1
|
Singh UB, Singh M, Rodrigues C, Christopher DJ, Mahajan N, Srivastav A, Singh KJ, Kanswal S, Rao MVV, Kazi M, Sawant D, Thangakunam B, Vijay CV, Shankar D, Bhatnagar A, Mohan A, Ahuja V. Multi-centric evaluation of Truenat MTB and MTB-RIF Dx assays for diagnosis of extrapulmonary tuberculosis. Sci Rep 2024; 14:15680. [PMID: 38977729 PMCID: PMC11231208 DOI: 10.1038/s41598-024-64688-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 06/12/2024] [Indexed: 07/10/2024] Open
Abstract
Extra-pulmonary TB (EPTB) is difficult to diagnose due to paucibacillary nature of disease. Current study evaluated accuracy of Truenat MTB and MTB-Rif Dx (TN), for detection of Mycobacterium tuberculosis and resistance to rifampicin. Samples were collected from 2103 treatment naive adults with presumptive EPTB, and tested by smear microscopy, liquid culture (LC) (MGIT-960) and GeneXpert MTB/RIF (GX) (Microbiological Reference Standards, MRS). TN results were compared to MRS and Composite Reference Standards (CRS, Microbiology, histopathology, radiology, clinical features prompting decision to treat, response to treatment). CRS grouped patients into 551 confirmed, 1096 unconfirmed, and 409 as unlikely TB. TN sensitivity and specificity was 73.7% and 90.4% against GX. Against LC, Overall sensitivity of GX was 67.6%, while that of TN was 62.3%. Highest sensitivity by TN was observed in pus samples (89%) and highest specificity (92%) in CSF samples, similar to GX. TN sensitivity was better in fluid and biopsy samples and slightly inferior for lymph node aspirates compared to GX. TN sensitivity for RIF resistance detection was slightly superior to GX. TN and GX results were further compared to Clinical Reference Standards. TN detected 170 TB patients initiated on treatment missed by GX, while GX detected 113 such patients missed by TN. Of 124 samples with RIF resistance discordance between GX and TN, GX reported 103/124 as sensitive, 3/124 as indeterminate and 18 as resistant (13/18 samples had low/very low DNA load) while TN reported RIF resistance indeterminate in 103/111 low/very low DNA load samples. Due to paucibacillary nature of EPTB samples, culture yield was poor and phenotypic drug susceptibility testing failed to resolve the discordance. The study establishes TN at par with GX and can be utilized for quick and accurate diagnosis of EPTB.
Collapse
Affiliation(s)
| | - Manjula Singh
- Division of Epidemiology and Communicable Diseases, ICMR, New Delhi, India
| | | | | | | | | | | | - Sunita Kanswal
- Department of Microbiology, AIIMS, New Delhi, India
- Centralized Core Research Facility, AIIMS, New Delhi, India
| | - M V V Rao
- National Institute of Medical Statistics, ICMR, New Delhi, India
| | - Mubin Kazi
- Department of Microbiology, P D Hinduja Hospital, Mumbai, India
| | - Damini Sawant
- Department of Microbiology, P D Hinduja Hospital, Mumbai, India
| | | | | | - Deepa Shankar
- Department of Pulmonary Medicine, CMC, Vellore, India
| | - Anuj Bhatnagar
- Department of Tuberculosis and Chest Diseases, Rajan Babu Institute for Pulmonary Medicine and Tuberculosis, New Delhi, India
| | - Anant Mohan
- Department of Pulmonary Medicine, AIIMS, New Delhi, India
| | - Vineet Ahuja
- Department of Gastroenterology, AIIMS, New Delhi, India
| |
Collapse
|
2
|
Deb S, Basu J, Choudhary M. An overview of next generation sequencing strategies and genomics tools used for tuberculosis research. J Appl Microbiol 2024; 135:lxae174. [PMID: 39003248 DOI: 10.1093/jambio/lxae174] [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: 04/15/2024] [Revised: 06/07/2024] [Accepted: 07/10/2024] [Indexed: 07/15/2024]
Abstract
Tuberculosis (TB) is a grave public health concern and is considered the foremost contributor to human mortality resulting from infectious disease. Due to the stringent clonality and extremely restricted genomic diversity, conventional methods prove inefficient for in-depth exploration of minor genomic variations and the evolutionary dynamics operating in Mycobacterium tuberculosis (M.tb) populations. Until now, the majority of reviews have primarily focused on delineating the application of whole-genome sequencing (WGS) in predicting antibiotic resistant genes, surveillance of drug resistance strains, and M.tb lineage classifications. Despite the growing use of next generation sequencing (NGS) and WGS analysis in TB research, there are limited studies that provide a comprehensive summary of there role in studying macroevolution, minor genetic variations, assessing mixed TB infections, and tracking transmission networks at an individual level. This highlights the need for systematic effort to fully explore the potential of WGS and its associated tools in advancing our understanding of TB epidemiology and disease transmission. We delve into the recent bioinformatics pipelines and NGS strategies that leverage various genetic features and simultaneous exploration of host-pathogen protein expression profile to decipher the genetic heterogeneity and host-pathogen interaction dynamics of the M.tb infections. This review highlights the potential benefits and limitations of NGS and bioinformatics tools and discusses their role in TB detection and epidemiology. Overall, this review could be a valuable resource for researchers and clinicians interested in NGS-based approaches in TB research.
