Department of Lung Diseases, Radboud Institute for Health Sciences, Radboud University Medical Center, Nijmegen, Netherlands
| | - Emmanuelle Cambau
- Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France, APHP-Hôpital Bichat, Mycobacteriology Laboratory, INSERM, University Paris Cite, IAME UMR1137, Paris, France
| | - Dumitru Chesov
- Department of Pneumology and Allergology, Nicolae Testemițanu State University of Medicine and Pharmacy, Chisinau, Moldova; Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
| | - Francesca Conradie
- Department of Clinical Medicine, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Vivian Cox
- Centre for Infectious Disease Epidemiology and Research, School of Public Health and Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa; Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene & Tropical Medicine, London, UK
| | - Andrii Dudnyk
- Department of Tuberculosis, Clinical Immunology and Allergy, National Pirogov Memorial Medical University, Vinnytsia, Ukraine; Public Health Center, Ministry of Health of Ukraine, Kyiv, Ukraine
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland; University of Basel, Basel, Switzerland
| | - Martin P Grobusch
- Center of Tropical Medicine and Travel Medicine, Department of Infectious Diseases, Amsterdam University Medical Centers, Amsterdam Infection & Immunity, Amsterdam Public Health, University of Amsterdam, Amsterdam, Netherlands
| | - Matthias I Gröschel
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany; Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Lorenzo Guglielmetti
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Irina Kontsevaya
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Berit Lange
- Department for Epidemiology, Helmholtz Centre for Infection Research, Braunschweig, Germany; German Centre for Infection Research, TI BBD, Braunschweig, Germany
| | - Frank van Leth
- Department of Health Sciences, Vrije Universiteit Amsterdam, Amsterdam, Netherlands; Amsterdam Public Health Research Institute, Amsterdam, Netherlands
| | - Christian Lienhardt
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK; UMI 233 IRD-U1175 INSERM - Université de Montpellier, Institut de Recherche pour le Développement, Montpellier, France
| | - Anna M Mandalakas
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Florian P Maurer
- National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Institute of Medical Microbiology, Virology and Hygiene, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Matthias Merker
- Division of Evolution of the Resistome, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany
| | - Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Barbara Molina-Moya
- Institut d'Investigació Germans Trias i Pujol, Universitat Autònoma de Barcelona, CIBER Enfermedades Respiratorias, INNOVA4TB Consortium, Barcelona, Spain
| | - Florence Morel
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Stefan Niemann
- Division of Molecular and Experimental Mycobacteriology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Department of Human, Biological and Translational Medical Sciences, School of Medicine, University of Namibia, Windhoek, Namibia
| | - Nicolas Veziris
- Sorbonne Université, INSERM, U1135, Centre d'Immunologie et des Maladies Infectieuses, (Cimi-Paris), APHP Sorbonne Université, Department of Bacteriology Hôpital Pitié-Salpêtrière, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Andrew Whitelaw
- Division of Medical Microbiology, Faculty of Medicine and Health Sciences, Stellenbosch University, South Africa; National Health Laboratory Service, Tygerberg Hospital, Cape Town, South Africa
| | - Charles R Horsburgh
- Departments of Epidemiology, Biostatistics, Global Health and Medicine, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Leibniz Lung Center, Borstel, Germany; German Center for Infection Research (DZIF), Partner Site Hamburg- Lübeck-Borstel-Riems, Borstel, Germany; Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany; Global TB Program, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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Syed RR, Catanzaro DG, Colman RE, Cooney CG, Linger Y, Kukhtin AV, Holmberg RC, Norville R, Crudu V, Ciobanu N, Codreanu A, Seifert M, Hillery N, Chiles P, Catanzaro A, Rodwell TC. Clinical Evaluation of the XDR-LFC Assay for the Molecular Detection of Isoniazid, Rifampin, Fluoroquinolone, Kanamycin, Capreomycin, and Amikacin Drug Resistance in a Prospective Cohort. J Clin Microbiol 2023; 61:e0147822. [PMID: 36757183 PMCID: PMC10035299 DOI: 10.1128/jcm.01478-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/11/2023] [Indexed: 02/10/2023] Open
Abstract
While the goal of universal drug susceptibility testing has been a key component of the WHO End TB Strategy, in practice, this remains inaccessible to many. Rapid molecular tests for tuberculosis (TB) and antituberculosis drug resistance could significantly improve access to testing. In this study, we evaluated the accuracy of the Akonni Biosystems XDR-TB (extensively drug-resistant TB) TruArray and lateral-flow-cell (XDR-LFC) assay (Akonni Biosystems, Inc., Frederick, MD, USA), a novel assay that detects mutations in seven genes associated with resistance to antituberculosis drugs: katG, the inhA promoter, and the ahpC promoter for isoniazid; rpoB for rifampin; gyrA for fluoroquinolones; rrs and the eis promoter for kanamycin; and rrs for capreomycin and amikacin. We evaluated assay performance using direct sputum samples from 566 participants recruited in a prospective cohort in Moldova over 2 years. The sensitivity and specificity against the phenotypic reference were both 100% for isoniazid, 99.2% and 97.9% for rifampin, 84.8% and 99.1% for fluoroquinolones, 87.0% and 84.1% for kanamycin, 54.3% and 100% for capreomycin, and 79.2% and 100% for amikacin, respectively. Whole-genome sequencing data for a subsample of 272 isolates showed 95 to 99% concordance with the XDR-LFC-reported suspected mutations. The XDR-LFC assay demonstrated a high level of accuracy for multiple drugs and met the WHO's minimum target product profile criteria for isoniazid and rifampin, while the sensitivity for fluoroquinolones and amikacin fell below target thresholds, likely due to the absence of a gyrB target in the assay. With optimization, the XDR-LFC shows promise as a novel near-patient technology to rapidly diagnose drug-resistant tuberculosis.
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Affiliation(s)
- Rehan R Syed
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Donald G Catanzaro
- Department of Biological Sciences, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rebecca E Colman
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | | | | | | | | | | | - Valeriu Crudu
- Phthisiopneumology Institute, Chișinău, Republic of Moldova
| | - Nelly Ciobanu
- Phthisiopneumology Institute, Chișinău, Republic of Moldova
| | | | - Marva Seifert
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Naomi Hillery
- Herbert Wertheim School of Public Health and Human Longevity Science, University of California, San Diego, La Jolla, California, USA
| | - Peter Chiles
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Antonino Catanzaro
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Timothy C Rodwell
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
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75
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D'Souza C, Kishore U, Tsolaki AG. The PE-PPE Family of Mycobacterium tuberculosis: Proteins in Disguise. Immunobiology 2023; 228:152321. [PMID: 36805109 DOI: 10.1016/j.imbio.2022.152321] [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: 06/28/2022] [Revised: 12/22/2022] [Accepted: 12/27/2022] [Indexed: 12/31/2022]
Abstract
Mycobacterium tuberculosis has thrived in parallel with humans for millennia, and despite our efforts, M. tuberculosis continues to plague us, currently infecting a third of the world's population. The success of M. tuberculosis has recently been attributed, in part, to the PE-PPE family; a unique collection of 168 proteins fundamentally involved in the pathogenesis of M. tuberculosis. The PE-PPE family proteins have been at the forefront of intense research efforts since their discovery in 1998 and whilst our knowledge and understanding has significantly advanced over the last two decades, many important questions remain to be elucidated. This review consolidates and examines the vast body of existing literature regarding the PE-PPE family proteins, with respect to the latest developments in elucidating their evolution, structure, subcellular localisation, function, and immunogenicity. This review also highlights significant inconsistencies and contradictions within the field. Additionally, possible explanations for these knowledge gaps are explored. Lastly, this review poses many important questions, which need to be addressed to complete our understanding of the PE-PPE family, as well as highlighting the challenges associated with studying this enigmatic family of proteins. Further research into the PE-PPE family, together with technological advancements in genomics and proteomics, will undoubtedly improve our understanding of the pathogenesis of M. tuberculosis, as well as identify key targets/candidates for the development of novel drugs, diagnostics, and vaccines.
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Affiliation(s)
- Christopher D'Souza
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom
| | - Uday Kishore
- Department of Veterinary Medicine, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Anthony G Tsolaki
- Biosciences, Department of Life Sciences, College of Health, Medicine and Life Sciences, Brunel University London, Uxbridge UB8 3PH, United Kingdom.
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76
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Yao L, Chen S, Sha W, Gu Y. The diagnostic performance of endobronchial ultrasound with Xpert MTB/RIF Ultra in smear-negative pulmonary tuberculosis. BMC Infect Dis 2023; 23:107. [PMID: 36814228 PMCID: PMC9945607 DOI: 10.1186/s12879-023-08073-7] [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: 11/29/2022] [Accepted: 02/10/2023] [Indexed: 02/24/2023] Open
Abstract
OBJECTIVE This study investigated the diagnostic performance of endobronchial ultrasound with Xpert MTB/RIF Ultra (Ultra) for detecting smear-negative pulmonary tuberculosis (TB). METHODS 143 patients suspected of sputum smear-negative pulmonary tuberculosis were enrolled in this study in Shanghai Pulmonary Hospital, China. These patients underwent endobronchial ultrasound with a guide sheath (EBUS-GS) or endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) based on their chest CT manifestations. We assessed the sensitivity and specificity of tissue specimens with Ultra in the TB group and non-TB group. Culture and clinical diagnosis were used as gold-standard for TB. RESULTS Among these 143 patients, 11 patients were culture-positive TB, 85 patients were diagnosed with culture-negative TB and 47 were with the non-TB diseases. Direct testing with microscopy (Acid-Fast Bacilli smear, AFB), liquid culture, pathology, Xpert MTB/RIF(Xpert) test and Ultra had a sensitivity of 8.3%, 11.5%, 42.7%, 64.6%, and 78.1% individually among all the TB patients. Ultra had a higher sensitivity than Xpert (P = 0.011). But Ultra had a specificity of 59.6% (95% CI 44.3-73.3), lower than that of Xpert (89.4%, 95% CI 76.1-96.0, P = 0.001). Ultra had the same sensitivity on specimens from EBUS-TBNA and EBUS-GS (P = 0.975). Ultra's positive predictive value and negative predictive value were 79.8% and 57.1% respectively. CONCLUSIONS Tissue specimens from interventional bronchoscopy combined with Ultra provide a sensitive method for diagnosing smear-negative pulmonary tuberculosis, but its specificity was lower than Xpert.
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Affiliation(s)
- Lan Yao
- grid.24516.340000000123704535Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Clinic and Research Center of Tuberculosis, Tongji University School of Medicine, Shanghai, 200433 China
| | - Shanhao Chen
- grid.24516.340000000123704535Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Clinic and Research Center of Tuberculosis, Tongji University School of Medicine, Shanghai, 200433 China
| | - Wei Sha
- Shanghai Key Laboratory of Tuberculosis, Shanghai Pulmonary Hospital, Clinic and Research Center of Tuberculosis, Tongji University School of Medicine, Shanghai, 200433, China.
| | - Ye Gu
- Department of Bronchoscopy, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, 200433, China.
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77
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Armstrong D, Fisher S, Totten M, Parrish N. An Analytic Feasibility Study of the BD MAX™ MDR-TB Assay for Testing of Non-Sputum Specimens for Detection of the Mycobacterium tuberculosis Complex (MTBC) and Isoniazid (INH) and Rifampin (RIF) Resistance. Diagn Microbiol Infect Dis 2023; 106:115925. [PMID: 36966629 DOI: 10.1016/j.diagmicrobio.2023.115925] [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: 10/27/2022] [Revised: 01/26/2023] [Accepted: 02/16/2023] [Indexed: 02/24/2023]
Abstract
Rapid diagnosis of tuberculosis and drug resistance in extrapulmonary specimens can be challenging. The BD MAX™ multidrug resistant (MDR)-TB assay (BD MAX™) has demonstrated high sensitivity and specificity for the detection of the Mycobacterium tuberculosis complex (MTBC) as well as resistance to INH and Rifampin (RIF) in pulmonary specimens but has not been rigorously assessed in extrapulmonary samples. We evaluated the diagnostic accuracy of the BD MAX™ assay for the detection of MTBC and drug resistance in extrapulmonary specimens spiked with MTBC from the Johns Hopkins strain collection. A total of 1083 tests were performed across multiple sample types, with an overall percent agreement of 94.8% (795/839) for detection of MTBC and 99% (379/383) and 96.4% (323/335) for determination of INH and RIF resistance-conferring mutations, respectively. The BD MAX™ assay provides same day detection of MTBC and drug-resistance results and could be a beneficial diagnostic test in extrapulmonary sample types.
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Affiliation(s)
- Derek Armstrong
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Stefanie Fisher
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Marissa Totten
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Nicole Parrish
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
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78
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Eom JS, Park S, Jang H, Kim S, Yoo WH, Kim SH, Mok J. Bronchial Washing Using a Thin Versus a Thick Bronchoscope to Diagnose Pulmonary Tuberculosis: A Randomized Trial. Clin Infect Dis 2023; 76:238-244. [PMID: 36151949 DOI: 10.1093/cid/ciac789] [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: 06/25/2022] [Revised: 09/14/2022] [Accepted: 09/20/2022] [Indexed: 01/18/2023] Open
Abstract
BACKGROUND This study was performed to evaluate the efficacy of using a thin bronchoscope for the diagnosis of pulmonary tuberculosis (PTB). METHODS Between March 2019 and November 2021, we prospectively enrolled participants with suspected PTB whose sputum acid-fast bacilli (AFB) smear and tuberculosis (TB) polymerase chain reaction (PCR) tests were negative or who could not produce self-expectorated sputum. Participants were randomized to a control group (bronchial washing [BW] using a 5.9-mm conventional bronchoscope guided by chest computed tomography) or an investigational group (BW using a 4.0-mm thin bronchoscope under virtual bronchoscopic navigation guidance). The primary outcome was detection of TB in BW fluid, defined as a positive result in the Xpert MTB/RIF assay. The secondary outcomes included AFB smear and Mycobacterium tuberculosis culture positivity, time to treatment initiation, and bronchoscopy-related complications. RESULTS In total, 85 participants were included in the final analysis (43 in the control group and 42 in the investigational group). Twenty-three and 29, respectively, were finally diagnosed with PTB. The TB detection rate in BW fluid was higher in the investigational group (72.4% vs 43.5%, P = .035). Mycobacterium tuberculosis culture positivity was also higher in the investigational group (79.3% vs 52.2%, P = .038). No participants required premature bronchoscopy termination because of complications. Of the participants with PTB, the time to treatment initiation was shorter in the investigational group (median, 2.0 days vs 4.0 days, P = .001). CONCLUSIONS BW using a thin bronchoscope increases the TB detection rate in patients with PTB compared to conventional bronchoscopy. Clinical Trials Registration.ȃNCT03802812.
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Affiliation(s)
- Jung Seop Eom
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea.,Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
| | - Seyeon Park
- Department of Internal Medicine, Daerim St Mary's Hospital, Seoul, Republic of Korea
| | - Hyojin Jang
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Saerom Kim
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Wan Ho Yoo
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Soo Han Kim
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea
| | - Jeongha Mok
- Department of Internal Medicine, Pusan National University Hospital, Busan, Republic of Korea.,Department of Internal Medicine, Pusan National University School of Medicine, Busan, Republic of Korea.,Biomedical Research Institute, Pusan National University Hospital, Busan, Republic of Korea
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79
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Loukman M, Olivier B, Vincent B, Rachid D, Cyril F, Morgane V, Nathalie CA. Epidemiology of tuberculosis and susceptibility to antituberculosis drugs in Reunion Island. BMC Infect Dis 2023; 23:4. [PMID: 36604621 PMCID: PMC9814425 DOI: 10.1186/s12879-022-07965-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 12/22/2022] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Tuberculosis is the first fatal infectious agent in the world with 1.2 million annual deaths for 10 million cases. Little is known about the epidemiology of tuberculosis and its resistance in Reunion Island, which is at the heart of migratory flows from highly endemic Indian Ocean territories. METHODS We carried out a retrospective observational study of cases of tuberculosis disease in Reunion Island between 2014 and 2018. The epidemiological, demographic, microbiological, clinical and social characteristics were analyzed from mandatory declarations, microbiology database and medical files. RESULTS 265 cases of tuberculosis disease were recorded over the period, ie an incidence of 6.2 / 100,000 inhabitants. 114 patients (43%) were born or resided > 6 months in the rest of the Indian Ocean area. The risk of infection was increased if birth in Madagascar (OR 23.5), Comoros (OR 8.9) or Mayotte (OR 6.8). The prevalence of HIV co-infection was low (2.5%). There were 31 cases (14.4%) of resistance to antituberculosis including 3 (1.4%) of multidrug-resistant tuberculosis and 0 case of extensively drug-resistant tuberculosis. The female gender (61.3% of resistant) was associated with resistance. The resistance rate was not significantly different depending on the geographic origin. CONCLUSION This is the first exhaustive epidemiological study of tuberculosis in Reunion Island. The incidence there is relatively low but increased for people with links to neighboring islands, particularly Madagascar. The prevalence of multidrug resistance is low, with no associated increased risk for patients from the Indian Ocean area.