Collapse
Affiliation(s)
- Sushanta Deb
- Department of Veterinary Microbiology and Pathology, College of Veterinary Medicine, Washington State University, Pullman 99164, WA, United States
- All India Institute of Medical Sciences, New Delhi 110029, India
| | - Jhinuk Basu
- Department of Clinical Immunology and Rheumatology, Kalinga Institute of Medical Sciences (KIMS), KIIT University, Bhubaneswar 751024, India
| | - Megha Choudhary
- All India Institute of Medical Sciences, New Delhi 110029, India
| |
Collapse
|
3
|
Ko SJ, Yoon KH, Lee SH. Performance of the BD MAX MDR-TB assay in a clinical setting and its impact on the clinical course of patients with pulmonary tuberculosis: a retrospective before-after study. JOURNAL OF YEUNGNAM MEDICAL SCIENCE 2024; 41:113-119. [PMID: 38576340 DOI: 10.12701/jyms.2024.00024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Accepted: 03/06/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Missing isoniazid (INH) resistance during tuberculosis (TB) diagnosis can worsen the outcomes of INH-resistant TB. The BD MAX MDR-TB assay (BD MAX) facilitates the rapid detection of TB and INH and rifampin (RIF) resistance; however, data related to its performance in clinical setting remain limited. Moreover, its effect on treatment outcomes has not yet been studied. METHODS We compared the performance of BD MAX for the detection of INH/RIF resistances to that of the line probe assay (LPA) in patients with pulmonary TB (PTB), using the results of a phenotypic drug sensitivity test as a reference standard. The treatment outcomes of patients who used BD MAX were compared with those of patients who did not. RESULTS Of the 83 patients included in the study, the BD MAX was used for an initial PTB diagnosis in 39 patients. The sensitivity of BD MAX for detecting PTB was 79.5%. The sensitivity and specificity of BD MAX for INH resistance were both 100%, whereas these were 50.0% and 95.8%, respectively, for RIF resistance. The sensitivity and specificity of BD MAX were comparable to those of LPA. The BD MAX group had a shorter time interval from specimen request to the initiation of anti-TB drugs (2.0 days vs. 5.5 days, p=0.001). CONCLUSION BD MAX showed comparable performance to conventional tests for detecting PTB and INH/RIF resistances. The implementation of BD MAX as a diagnostic tool for PTB resulted in a shorter turnaround time for the initiation of PTB treatment.
Collapse
Affiliation(s)
- Sung Jun Ko
- Department of Internal Medicine, Wonkwang University Sanbon Hospital, Gunpo, Korea
| | - Kui Hyun Yoon
- Department of Laboratory Medicine, Wonkwang University Sanbon Hospital, Gunpo, Korea
| | - Sang Hee Lee
- Department of Internal Medicine, Wonkwang University Sanbon Hospital, Gunpo, Korea
| |
Collapse
|
4
|
Arbués MD, Rossetti MLR. Evaluation of the GeneXpert MTB/RIF to diagnose tuberculosis in a public health laboratory. Rev Saude Publica 2024; 58:03. [PMID: 38381893 PMCID: PMC10878686 DOI: 10.11606/s1518-8787.2024058005306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Accepted: 03/31/2023] [Indexed: 02/23/2024] Open
Abstract
OBJECTIVES To evaluate the performance of geneXpert MTB/Rif versus conventional methods (bacilloscopy and culture) in the diagnosis of tuberculosis in a Central Public Health Laboratory (LACEN, Tocantins), Northern Brazil. METHODS Retrospective study, with information from 1,973 suspected cases of tuberculosis from patients treated from January 2015 to December 2020. RESULTS From the culture (reference standard), the sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of the geneXpert MTB/Rif were 100%, 97%, 74%, 100%, and 97%, respectively, against 85%, 98%, 80%, 98%, and 97% of bacilloscopy. CONCLUSIONS The geneXpert MTB/Rif performed similarly to culture and better than bacilloscopy. Although positive cases with negative culture should be evaluated with caution, its routine use is important for the early detection of tuberculosis.
Collapse
Affiliation(s)
- Mohanna Damasceno Arbués
- Universidade Luterana do BrasilPrograma de Doutorado em Biologia Molecular e Celular Aplicada à SaúdeCanoasRSBrasilUniversidade Luterana do Brasil. Programa de Doutorado em Biologia Molecular e Celular Aplicada à Saúde. Canoas, RS, Brasil
| | - Maria Lúcia Rosa Rossetti
- Universidade Luterana do BrasilPrograma de Doutorado em Biologia Molecular e Celular Aplicada à SaúdeCanoasRSBrasilUniversidade Luterana do Brasil. Programa de Doutorado em Biologia Molecular e Celular Aplicada à Saúde. Canoas, RS, Brasil
| |
Collapse
|
5
|
Komakech K, Nakiyingi L, Fred A, Achan B, Joloba M, Kirenga BJ, Ssengooba W. Effect of mixed Mycobacterium tuberculosis infection on rapid molecular diagnostics among patients starting MDR-TB treatment in Uganda. BMC Infect Dis 2024; 24:70. [PMID: 38200467 PMCID: PMC10782568 DOI: 10.1186/s12879-023-08968-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 12/30/2023] [Indexed: 01/12/2024] Open
Abstract
BACKGROUND Mixed M. tuberculosis (MTB) infection occurs when one is infected with more than one clonally distinct MTB strain. This form of infection can assist MTB strains to acquire additional mutations, facilitate the spread of drug-resistant strains, and boost the rate of treatment failure. Hence, the presence of mixed MTB infection could affect the performance of some rapid molecular diagnostic tests such as Line Probe Assay (LPA) and GeneXpert MTB/RIF (Xpert) assays. METHODS This was a cross-sectional study that used sputum specimens collected from participants screened for STREAM 2 clinical trial between October 2017 and October 2019. Samples from 62 MTB smear-positive patients and rifampicin-resistant patients from peripheral health facilities were processed for Xpert and LPA as screening tests for eligibility in the trial. From November 2020, processed stored sputum samples were retrieved and genotyped to determine the presence of mixed-MTB strain infection using a standard 24-locus Mycobacterial Interspersed Repetitive Unit-Variable Number Tandem-Repeat (MIRU-VNTR). Samples with at least 20/24 MIRU-VNTR loci amplified were considered for analysis. Agar proportional Drug Susceptibility Test (DST) was performed on culture isolates of samples that had discordant results between LPA and Xpert. The impact of the presence of mixed-MTB strain on Xpert and LPA test interpretation was analyzed. RESULTS A total of 53/62 (85%) samples had analyzable results from MIRU-VNTR. The overall prevalence of mixed-MTB infection was 5/53 (9.4%). The prevalence was highest among male's 3/31 (9.7%) and among middle-aged adults, 4/30 (33.3%). Lineage 4 of MTB contributed 3/5 (60.0%) of the mixed-MTB infection prevalence. Having mixed MTB strain infection increased the odds of false susceptible Xpert test results (OR 7.556, 95% CI 0.88-64.44) but not for LPA. Being HIV-positive (P = 0.04) independently predicted the presence of mixed MTB infection. CONCLUSIONS The presence of mixed-MTB strain infection may affect the performance of the GeneXpert test but not for LPA. For patients with high pre-test probability of rifampicin resistance, an alternative rapid method such as LPA should be considered.
Collapse
Affiliation(s)
- Kevin Komakech
- Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Makerere University, Kampala, Uganda
| | - Lydia Nakiyingi
- Department of Medicine, School of Medicine, Makerere University, Kampala, Uganda
| | - Ashab Fred
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Beatrice Achan
- Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Makerere University, Kampala, Uganda
| | - Moses Joloba
- Department of Immunology and Molecular Biology, Makerere University, Kampala, Uganda
| | - Bruce J Kirenga
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda
| | - Willy Ssengooba
- Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, Makerere University, Kampala, Uganda.