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Affiliation(s)
- Moreea Loukman
- Service de Pneumologie, Centre Hospitalo-Universitaire Réunion, Allée des topazes CS 11021, 97400 Site St. Denis, France
| | - Belmonte Olivier
- Service de Microbiologie, Centre Hospitalo-Universitaire Réunion, Site St. Denis, France
| | - Boulay Vincent
- Centre de Lutte Anti Tuberculeuse Sud Réunion, St. Denis, France
| | - Dekkak Rachid
- Centre de Lutte Anti Tuberculeuse Ouest Réunion, St. Denis, France
| | - Ferdynus Cyril
- Methodological Support Unit, Saint-Denis University Hospital, St Denis, France ,grid.7429.80000000121866389Clinical Research Department, INSERM, CIC1410, 97410 Saint-Pierre, France
| | - Verduyn Morgane
- Service de Pneumologie, Centre Hospitalo-Universitaire Réunion, Allée des topazes CS 11021, 97400 Site St. Denis, France ,Centre de Lutte Anti Tuberculeuse Nord-Est Réunion, St. Denis, France
| | - Coolen-Allou Nathalie
- Service de Pneumologie, Centre Hospitalo-Universitaire Réunion, Allée des topazes CS 11021, 97400 Site St. Denis, France ,Centre de Lutte Anti Tuberculeuse Nord-Est Réunion, St. Denis, France
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80
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Boldi MO, Denis-Lessard J, Neziri R, Brouillet R, von-Garnier C, Chavez V, Mazza-Stalder J, Jaton K, Greub G, Opota O. Performance of microbiological tests for tuberculosis diagnostic according to the type of respiratory specimen: A 10-year retrospective study. Front Cell Infect Microbiol 2023; 13:1131241. [PMID: 36936773 PMCID: PMC10017756 DOI: 10.3389/fcimb.2023.1131241] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 02/03/2023] [Indexed: 03/06/2023] Open
Abstract
Background The microbial diagnosis of tuberculosis (TB) remains challenging and relies on multiple microbiological tests performed on different clinical specimens. Polymerase chain reactions (PCRs), introduced in the last decades has had a significant impact on the diagnosis of TB. However, questions remain about the use of PCRs in combination with conventional tests for TB, namely microscopy and culture. We aimed to determine the performance of microscopy, culture and PCR for the diagnosis of pulmonary tuberculosis according to the type of clinical specimen in order to improve the diagnostic yield and to avoid unnecessary, time and labor-intensive tests. Methods We conducted a retrospective study (2008-2018) on analysis (34'429 specimens, 14'358 patients) performed in our diagnostic laboratory located in the Lausanne University Hospital to compare the performance of microbiological tests on sputum, induced sputum, bronchial aspirate and bronchoalveolar lavage (BAL). We analysed the performance using a classical "per specimen" approach and a "per patient" approach for paired specimens collected from the same patient. Results The overall sensitivities of microscopy, PCR and culture were 0.523 (0.489, 0.557), 0.798 (0.755, 0.836) and 0.988 (0.978, 0.994) and the specificity were 0.994 (0.993, 0.995), 1 (0.999, 1) and 1 (1, 1). Microscopy displayed no significant differences in sensitivity according to the type of sample. The sensitivities of PCR for sputum, induced sputum, bronchial aspirate and BAL were, 0.821 (0.762, 0.871), 0.643 (0.480, 0.784), 0.837 (0.748, 0.904) and 0.759 (0.624, 0.865) respectively and the sensitivity of culture were, 0.993 (0.981, 0.998), 0.980 (0.931, 0.998), 0.965 (0.919, 0.988), and 1 (0.961, 1) respectively. Pairwise comparison of specimens collected from the same patient reported a significantly higher sensitivity of PCR on bronchial aspirate over BAL (p < 0.001) and sputum (p < 0.05) and a significantly higher sensitivity of culture on bronchial aspirate over BAL (p < 0.0001). Conclusions PCR displayed a higher sensitivity and specificity than microscopy for all respiratory specimens, a rational for a smear-independent PCR-based approach to initiate tuberculosis microbial diagnostic. The diagnosis yield of bronchial aspirate was higher than BAL. Therefore, PCR should be systematically performed also on bronchial aspirates when available.
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Affiliation(s)
- Marc-Olivier Boldi
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Justin Denis-Lessard
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Rina Neziri
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - René Brouillet
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Christophe von-Garnier
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Valérie Chavez
- Faculty of Business and Economics, University of Lausanne, Lausanne, Switzerland
| | - Jesica Mazza-Stalder
- Division of Pulmonology, Department of Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland
| | - Katia Jaton
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
| | - Onya Opota
- Institute of Microbiology, Lausanne University and University Hospital of Lausanne, Lausanne, Switzerland
- *Correspondence: Onya Opota,
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81
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Yu Y, Jiang XX, Li JC. Biomarker discovery for tuberculosis using metabolomics. Front Mol Biosci 2023; 10:1099654. [PMID: 36891238 PMCID: PMC9986447 DOI: 10.3389/fmolb.2023.1099654] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Accepted: 02/06/2023] [Indexed: 02/22/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death among infectious diseases, and the ratio of cases in which its pathogen Mycobacterium tuberculosis (Mtb) is drug resistant has been increasing worldwide, whereas latent tuberculosis infection (LTBI) may develop into active TB. Thus it is important to understand the mechanism of drug resistance, find new drugs, and find biomarkers for TB diagnosis. The rapid progress of metabolomics has enabled quantitative metabolite profiling of both the host and the pathogen. In this context, we provide recent progress in the application of metabolomics toward biomarker discovery for tuberculosis. In particular, we first focus on biomarkers based on blood or other body fluids for diagnosing active TB, identifying LTBI and predicting the risk of developing active TB, as well as monitoring the effectiveness of anti-TB drugs. Then we discuss the pathogen-based biomarker research for identifying drug resistant TB. While there have been many reports of potential candidate biomarkers, validations and clinical testing as well as improved bioinformatics analysis are needed to further substantiate and select key biomarkers before they can be made clinically applicable.