- Makerere University Lung Institute, Makerere University College of Health Sciences, Kampala, Uganda.
| |
Collapse
|
6
|
Walter KS, Cohen T, Mathema B, Colijn C, Sobkowiak B, Comas I, Goig GA, Croda J, Andrews JR. Signatures of transmission in within-host M. tuberculosis variation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.28.23300451. [PMID: 38234741 PMCID: PMC10793532 DOI: 10.1101/2023.12.28.23300451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Background Because M. tuberculosis evolves slowly, transmission clusters often contain multiple individuals with identical consensus genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared M. tuberculosis variation could help overcome this problem. Previous studies have reported M. tuberculosis diversity within infected individuals; however, whether within-host variation improves transmission inferences remains unclear. Methods To evaluate the transmission information present in within-host M. tuberculosis variation, we re-analyzed publicly available sequence data from three household transmission studies, using household membership as a proxy for transmission linkage between donor-recipient pairs. Findings We found moderate levels of minority variation present in M. tuberculosis sequence data from cultured isolates that varied significantly across studies (mean: 6, 7, and 170 minority variants above a 1% minor allele frequency threshold, outside of PE/PPE genes). Isolates from household members shared more minority variants than did isolates from unlinked individuals in the three studies (mean 98 shared minority variants vs. 10; 0.8 vs. 0.2, and 0.7 vs. 0.2, respectively). Shared within-host variation was significantly associated with household membership (OR: 1.51 [1.30,1.71], for one standard deviation increase in shared minority variants). Models that included shared within-host variation improved the accuracy of predicting household membership in all three studies as compared to models without within-host variation (AUC: 0.95 versus 0.92, 0.99 versus 0.95, and 0.93 versus 0.91). Interpretation Within-host M. tuberculosis variation persists through culture and could enhance the resolution of transmission inferences. The substantial differences in minority variation recovered across studies highlights the need to optimize approaches to recover and incorporate within-host variation into automated phylogenetic and transmission inference. Funding NIAID: 5K01AI173385.
Collapse
Affiliation(s)
| | - Ted Cohen
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Barun Mathema
- Department of Epidemiology, Columbia University Mailman School of Public Health; New York, United States
| | - Caroline Colijn
- Department of Mathematics, Simon Fraser University; Burnaby, Canada
| | - Benjamin Sobkowiak
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (CSIC), Valencia, Spain
| | - Galo A Goig
- Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Julio Croda
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, USA
- Federal University of Mato Grosso do Sul - UFMS, Campo Grande, MS, Brazil
- Oswaldo Cruz Foundation Mato Grosso do Sul, Mato Grosso do Sul, Brazil
| | - Jason R Andrews
- Division of Infectious Diseases and Geographic Medicine, Stanford University School of Medicine, Stanford, CA, USA
| |
Collapse
|
7
|
Nie Q, Sun D, Zhu M, Tu S, Chen N, Chen H, Zhou Y, Yao G, Zhang X, Zhang T, Yang C, Tao L. Phenotypic drug susceptibility characterization and clinical outcomes of tuberculosis strains with A-probe mutation by GeneXpert MTB/RIF. BMC Infect Dis 2023; 23:832. [PMID: 38012619 PMCID: PMC10680243 DOI: 10.1186/s12879-023-08509-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 08/03/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND GeneXpert MTB/RIF (Xpert) assay was applied widely to detect Mycobacterium tuberculosis (MTB) and rifampicin resistance. METHODS Retrospectively investigated the association among treatment histories, phenotypic drug susceptibility testing (pDST) results, and clinical outcomes of patients infected with probe A absent mutation isolate confirmed by Xpert. RESULTS 63 patients with only probe A absent mutation and 40 with additional pDST results were analyzed. 24 (60.0%) patients had molecular-phenotypic discordant rifampicin (RIF) susceptibility testing results, including 12 (12/13, 92.3%) new tuberculosis (TB) patients and 12 (12/27, 44.4%) retreated ones. 28 (28/39, 71.8%) retreated patients received first-line treatment regime within two years with failed outcomes. New patients had better treatment outcomes than retreated ones (successful: 83.3% VS. 53.8%; P value = 0.02). The clinical results of RIF-susceptible TB confirmed by pDST were not better than RIF-resistant TB (successful: 62.5% VS. 50.0%; P value = 0.43). INH-resistant TB and INH-susceptible TB had similar treatment outcomes too (successful: 61.5% VS. 50.0%; P value = 0.48). 11 (11/12, 91.7%) new patients treated with the short treatment regimen (STR) had successful outcomes. CONCLUSIONS More than half of mono probe A absent isolates had RIF molecular-phenotypic discordance results, especially in new patients. Probe A mutations were significantly associated with unsuccessful clinical outcomes, whether the pDST results were RIF susceptible or not. STR was the best choice for new patients. TRIAL REGISTRATION retrospectively registered in Wuhan Jinyintan Hospital (No. 2021-KY-16).