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Affiliation(s)
- Yi Yu
- Center for Analyses and Measurements, College of Chemical Engineering, Zhejiang University of Technology, Hangzhou, China
| | - Xin-Xin Jiang
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China
| | - Ji-Cheng Li
- Clinical Research Laboratory, Shaoxing Seventh People's Hospital, Shaoxing, China.,Institute of Cell Biology, Zhejiang University Medical School, Hangzhou, China
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82
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van Ginneken B. Tuberculosis Detection from Chest Radiographs: Stop Training Radiologists Now. Radiology 2023; 306:138-139. [PMID: 36066371 DOI: 10.1148/radiol.221769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Bram van Ginneken
- From the Radboud University Medical Center, Geert Grooteplein Zuid 10, 6525 GA Nijmegen, the Netherlands
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83
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Ali GA, Goravey W, Howady FS, Ali M, Alshurafa A, Abdalhadi AM, Hajmusa M, Daghfal J, Khal AA, Maslamani MA, Soub HA, Omrani AS. The Role of Post-Bronchoscopy Sputum Examination in Screening for Active Tuberculosis. Trop Med Infect Dis 2022; 8:tropicalmed8010013. [PMID: 36668920 PMCID: PMC9864813 DOI: 10.3390/tropicalmed8010013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/28/2022] Open
Abstract
Early diagnosis is a fundamental component of global tuberculosis control. The objective of this study was to evaluate the diagnostic yield of post-bronchoscopy sputum (PBS) testing as part of a tuberculosis diagnostic work-up. All new residents in the State of Qatar undergo a tuberculosis (TB) screening program. Those with abnormal chest radiology, negative sputum acid-fast bacilli (AFB) smears, and nucleic acid amplification testing (NAAT) for M. tuberculosis, undergo an additional bronchoscopic evaluation for TB. We prospectively enrolled individuals who were going to undergo bronchoscopy to provide two PBS samples for AFB smears and mycobacterial cultures between 18 September 2018 and 12 March 2021. A total of 495 individuals, with a median age of 31 years, were included. The majority of the patients were males (329, 66.5%). The most frequent country of origin was India (131, 26.5%) followed by the Philippines (123, 24.8%). The addition of PBS to bronchoalveolar lavage (BAL) testing allowed microbiological confirmation of tuberculosis in an additional 13 patients (3.9%), resulting in improved sensitivity (from 77.9% to 81.9%), negative predictive value (from 69.2% to 73.2%), and negative likelihood ratio (from 0.22 to 0.18). Where resources are available, the incorporation of routine PBS examination as part of tuberculosis diagnostic work-up can enhance the diagnostic yield.
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Affiliation(s)
- Gawahir A. Ali
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Wael Goravey
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
- Correspondence:
| | - Faraj S. Howady
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Maisa Ali
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Awni Alshurafa
- Division of Internal Medicine, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
| | - Ahmed M. Abdalhadi
- Division of Internal Medicine, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
| | - Muhammed Hajmusa
- Division of Internal Medicine, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
| | - Joanne Daghfal
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
| | - Abdullatif Al Khal
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Muna Al Maslamani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Hussam Al Soub
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
| | - Ali S. Omrani
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha 3050, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha 3050, Qatar
- College of Medicine, Qatar University, Doha 2713, Qatar
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84
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Wang Y, Tan J, Lei L, Yuan Y, Li W, Zhao Y, Wang Y, Niu X, Li Z, Wei L, Han Y, Cheng M, Guo X, Han X, Wang W. The value of Xpert MTB/RIF assay of urine samples in the early diagnosis of smear-negative urinary tuberculosis. Eur J Med Res 2022; 27:300. [PMID: 36539899 PMCID: PMC9764486 DOI: 10.1186/s40001-022-00947-x] [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: 10/15/2022] [Accepted: 12/12/2022] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND According to reports, between 30 and 40 percent of extrapulmonary tuberculosis (EPTB) cases are caused by urinary tract tuberculosis (UTB). It is critical to identify UTB quickly since it frequently precedes delayed medical attention, which can have detrimental effects. This study examined the use of Xpert MTB/RIF, a PCR test that can detect MTB as well as resistance to an important drug, rifampicin (RIF), in UTB particularly, for the early identification of UTB. METHODS 180 participants with clinically presumptive UTB whose urine samples were chosen for urine sediment smear, culture, Xpert MTB/RIF, and TB-DNA testing at Henan Chest Hospital between January 2019 and July 2022. Evaluation of test performance using Composite Reference Standards (CRSs). We studied and compared the positivity rate for various tests using the t-test. The effectiveness of smear, culture, Xpert MTB/RIF, and TB-DNA was assessed using McNemar test. RESULTS In this subject, a total of 108 participants were diagnosed with UTB, and the positivity rate was 67.1%. Compared with CRS, the positivity rate of Xpert MTB/RIF, smear, culture, and TB-DNA was 29.69% (19/64, P < 0.001), 7.56% (9/119, P < 0.1), 12.12% (4/33, P > 0.05), and 18.75% (6/32, P < 0.1), respectively. The sensitivity of Xpert MTB/RIF assay was significantly better than that of smear and culture tests (78.9% vs. 77.8%, P < 0.05; 78.9% vs. 75%, P < 0.05). Under CRS, the positivity rate for Xpert, culture, and TB-DNA was 31.6% (6/19, P < 0.1), 6.2% (1/16, P > 0.05), and 26.7% (4/15, P > 0.05) for TB-DNA, respectively, compared to smear negative. Xpert MTB/RIF assay specificity was significant for culture and TB-DNA (53.6% vs. 25%, P < 0.01; 53.6% vs. 38.9%, P < 0.05), and Xpert MTB/RIF assay FPV was significant for culture and TB-DNA (53.6% vs. 0%, P < 0.001; 53.6% vs. 0%, P < 0.001). CONCLUSION Xpert MTB/RIF outperforms smear, cultures, and TB-DNA in detecting UTB, plus Xpert MTB/RIF is better suited for early diagnosis in smear-negative UTB.
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Affiliation(s)
- Yachun Wang
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Jiao Tan
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Lei Lei
- Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China ,grid.459614.bDepartment of Family Medicine, Henan Provincial Chest Hospital, Zhengzhou, 450003 China
| | - Yingying Yuan
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Wenbo Li
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Yue Zhao
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Yali Wang
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Xiaodong Niu
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Zheng Li
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Lukuan Wei
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Yungang Han
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Meijing Cheng
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Xu Guo
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Xue Han
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
| | - Wei Wang
- grid.207374.50000 0001 2189 3846Medical Laboratory, Henan Provincial Chest Hospital, Zhengzhou University, Zhengzhou, 450003 China ,Henan Provincial Key Laboratory of Tuberculosis Diagnostic Medicine, Zhengzhou, 450003 China ,Henan Provincial Infectious Diseases (Tuberculosis) Clinical Medical Research Center, Zhengzhou, 450003 China
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Ou X, Zhang Z, Zhao B, Song Z, Wang S, He W, Pei S, Liu D, Xing R, Xia H, Zhao Y. Evaluation Study of xMAP TIER Assay on a Microsphere-Based Platform for Detecting First-Line Anti-Tuberculosis Drug Resistance. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph192417068. [PMID: 36554951 PMCID: PMC9779588 DOI: 10.3390/ijerph192417068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 05/09/2023]
Abstract
Early diagnosis of drug susceptibility for tuberculosis (TB) patients could guide the timely initiation of effective treatment. We evaluated a novel multiplex xMAP TIER (Tuberculosis-Isoniazid-Ethambutol-Rifampicin) assay based on the Luminex xMAP system to detect first-line anti-tuberculous drug resistance. Deoxyribonucleic acid samples from 353 Mycobacterium tuberculosis clinical isolates were amplified by multiplex polymerase chain reaction, followed by hybridization and analysis through the xMAP system. Compared with the broth microdilution method, the sensitivity and specificity of the xMAP TIER assay for detecting resistance was 94.9% (95%CI, 90.0-99.8%) and 98.9% (95%CI, 97.7-100.0%) for rifampicin; 89.1% (95%CI, 83.9-94.3%) and 100.0% (95%CI, 100.0-100.0%) for isoniazid; 82.1% (95% CI, 68.0-96.3%) and 99.7% (95% CI, 99.0-100.0%) for ethambutol. With DNA sequencing as the reference standard, the sensitivity and specificity of xMAP TIER for detecting resistance were 95.0% (95% CI, 90.2-99.8%) and 99.6% (95% CI, 98.9-100.0%) for rifampicin; 96.9% (95% CI, 93.8-99.9%) and 100.0% (95% CI, 100.0-100.0%) for isoniazid; 86.1% (95% CI, 74.8-97.4%) and 100.0% (95% CI, 100.0-100.0%) for ethambutol. The results achieved showed that the xMAP TIER assay had good performance for detecting first-line anti-tuberculosis drug resistance, and it has the potential to diagnose drug-resistant tuberculosis more accurately due to the addition of more optimal design primers and probes on open architecture xMAP system.
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Affiliation(s)
- Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zhiguo Zhang
- Tuberculosis Dispensary of Changping District, Beijing 102202, China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Zexuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Shaojun Pei
- School of Public Health, Peking University, Beijing 100191, China
| | - Dongxin Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ruida Xing
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Correspondence:
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Lin JJ, Xi XH, Xia L, Tan YJ, Chen Y, Di HQ, Chen ZH, Yu T, Wei JH, Fang P, Lin XM, Su BY, Yan MZ, Yu YM, Okada K, Noguchi N, Annaka T, Liu XH, Lu SH. Diagnostic accuracy of loop-mediated isothermal amplification for pulmonary tuberculosis in China. FRONTIERS IN TROPICAL DISEASES 2022. [DOI: 10.3389/fitd.2022.1046948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
ObjectivesTo evaluate the diagnostic accuracy of Loop-Mediated Isothermal Amplification Platform (LAMP) in detecting pulmonary tuberculosis (PTB).MethodsThis multicenter prospective study was conducted at six sites in China from June, 2018 to December, 2019. Patients with suspected PTB were consecutively recruited and respiratory samples were collected from all patients. LAMP, Xpert MTB/RIF assay (Xpert), fluorescence smear microscopy, and BACTEC MGIT 960 liquid culture (Mtb culture) were performed for each sample. Diagnostic accuracy indices were calculated against Mtb culture results.ResultsA total of 845 participants were enrolled, but only 799 were included in the analysis. The sensitivities of LAMP, Xpert, and smear microscopy were 78.6% (239/304), 82.2% (250/304), and 63.8% (194/304), respectively, and their specificities were 88.7% (439/495), 86.1% (426/495), and 94.9% (470/495), respectively. The LAMP assay showed substantial agreement with other tests (kappa 0.64–0.79).ConclusionThe LAMP assay performs as well as Xpert MTB/RIF assay and Mtb culture in tertiary-care hospitals. It can be used as an alternative test for detecting PTB with the advantages of being fast, inexpensive, and easy to operate.
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Diriba G, Alemu A, Tola HH, Eshetu K, Yenew B, Amare M, Dagne B, Mollalign H, Sinshaw W, Abebaw Y, Seid G, Tadesse M, Zerihun B, Getu M, Moga S, Meaza A, Gamtesa DF, Tefera Z, Wondimu A, Hailu M, Buta B, Getahun M, Kebede A. Detection of Mycobacterium tuberculosis and rifampicin resistance by Xpert® MTB/RIF assay among presumptive tuberculosis patients in Addis Ababa, Ethiopia from 2014 to 2021. IJID REGIONS 2022; 5:97-103. [PMID: 36247095 PMCID: PMC9556786 DOI: 10.1016/j.ijregi.2022.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 12/02/2022]
Abstract
Objective This study aimed to determine the frequencies and trends of Mycobacterium tuberculosis and rifampicin resistance among presumptive tuberculosis patients in Ethiopia, who were tested using the Xpert MTB/RIF assay between 2014 and 2021. Methods Data were collected retrospectively from patient registries. Laboratory-based data were extracted from the national tuberculosis (TB) referral laboratory database. All patients referred to the National Tuberculosis Reference Laboratory (NTRL) for TB diagnosis from all over the country between March 1, 2014 and September 30, 2021, and tested using the Xpert MTB/RIF assay, were included. The extracted data were entered into a Microsoft Excel sheet and analyzed by Statistical Package for Social Sciences (SPSS) version 23. Results Among a total of 13 772 individuals tested using the Xpert MTB/RIF assay, the majority (8223; 59.7%) were males, and 48.5% (6678) of the individuals were aged between 15 and 39 years. Mycobacterium tuberculosis (MTB) was detected in 17.0% (2347) of the examined individuals. Of the detected MTB cases, nearly 9.9% (233) were rifampicin resistant (RR-TB), while 24 (1.0%) were RR-intermediate. Among all RR-TB cases, more than half (125; 53.6%) were detected in males, and 105 were new TB cases. Extrapulmonary (EPTB) patients had a greater rate of rifampicin resistance (11.0%) than pulmonary (PTB) patients (9.6%). Conclusion The frequency of TB and RR-TB remains high in the study setting. RR-TB was found to have a statistically significant association with previous anti-TB medication treatment. As a result, improving treatment adherence in recognized instances could assist in preventing MTB and RR-TB cases.
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Key Words
- EPHI, Ethiopian Public Health Institute
- EPTB, extrapulmonary tuberculosis
- MDR, multidrug resistance
- MTB, Mycobacterium tuberculosis
- MTBC, Mycobacterium tuberculosis complex
- Mycobacterium tuberculosis
- NTRL, National Tuberculosis Reference Laboratory
- PTB, pulmonary tuberculosis
- RIF, rifampicin
- RR-TB, rifampicin-resistant tuberculosis
- SPSS, Statistical Package for Social Sciences
- TB, tuberculosis
- WHO, World Health Organization
- Xpert MTB/RIF
- frequency
- rifampicin resistance
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Affiliation(s)
- Getu Diriba
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Ayinalem Alemu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Habteyes Hailu Tola
- Department of Public Health, College of Health Sciences, Selale University, Fiche, Ethiopia
| | - Kirubel Eshetu
- USAID Eliminate TB Project, Management Sciences for Health, Addis Ababa, Ethiopia
| | - Bazezew Yenew
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Misikir Amare
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Biniyam Dagne
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Hilina Mollalign
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Waganeh Sinshaw
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Yeshiwork Abebaw
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Getachew Seid
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Mengistu Tadesse
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Betselot Zerihun
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Melak Getu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Shewki Moga
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abyot Meaza
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Dinka Fekadu Gamtesa
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Zigba Tefera
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Amanuel Wondimu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Michael Hailu
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Bedo Buta
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Muluwork Getahun
- National Tuberculosis Reference Laboratory, Ethiopian Public Health Institute, Addis Ababa, Ethiopia
| | - Abebaw Kebede
- Department of Microbial, Cellular and Molecular Biology, College of Natural and Computational Sciences, Addis Ababa University, Addis Ababa, Ethiopia
- Africa Centers for Disease Control and Prevention, Addis Ababa, Ethiopia
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Busatto C, Bierhals DV, Vianna JS, da Silva PEA, Possuelo LG, Ramis IB. Epidemiology and control strategies for tuberculosis in countries with the largest prison populations. Rev Soc Bras Med Trop 2022; 55:e00602022. [PMID: 36417620 PMCID: PMC9757719 DOI: 10.1590/0037-8682-0060-2022] [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] [Indexed: 11/22/2022] Open
Abstract
Tuberculosis (TB) is a serious infectious disease, and its control is considered a challenge, especially among vulnerable populations such as prisoners. The occurrence of TB in prisons is an alarming public health problem in many countries. This integrative review aims to describe the epidemiology of TB and control strategies for this disease in countries with the largest prison populations. Studies have shown that it is essential to know the prevalence of TB in prisons of each country. This is because it can serve as an indication of the need for action in prisons to reduce TB rates, including improving the structure of prison environments, rapidly and accurately diagnosing new cases, identifying drug-resistant strains, and implementing effective and directly observed treatment for TB.
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Affiliation(s)
- Caroline Busatto
- Universidade Federal do Rio Grande, Programa de Pós-Graduação em Ciências da Saúde, Rio Grande, RS, Brasil
| | - Dienefer Venske Bierhals
- Universidade Federal do Rio Grande, Programa de Pós-Graduação em Ciências da Saúde, Rio Grande, RS, Brasil
| | - Julia Silveira Vianna
- Universidade Federal do Rio Grande, Programa de Pós-Graduação em Ciências da Saúde, Rio Grande, RS, Brasil
| | | | - Lia Gonçalves Possuelo
- Universidade de Santa Cruz do Sul, Programa de Pós-Graduação em Promoção da Saúde, Santa Cruz do Sul, RS, Brasil
| | - Ivy Bastos Ramis
- Universidade Federal do Rio Grande, Programa de Pós-Graduação em Ciências da Saúde, Rio Grande, RS, Brasil
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Boko CK, Zoclanclounon AR, Adoligbe CM, Dedehouanou H, M'Po M, Mantip S, Farougou S. Molecular diagnosis of bovine tuberculosis on postmortem carcasses during routine meat inspection in Benin: GeneXpert® testing to improve diagnostic scheme. Vet World 2022; 15:2506-2510. [DOI: 10.14202/vetworld.2022.2506-2510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Background and Aim: Bovine tuberculosis (TB) is a zoonotic disease of major public health importance, particularly in African countries, where control measures are limited or largely not applied. This study aimed to determine the accuracy of the currently used bovine TB diagnostic method at slaughterhouses in Benin; this is to contribute to the betterment and improvement in the epidemiological surveillance of the disease in the country.