Collapse
Affiliation(s)
- Qi Nie
- College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, China
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Dan Sun
- Department of Interventional therapy, Wuhan Pulmonary Hospital, Hubei, China
| | - Muxin Zhu
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Shengjin Tu
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Nanshan Chen
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Hua Chen
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Yong Zhou
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Ge Yao
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Xiaoqing Zhang
- Department of MDR/RR-TB, Wuhan Jinyintan Hospital, Tongji Medical College of Huazhong, Wuhan Research Center for Communicable Disease Diagnosis and Treatment, University of Science and Technology, Hubei Clinical Research Center for Infectious Diseases, Chinese Academy of Medical Sciences, Hubei, China
| | - Tongcun Zhang
- College of Life Sciences and Health, Wuhan University of Science and Technology, Hubei, China.
| | - Chengfeng Yang
- Hubei Provincial Center for Disease Control and Prevention, Hubei, China.
| | - Lixuan Tao
- Emergency Department, Puren Hospital, Wuhan University of science and technology, Hubei, China.
| |
Collapse
|
8
|
Molldrem S, Bagani S, Subrahmanyam V, Permar R, Matsiri O, Caiphus C, Kizito B, Modongo C, Shin SS. Botswana tuberculosis (TB) stakeholders broadly support scaling up next-generation whole genome sequencing: Ethical and practical considerations for Botswana and global health. PLOS GLOBAL PUBLIC HEALTH 2023; 3:e0002479. [PMID: 37967081 PMCID: PMC10651001 DOI: 10.1371/journal.pgph.0002479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/16/2023] [Indexed: 11/17/2023]
Abstract
Global health agencies are increasingly promoting the scale-up of next-generation whole genome sequencing (NG-WGS) of pathogens into infectious disease control programs, including for tuberculosis (TB). However, little is known about how stakeholders in low-to-middle income countries (LMICs) understand the ethics, benefits, and risks of these proposals. We conducted a qualitative study in Greater Gaborone, Botswana to learn how TB stakeholders there viewed a potential scale-up of NG-WGS into Botswana's TB program. We conducted 30 interviews and four deliberative dialogues with TB stakeholders based in Greater Gaborone, the country's largest city and capital. We created and showed participants an animated video series about a fictional family that experienced TB diagnosis, treatment, contact tracing, and data uses that were informed by NG-WGS. We analyzed transcripts using reflexive thematic analysis. We found broad support for the scale-up of TB NG-WGS in Botswana, owing to perceived benefits. Support was qualified with statements about ensuring adequate planning, resource-allocation, community and stakeholder engagement, capacity-building, and assessing ethical norms around publishing data. Our results suggest that scaling up NG-WGS for TB in Botswana would be supported by stakeholders there, contingent upon the government and other entities adequately investing in the initiative. These findings are relevant to other LMICs considering scale-ups of NG-WGS and related technologies for infectious diseases and suggest the need for sustained research into the acceptability of pathogen sequencing in other contexts.
Collapse
Affiliation(s)
- Stephen Molldrem
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | | | - Vishnu Subrahmanyam
- Institute for Bioethics and Health Humanities, University of Texas Medical Branch, Galveston, Texas, United States of America
| | - Rebecca Permar
- Program for Leadership and Character, Office of Academic Advising, Wake Forest University, Winston-Salem, North Carolina, United States of America
| | | | | | | | | | - Sanghyuk S. Shin
- Sue & Bill Gross School of Nursing, University of California, Irvine, California, United States of America
| |
Collapse
|
9
|
Shah I, Bhamre R, Shetty NS. Accuracy of Xpert® MTB/RIF in diagnosing extrapulmonary tuberculosis in Indian children. THE NATIONAL MEDICAL JOURNAL OF INDIA 2023; 35:334-337. [PMID: 37167509 DOI: 10.25259/nmji_35_6_334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Background Diagnosing extrapulmonary tuberculosis (EPTB) can be challenging because of a variety of presentations. We assessed the accuracy of the Xpert MTB/RIF assay in diagnosing EPTB in children. Methods Of the 255 children diagnosed to have tuberculosis (TB) who underwent testing by the Xpert MTB/ RIF assay at the TB clinic from December 2014 to April 2017, 182 had EPTB and were included in the study. The diagnostic accuracy, specificity and sensitivity of the Xpert assay were calculated with Mycobacterium growth indicator tube (MGIT) as a reference standard. Results Lymph node TB was present in 58 (32%) children, 37 (20%) had neurological TB, 36 (20%) had bone TB, 31 (17%) had pleural TB, 15 (8%) had abdominal TB, 2 (1%) had abscess, 2 (1%) had congenital TB and disseminated TB was seen in 1 (0.4%) child. Xpert MTB/RIF assay was positive in 84 (46.2%) patients. The sensitivity and specificity of the Xpert MTB/RIF assay were 72% and 72.04%, respectively. Compared to MGIT, a kappa coefficient of 0.44 shows moderate agreement between the Xpert assay and MGIT. The sensitivity of Xpert MTB/RIF assay in abdominal TB, bone TB, lymph node TB, neurological TB and pleural TB was 50% (15%-85%), 72.7% (15.9%- 86.9%), 80.8% (62.1%-91.5%), 75% (50.5%-90%) and 25% (4.6%-70%), respectively. The specificity of abdominal TB, bone TB, lymph node TB, neurological TB and pleural TB was 83.3% (43.7%-97%), 69.2% (42.4%- 87.3%), 55.2% (37.6%-71.6%), 85% (64%-94.8%) and 82.6% (62.9%-93%), respectively. Forty-seven (26%) patients had drug-resistant TB (DR-TB), of which 15 (8%) were rifampicin-resistant (RR), 2 (1%) were polyresistant, 14 (8%) had multi-DR (MDR), 15 (8%) had pre-extremely DR (XDR) and 1 (1%) had XDR-TB. Of the 15 patients with MDR-TB, Xpert MTB/RIF assay detected only 10 (71%) as RR (p=0.06). Of the 15 pre-XDR cases, Xpert MTB/RIF detected only 8 (53%) as RR (p=0.02). Conclusion Xpert MTB/RIF assay is useful in the diagnosis of EPTB. It shows good concordance with MGIT. However, it may be negative in patients with DR-TB.
Collapse
Affiliation(s)
- Ira Shah
- Department of Paediatrics, B.J. Wadia Hospital for Children, Mumbai, Maharashtra, India
| | - Rasika Bhamre
- Department of Paediatrics, B.J. Wadia Hospital for Children, Mumbai, Maharashtra, India
| | - Naman S Shetty
- Department of Paediatrics, B.J. Wadia Hospital for Children, Mumbai, Maharashtra, India
| |
Collapse
|
10
|
Faye LM, Hosu MC, Oostvogels S, Dippenaar A, Warren RM, Sineke N, Vasaikar S, Apalata T. The Detection of Mutations and Genotyping of Drug-Resistant Mycobacterium tuberculosis Strains Isolated from Patients in the Rural Eastern Cape Province. Infect Dis Rep 2023; 15:403-416. [PMID: 37489395 PMCID: PMC10366782 DOI: 10.3390/idr15040041] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/26/2023] Open
Abstract
Drug-resistant tuberculosis (DR-TB) is still a major public health concern in South Africa. Mutations in M. tuberculosis can cause varying levels of phenotypic resistance to anti-TB medications. There have been no prior studies on gene mutations and the genotyping of DR-TB in the rural Eastern Cape Province; hence, we aimed to identify DR-TB mutations, genetic diversity, and allocated lineages among patients in this area. Using Xpert® MTB/RIF, we assessed the rifampin resistance of sputum samples collected from 1157 patients suspected of having tuberculosis. GenoType MTBDR plus VER 2.0 was used for the detection of mutations causing resistance to anti-TB medications. The next step was to spoligotype 441 isolates. The most prevalent rifampin resistance-conferring mutations were in rpoB codon S531L in INH-resistant strains; the katG gene at codon S315TB and the inhA gene at codon C-15TB had the most mutations; 54.5% and 24.7%, respectively. In addition, 24.6% of strains showed mutations in both the rpoB and inhA genes, while 69.9% of strains showed mutations in both the katG and rpoB genes. Heteroresistance was seen in 17.9% of all cases in the study. According to spoligotyping analysis, Beijing families predominated. Investigation of the evolutionary lineages of M. tuberculosis isolates can be carried out using the information provided by the study's diversity of mutations. In locations wherein these mutations have been discovered, decision-making regarding the standardization of treatment regimens or individualized treatment may be aided by the detection frequency of rpoB, katG, and inhA mutations in various study areas.