Materials and Methods: A total of 40 tissue samples were collected from meat/viscera (lung, liver, heart, kidney, and the gastro-intestinal tract tissues) at Cotonou slaughterhouses from ruminants suspected to be infected with bovine TB during routine meat inspection. The collected samples were analyzed using GeneXpert testing technique as a reference method.
Results: Twenty-six samples tested positive out of the 40 suspected tissue samples collected by GeneXpert diagnostic technique; this shows the limitation of the routine meat inspection in detecting bovine TB as currently performed in Benin.
Conclusion: The outcome of the use of the molecular technique, therefore, supports the importance of the use of a molecular tool alongside the routine meat inspection for a better understanding of the epidemiology of bovine TB in Benin. However, more robust technical and policy efforts are needed for a sustainable implementation of such a strategy.
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Affiliation(s)
- Cyrille K. Boko
- Research Unit in Transmissible Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01BP 2009, Cotonou, Benin
| | - Ange-Régis Zoclanclounon
- Research Unit in Transmissible Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01BP 2009, Cotonou, Benin
| | - Camus M. Adoligbe
- Research Unit in Transmissible Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01BP 2009, Cotonou, Benin
| | | | - Marguéritte M'Po
- Research Unit in Transmissible Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01BP 2009, Cotonou, Benin
| | - Samuel Mantip
- Virology Division, National Veterinary Research Institute, PMB 0001, Vom, Nigeria
| | - Souaïbou Farougou
- Research Unit in Transmissible Diseases, Polytechnic School of Abomey-Calavi, University of Abomey-Calavi, 01BP 2009, Cotonou, Benin
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90
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Li Z. The Value of GeneXpert MTB/RIF for Detection in Tuberculosis: A Bibliometrics-Based Analysis and Review. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2022; 2022:2915018. [PMID: 36284547 PMCID: PMC9588380 DOI: 10.1155/2022/2915018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 09/26/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
With the continuous development of medical science and technology, especially with the advent of the era of precision diagnosis and treatment, molecular biology detection technology is widely valued and applied as an aid to early diagnosis of tuberculosis. The GeneXpert Mycobacterium tuberculosis Branching (MTB) technology is a suite of semi-nested real-time fluorescent quantitative PCR in vitro diagnostic technologies developed by Cepheid Inc. It targets the rifampicin resistance gene, rpoB, and can detect both MTB and resistance to rifampicin within 2 h. This review analyzed the papers related to GeneXpert using bibliometric software CiteSpace and Bibliometrix. A total of 151 articles were analyzed, spanning from 2011 to 2021. This bibliometrics-based review summarizes the history of the development of GeneXpert in tuberculosis diagnosis and its current status. Contributions of different countries to the topic, journal analysis, key paper analysis, and clustering of keywords were used to analyze this topic.
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Affiliation(s)
- Zhiyi Li
- Laboratory Medicine, Nanan Hospital, Nanan, Quanzhou 362300, Fujian, China
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Brankin AE, Fowler PW. Predicting antibiotic resistance in complex protein targets using alchemical free energy methods. J Comput Chem 2022; 43:1771-1782. [PMID: 36054249 PMCID: PMC9545121 DOI: 10.1002/jcc.26979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 07/26/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022]
Abstract
Drug resistant Mycobacterium tuberculosis, which mostly results from single nucleotide polymorphisms in antibiotic target genes, poses a major threat to tuberculosis treatment outcomes. Relative binding free energy (RBFE) calculations can rapidly predict the effects of mutations, but this approach has not been tested on large, complex proteins. We use RBFE calculations to predict the effects of M. tuberculosis RNA polymerase and DNA gyrase mutations on rifampicin and moxifloxacin susceptibility respectively. These mutations encompass a range of amino acid substitutions with known effects and include large steric perturbations and charged moieties. We find that moderate numbers (n = 3-15) of short RBFE calculations can predict resistance in cases where the mutation results in a large change in the binding free energy. We show that the method lacks discrimination in cases with either a small change in energy or that involve charged amino acids, and we investigate how these calculation errors may be decreased.
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Affiliation(s)
- Alice E. Brankin
- Nuffield Department of Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
| | - Philip W. Fowler
- Nuffield Department of Medicine, John Radcliffe HospitalUniversity of OxfordOxfordUK
- National Institute of Health Research Oxford Biomedical Research CentreJohn Radcliffe HospitalOxfordUK
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92
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Zeng Y, Qi P, Zhou Y, Wang Y, Xin Y, Sun Y, Zhang D. Multi pathogenic microorganisms determination using DNA composites-encapsulated DNA silver nanocluster/graphene oxide-based system through rolling cycle amplification. Mikrochim Acta 2022; 189:403. [PMID: 36197586 DOI: 10.1007/s00604-022-05505-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/19/2022] [Indexed: 11/29/2022]
Abstract
A multi pathogenic microorganisms determination method is reported using DNA composites encapsulated DNA silver nanocluster (AgNCs)/graphene oxide (GO)-based system through rolling cycle (RCA) amplification. Firstly, two different RCA-based DNA composites are assembled, coupled with thousands of DNA-stabilized AgNCs probe and ssDNA aptamer specific for two pathogen bacteria targets. GO was then introduced into the system to capture ssDNA aptamer of DNA composites and as a selective fluorescence quencher of DNA/AgNCs. Upon recognizing the target bacteria, ssDNA aptamer part would combine with bacteria and release from the surface of GO. Thus, DNA/AgNCs of RCA-based DNA composites can generate strong fluorescence signal. With the fluorescent report of RCADNA-AgNCs/530 and RCADNA-AgNCs/625, the assay successfully detect Escherichia coli and Staphylococcus aureus at concentrations as low as 38 CFU/mL, and a highly selective and efficient sensing platform was achieved. Therefore, this RCA/DNA-AgNCs/GO-based platform shows excellent application in multi pathogenic microorganisms determination and potential clinic therapy.
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Affiliation(s)
- Yan Zeng
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Peng Qi
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China. .,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
| | - Yanan Zhou
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Yingwen Wang
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Yue Xin
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,University of the Chinese Academy of Sciences, Beijing, 100039, China
| | - Yan Sun
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China.,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China
| | - Dun Zhang
- Key Laboratory of Marine Environmental Corrosion and Bio-Fouling, Institute of Oceanology, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China. .,Open Studio for Marine Corrosion and Protection, Qingdao National Laboratory for Marine Science and Technology, 1 Wenhai Road, Qingdao, 266237, China. .,Center for Ocean Mega-Science, Chinese Academy of Sciences, 7 Nanhai Road, Qingdao, 266071, China.
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93
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Stanley S, Liu Q, Fortune SM. Mycobacterium tuberculosis functional genetic diversity, altered drug sensitivity, and precision medicine. Front Cell Infect Microbiol 2022; 12:1007958. [PMID: 36262182 PMCID: PMC9574059 DOI: 10.3389/fcimb.2022.1007958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 09/14/2022] [Indexed: 01/27/2023] Open
Abstract
In the face of the unrelenting global burden of tuberculosis (TB), antibiotics remain our most effective tools to save lives and control the spread of Mycobacterium tuberculosis (Mtb). However, we confront a dual challenge in our use of antibiotics: simplifying and shortening the TB drug regimen while also limiting the emergence and propagation of antibiotic resistance. This task is now more feasible due to the increasing availability of bacterial genomic data at or near the point of care. These resources create an opportunity to envision how integration of bacterial genetic determinants of antibiotic response into treatment algorithms might transform TB care. Historically, Mtb drug resistance studies focused on mutations in genes encoding antibiotic targets and the resulting increases in the minimal inhibitory concentrations (MICs) above a breakpoint value. But recent progress in elucidating the effects of functional genetic diversity in Mtb has revealed various genetic loci that are associated with drug phenotypes such as low-level MIC increases and tolerance which predict the development of resistance and treatment failure. As a result, we are now poised to advance precision medicine approaches in TB treatment. By incorporating information regarding Mtb genetic characteristics into the development of drug regimens, clinical care which tailors antibiotic treatment to maximize the likelihood of success has come into reach.