Collapse
Affiliation(s)
- Lindiwe M Faye
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Mojisola C Hosu
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Selien Oostvogels
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Anzaan Dippenaar
- Family Medicine and Population Health (FAMPOP), Faculty of Medicine and Health Sciences, University of Antwerp, BE-2000 Antwerp, Belgium
| | - Robin M Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council, Parowvallei, Cape Town 7505, South Africa
- Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 7505, South Africa
| | - Ncomeka Sineke
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Sandeep Vasaikar
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| | - Teke Apalata
- Department of Laboratory Medicine and Pathology, Walter Sisulu University, Mthatha 5099, South Africa
- National Health Laboratory Services (NHLS), Mthatha 5099, South Africa
| |
Collapse
|
11
|
Chen Y, Jiang Q, Liu Q, Gan M, Takiff HE, Gao Q. Whole-Genome Sequencing Exhibits Better Diagnostic Performance than Variable-Number Tandem Repeats for Identifying Mixed Infections of Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0357022. [PMID: 37098911 PMCID: PMC10269500 DOI: 10.1128/spectrum.03570-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 04/10/2023] [Indexed: 04/27/2023] Open
Abstract
Mixed infections of Mycobacterium tuberculosis, defined as the coexistence of multiple genetically distinct strains within a single host, have been associated with unfavorable treatment outcomes. Different methods have been used to detect mixed infections, but their performances have not been carefully evaluated. To compare the sensitivity of whole-genome sequencing (WGS) and variable-number tandem repeats (VNTR) typing to detect mixed infections, we prepared 10 artificial samples composed of DNA mixtures from two strains in different proportions and retrospectively collected 1,084 clinical isolates. The limit of detection (LOD) for the presence of a minor strain was 5% for both WGS and VNTR typing. The overall clinical detection rate of mixed infections was 3.7% (40/1,084) for the two methods combined, WGS identified 37/1,084 (3.4%), and VNTR typing identified 14/1,084 (1.3%), including 11 also identified by WGS. Multivariate analysis demonstrated that retreatment patients had a 2.7 times (95% confidence interval [CI], 1.2 to 6.0) higher risk of mixed infections than new cases. Collectively, WGS is a more reliable tool to identify mixed infections than VNTR typing, and mixed infections are more common in retreated patients. IMPORTANCE Mixed infections of M. tuberculosis have the potential to render treatment regimens ineffective and affect the transmission dynamics of the disease. VNTR typing, currently the most widely used method for the detection of mixed infections, detects mixed infections only by interrogating a small fraction of the M. tuberculosis genome, which necessarily limits sensitivity. With the introduction of WGS, it became possible to study the entire genome, but no quantitative comparison has yet been undertaken. Our systematic comparison of the ability of WGS and VNTR typing to detect mixed infections, using both artificial samples and clinical isolates, revealed the superior performance of WGS at a high sequencing depth (~100×) and found that mixed infections are more common in patients being retreated for tuberculosis (TB) in the populations studied. This provides valuable information for the application of WGS in the detection of mixed infections and the implications of mixed infections for tuberculosis control.