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Affiliation(s)
| | | | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA, United States
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94
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Li Y, de Macedo Couto R, Pelissari DM, Costa Alves L, Bartholomay P, Maciel EL, Sanchez M, Castro MC, Cohen T, Menzies NA. Excess tuberculosis cases and deaths following an economic recession in Brazil: an analysis of nationally representative disease registry data. Lancet Glob Health 2022; 10:e1463-e1472. [PMID: 36049488 PMCID: PMC9472578 DOI: 10.1016/s2214-109x(22)00320-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 06/22/2022] [Accepted: 07/05/2022] [Indexed: 01/05/2023]
Abstract
BACKGROUND In 2019, tuberculosis incidence and mortality in Brazil were 46 and 3·3 per 100 000 population, respectively, and the country has reported rising tuberculosis case rates since 2016, following an economic crisis beginning in mid-2014. We aimed to estimate the number of excess tuberculosis cases and deaths during the recession period, and assessed potential causes. METHODS In this multi-level regression modelling study, we extracted tuberculosis case notifications from Brazil's National Notifiable Disease Information System (known as SINAN), and tuberculosis deaths from the Mortality Information System (known as SIM), for all ages. We fitted mixed-effects regression models estimating trends in these outcomes-stratified by sex, age group, and state-during the pre-recession period (Jan 1, 2010-Dec 31, 2014). We calculated excess cases and deaths between Jan 1, 2015, and Dec 31, 2019 (the recession period) as the difference between reported values and a counterfactual of continued pre-recession trends. We examined the relationship between excess cases and possible explanatory factors using ordinary least squares regression. We tested the robustness of our findings to alternative model specifications related to the pre-recession period and criteria for defining tuberculosis deaths. FINDINGS We estimated 22 900 excess tuberculosis cases (95% uncertainty interval 18 100-27 500) during 2015-19. By 2019, reported cases were 12% (10-13) higher than predicted by historical trends. 54% (44-66) of excess cases occurred among 20-29-year-old men. In this group, reported cases in 2019 were 30% (25-36) higher than predicted. Excess cases were positively associated with an increasing fraction of cases among incarcerated individuals (p=0·001) and higher unemployment (p=0·04) at the state level. Estimated excess deaths for 2015-19 were not statistically significant from 0 (-600 [-2100 to 1000]). These results were robust to alternative definitions of the pre-recession period and criteria for defining tuberculosis deaths. INTERPRETATION Tuberculosis cases in Brazil rose substantially in 2015-19 during the recession, largely affecting young men. This increase seems to be linked to increasing tuberculosis transmission among incarcerated populations. Rising tuberculosis case rates threaten tuberculosis control in Brazil, and highlight the threat posed by prison-based tuberculosis transmission. FUNDING US National Institutes of Health. TRANSLATION For the Portuguese translation of the abstract see Supplementary Materials section.
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Affiliation(s)
- Yunfei Li
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA.
| | | | | | | | | | - Ethel L Maciel
- Laboratorio de Epidemiologia, Universidade Federal do Espirito Santo, Vitória, Brazil
| | - Mauro Sanchez
- Department of Tropical Medicine, University of Brasilia, Brasilia, Brazil
| | - Marcia C Castro
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Nicolas A Menzies
- Department of Global Health and Population, Harvard T H Chan School of Public Health, Boston, MA, USA
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95
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Sidiq Z, Hanif M, Dwivedi KK, Chopra KK, Khanna A, Vashishat BK. Effectiveness of Xpert MTB/RIF for the diagnosis of extrapulmonary tuberculosis at various stand-alone laboratories in Delhi. Indian J Tuberc 2022; 69:530-534. [PMID: 36460384 DOI: 10.1016/j.ijtb.2021.08.011] [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: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 06/17/2023]
Abstract
BACKGROUND Globally, EPTB accounts for 15% of the notified incident TB cases. Laboratory confirmation of EPTB is challenging and majority of the cases remain undetected for a longer time. A major breakthrough in the diagnosis of EPTB was the introduction of nucleic acid amplification tests (NAAT). One such test-the Xpert MTB/RIF assay also known as Cartridge based nucleic acid amplification test (CBNAAT) was endorsed by the Scientific and Technical Advisory Board of the WHO for the diagnosis of Tuberculosis. The present study was conduct to evaluate the outcome of various extrapulmonary samples tested in the year 2019 at different standalone NAAT laboratories in Delhi. MATERIALS AND METHODS A total of 20,238 samples consisting mainly of Pus (21.77%), Cerebrospinal fluid (CSF) (14.96%), Biopsies (13.87%), Pleural fluid (10.49%), Lymph node aspirations (FNAC aspirates) (6.75%), synovial fluid (0.54%) and gastric aspirates (26.4%) tested at 22 standalone NAAT laboratories were included in this study. RESULTS Mycobacterium tuberculosis was detected in 3496 samples and resistance to rifampicin was detected in 329 of the samples. The overall yield of all the specimens combined was 17.2%. Highest yield was seen in Lymph nodes aspirates (FNAC) (36.0%), followed by pus (35.4%), tissues (15.7%), synovial fluid (13.5%), Endometrial tissues (10.7%), Pleural fluid (9.5%), Gastric aspirates (9.4%) and CSF (6.5%). The lowest yield was seen in Cavitary fluids (6.2%). CONCLUSION The results of this study highlight the usefulness of Xpert MTB/RIF assay in the diagnosis of EPTB. In particular, this assay proved to be of great utility while testing pus samples, tissue samples and lymph node FNACs.
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Affiliation(s)
- Zeeshan Sidiq
- New Delhi Tuberculosis Centre, Jawaharlal Nehru Marg, Delhi Gate, New Delhi, 110002, India
| | - M Hanif
- New Delhi Tuberculosis Centre, Jawaharlal Nehru Marg, Delhi Gate, New Delhi, 110002, India.
| | - Kaushal Kumar Dwivedi
- New Delhi Tuberculosis Centre, Jawaharlal Nehru Marg, Delhi Gate, New Delhi, 110002, India
| | - Kamal Kishore Chopra
- New Delhi Tuberculosis Centre, Jawaharlal Nehru Marg, Delhi Gate, New Delhi, 110002, India
| | - Ashwani Khanna
- State TB Cell, NTEP Delhi, Health Centre Building, Delhi Government Colony, Gulabi Bagh, Delhi, 110007, India
| | - B K Vashishat
- State TB Cell, NTEP Delhi, Health Centre Building, Delhi Government Colony, Gulabi Bagh, Delhi, 110007, India
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96
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Huang Y, Ai L, Wang X, Sun Z, Wang F. Review and Updates on the Diagnosis of Tuberculosis. J Clin Med 2022; 11:jcm11195826. [PMID: 36233689 PMCID: PMC9570811 DOI: 10.3390/jcm11195826] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022] Open
Abstract
Diagnosis of tuberculosis, and especially the diagnosis of extrapulmonary tuberculosis, still faces challenges in clinical practice. There are several reasons for this. Methods based on the detection of Mycobacterium tuberculosis (Mtb) are insufficiently sensitive, methods based on the detection of Mtb-specific immune responses cannot always differentiate active disease from latent infection, and some of the serological markers of infection with Mtb are insufficiently specific to differentiate tuberculosis from other inflammatory diseases. New tools based on technologies such as flow cytometry, mass spectrometry, high-throughput sequencing, and artificial intelligence have the potential to solve this dilemma. The aim of this review was to provide an updated overview of current efforts to optimize classical diagnostic methods, as well as new molecular and other methodologies, for accurate diagnosis of patients with Mtb infection.
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97
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Gordhan BG, Sewcharran A, Letsoalo M, Chinappa T, Yende-Zuma N, Padayatchi N, Naidoo K, Kana BD. Detection of differentially culturable tubercle bacteria in sputum from drug-resistant tuberculosis patients. Front Cell Infect Microbiol 2022; 12:949370. [PMID: 36159642 PMCID: PMC9500503 DOI: 10.3389/fcimb.2022.949370] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 08/15/2022] [Indexed: 11/13/2022] Open
Abstract
Several studies described the presence of non-replicating, drug-tolerant differentially culturable tubercle bacteria (DCTB) in sputum from patients with active tuberculosis (TB). These organisms are unable to form colonies on agar but can be recovered in liquid media supplemented with culture filtrate as a source of growth factors. Herein, we undertook to investigate the response of DCTB during the treatment of individuals with drug-resistant TB. A cohort of 100 participants diagnosed with rifampicin-resistant TB were enrolled and prospectively followed to monitor response to therapy using routine culture and limiting dilution assays, supplemented with culture filtrate (CF) to quantify DCTB. Fifteen participants were excluded due to contamination, and of the remaining 85 participants, 29, 49, and 7 were infected with rifampicin mono-resistant (RMR), multidrug-resistant (MDR), or extremely drug-resistant (XDR) TB, respectively. Analysis of baseline sputum demonstrated that CF supplementation of limiting dilution assays detected notable amounts of DCTB. Prevalence of DCTB was not influenced by smear status or mycobacterial growth indicator tube time to positivity. CF devoid of resuscitation promoting factors (Rpfs) yielded a greater amount of DCTB in sputum from participants with MDR-TB compared with those with RMR-TB. A similar effect was noted in DCTB assays without CF supplementation, suggesting that CF is dispensable for the detection of DCTB from drug-resistant strains. The HIV status of participants, and CD4 count, did not affect the amount of DCTB recovered. During treatment with second-line drug regimens, the probability of detecting DCTB from sputum specimens in liquid media with or without CF was higher compared with colony forming units, with DCTB detected up to 16 weeks post treatment. Collectively, these data point to differences in the ability of drug-resistant strains to respond to CF and Rpfs. Our findings demonstrate the possible utility of DCTB assays to diagnose and monitor treatment response for drug-resistant TB, particularly in immune compromised individuals with low CD4 counts.
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Affiliation(s)
- Bhavna G. Gordhan
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Astika Sewcharran
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
| | - Marothi Letsoalo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Thilgavathy Chinappa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nonhlanhla Yende-Zuma
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, 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)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, 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)-Centre for the AIDS Programme of Research in South Africa (CAPRISA) Human Immunodeficiency Virus- Tuberculosis (HIV-TB) Pathogenesis and Treatment Research Unit, University of KwaZulu-Natal, Durban, South Africa
| | - Bavesh D. Kana
- Department of Science and Technology/National Research Foundation Centre of Excellence for Biomedical Tuberculosis (TB) Research, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand and the National Health Laboratory Service, Johannesburg, South Africa
- *Correspondence: Bavesh D. Kana,
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98
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Mukhida S, Vyawahare CR, Mirza SB, Gandham NR, Khan S, Kannuri S, Bhaumi S. Role of GeneXpert MTB/RIF assay for the diagnosis of cervical lymph node tuberculosis and rifampicin resistance. Tzu Chi Med J 2022; 34:418-422. [PMID: 36578636 PMCID: PMC9791852 DOI: 10.4103/tcmj.tcmj_86_22] [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: 03/30/2022] [Revised: 06/03/2022] [Accepted: 07/20/2022] [Indexed: 12/31/2022] Open
Abstract
Objectives Tuberculosis (TB) of lymph node (TB lymphadenitis) is one of the most common forms of extrapulmonary TB (EPTB) whose diagnosis is critically challenging. Although new diagnostic methods have been developed, especially in patients without a history of TB, the cervical tuberculous lymphadenitis diagnosis is still elusive. This study assessed the applicability of GeneXpert in early diagnosis of EPTB, especially cervical lymphadenopathy. Materials and Methods The study was conducted in a tertiary care hospital from January 2018 to December 2020 at the department of microbiology. All the samples of cervical lymph node tissue and lymph node aspirate were followed as per the routine protocol for mycobacterial identification. The sample was divided into two parts: one was used for the new molecular-based GeneXpert MTB/RIF assay and the second one was tested by direct and concentrated acid-fast bacilli microscopy by Z-N staining and culture for the detection of MTB. Results Among the 145 samples tested, the GeneXpert detected the DNA of MTB in 89 samples (61.37%), whereas the culture test was positive in 42 (28.93%) specimens. GeneXpert also detected 7 rifampicin resistance cases. GeneXpert sensitivity and specificity results were assessed according to culture results. The sensitivity and specificity of the GeneXpert assay were 85.71% and 48.54%, respectively. Conclusion GeneXpert MTB/RIF should be used in conjunction with clinical presentation and other molecular investigation in nonrespiratory specimens.
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Affiliation(s)
- Sahjid Mukhida
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Chanda R. Vyawahare
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India,Address for correspondence: Dr. Chanda R. Vyawahare, Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pimpri, Pune - 411 018, Maharashtra, India. E-mail:
| | - Shahzad Beg Mirza
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Nageswari R. Gandham
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Sameena Khan
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Sriram Kannuri
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
| | - Shalini Bhaumi
- Department of Microbiology, Dr. D. Y. Patil Medical College, Hospital and Research Centre (D. Y. Patil Vidyapeeth), Pune, Maharashtra, India
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99
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Ullah U, Tahir Z, Qazi O, Mirza S, Cheema MI. Raman spectroscopy and machine learning-based optical probe for tuberculosis diagnosis via sputum. Tuberculosis (Edinb) 2022; 136:102251. [DOI: 10.1016/j.tube.2022.102251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Revised: 08/10/2022] [Accepted: 08/24/2022] [Indexed: 11/26/2022]
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100
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Burger Z, Aung HT, Seifert M, Mar TT, Harris V, Colman RE, Rodwell TC, Aung ST. Contributions of GeneXpert ® to TB diagnosis in Myanmar. Int J Tuberc Lung Dis 2022; 26:875-879. [PMID: 35996278 PMCID: PMC9423018 DOI: 10.5588/ijtld.22.0009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND: Xpert® MTB/RIF, a rapid, molecular TB diagnostic assay, can detect Mycobacterium tuberculosis and rifampin resistance directly from clinical sputum samples in <2 h with high sensitivity and specificity. The added diagnostic value of Xpert over smear microscopy at a national level in Myanmar has not been previously reported.METHODS: We evaluated 339,358 Xpert and demographic records captured from January 2015 to December 2018 as part of the Myanmar National TB Program Data Utilization and Connectivity Project to examine the additional diagnostic yield of Xpert relative to smear for the detection of M. tuberculosis for TB diagnosis in Myanmar, with a focus on people living with HIV (PLHIV) and sample type.RESULTS: Use of Xpert increased TB case detection by 40% compared to smear microscopy results. Among PLHIV, use of Xpert increased TB case detection by almost 100% compared to smear microscopy results.CONCLUSION: Xpert testing identified more patients with TB than smear microscopy alone, particularly in cohorts with significant proportions of PLHIV. The use of Xpert as a screening tool in countries with a high burden of TB could lead to significantly increased diagnosis of TB at a regional and national level.
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Affiliation(s)
- Z Burger
- University of California San Diego, La Jolla, CA, USA
| | - H T Aung
- Clinton Health Access Initiative, Yangon, Myanmar
| | - M Seifert
- University of California San Diego, La Jolla, CA, USA
| | - T T Mar
- Ministry of Health and Sports, Naypyitaw, Myanmar
| | - V Harris
- Foundation for Innovative New Diagnostics, Geneva, Switzerland
| | - R E Colman
- University of California San Diego, La Jolla, CA, USA
| | - T C Rodwell
- University of California San Diego, La Jolla, CA, USA
| | - S T Aung
- Ministry of Health and Sports, Naypyitaw, Myanmar
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