Collapse
Affiliation(s)
- Yiwang Chen
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Qi Jiang
- School of Public Health, Public Health Research Institute of Renmin Hospital, Wuhan University, Wuhan, China
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Mingyu Gan
- Molecular Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Howard E. Takiff
- Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas, Venezuela
| | - Qian Gao
- National Clinical Research Center for Infectious Diseases, Shenzhen Third People’s Hospital, Shenzhen, Guangdong, China
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| |
Collapse
|
12
|
Huang W, Lee MKT, Sin ATK, Nazari RS, Chua SY, Sng LH. Evaluation of Xpert MTB/RIF ultra assay for detection of Mycobacterium tuberculosis and rifampicin resistance. Pathology 2023:S0031-3025(23)00116-2. [PMID: 37268484 DOI: 10.1016/j.pathol.2023.03.002] [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: 09/13/2022] [Revised: 01/05/2023] [Accepted: 03/14/2023] [Indexed: 06/04/2023]
Abstract
Tuberculosis (TB) is a public health challenge globally, and molecular testing is recommended to expedite diagnosis. Concerns that Xpert MTB/RIF assay (Xpert) may be less sensitive when testing paucibacillary samples led to the development of the Xpert MTB/RIF Ultra assay (Ultra). We evaluated the performance of Ultra against Xpert on clinical samples sent to the national reference laboratory in Singapore. In total, 149 samples collected between January 2019 and November 2020 were analysed. Mycobacterium tuberculosis complex (MTBC) was isolated from 55 cultures. Using culture as the reference standard, Ultra demonstrated higher sensitivity (96.4% vs 85.5%) and marginally lower specificity (88.3% vs 89.4%) compared to Xpert in the full cohort. When considering only paucibacillary specimens such as extrapulmonary and smear-negative samples, similar results were obtained. Reclassifying Ultra trace results (low levels of MTB are detected but no rifampicin resistant result is detected) as negative in the full cohort led to a decrease in sensitivity by 10.9% and a marginal increase in specificity by 1.1%. In instances of low bacillary load, Ultra also identified rifampicin resistance more accurately than Xpert, when corroborated against other methods such as broth microdilution, line probe assay and whole genome sequencing (WGS). One isolate tested rifampicin-resistant using Xpert and Ultra, but was phenotypically susceptible and WGS demonstrated the presence of the silent mutation Thr444Thr. Ultra is more sensitive than Xpert in the detection of MTBC and rifampicin resistance in our local setting. Nevertheless, the results of molecular testing should still be correlated with phenotypic studies.
Collapse
Affiliation(s)
- Wenjie Huang
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore.
| | - Melody Kee Tai Lee
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Amanda Teo Kai Sin
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | | | - Syn Yu Chua
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| | - Li-Hwei Sng
- Central Tuberculosis Laboratory, Department of Microbiology, Singapore General Hospital, Singapore
| |
Collapse
|
13
|
Owusu W, van Vliet AHM, Riddell NE, Stewart G, Akwani WC, Aryeetey S, Arthur RA, Sylverken AA, Hingley-Wilson SM. A multiplex PCR assay for the differentiation of Mycobacterium tuberculosis complex reveals high rates of mixed-lineage tuberculosis infections among patients in Ghana. Front Cell Infect Microbiol 2023; 13:1125079. [PMID: 37077529 PMCID: PMC10108843 DOI: 10.3389/fcimb.2023.1125079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 03/17/2023] [Indexed: 04/05/2023] Open
Abstract
In low-resource settings with high tuberculosis (TB) burdens, lack of rapid diagnostic methods for detection and differentiation of Mycobacterium tuberculosis complex (MTBC) is a major challenge affecting TB management. This study utilized comparative genomic analyses of MTBC lineages; M. tuberculosis, M. africanum Lineages 5/6 and M. bovis to identify lineage-specific genes. Primers were designed for the development of a Multiplex PCR assay which was successful in differentiating the MTBC lineages. There was no cross-reaction with other respiratory pathogens tested. Validation of the assay using clinical samples was performed with sputum DNA extracts from 341 clinically confirmed active TB patients. It was observed that 24.9% of cases were caused by M. tuberculosis, while M. africanum L5 & L6 reported 9.0% and 14.4%, respectively. M. bovis infection was the least frequently detected lineage with 1.8%. Also, 27.0% and 17.0% of the cases were PCR negative and unspeciated, respectively. However, mixed-lineage TB infections were recorded at a surprising 5.9%. This multiplex PCR assay will allow speciation of MTBC lineages in low-resource regions, providing rapid differentiation of TB infections to select appropriate medication at the earliest possible time point. It will also be useful in epidemiological surveillance studies providing reliable information on the prevalence of TB lineages as well as identifying difficult to treat cases of mixed-lineage tuberculosis infections.
Collapse
Affiliation(s)
- Wellington Owusu
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Arnoud H. M. van Vliet
- Department of Comparative Biomedical Sciences, School of Veterinary Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Natalie E. Riddell
- Department of Biochemical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, United Kingdom
| | - Graham Stewart
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Winifred C. Akwani
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| | - Sherihane Aryeetey
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Rejoice Agyeiwaa Arthur
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research in Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
- Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Suzanne M. Hingley-Wilson
- Department of Microbial Sciences, School of Biosciences, Faculty of Health and Medical Sciences, University of Surrey, Guildford, United Kingdom
| |
Collapse
|
14
|
Karuniawati A, Burhan E, Koendhori EB, Sari D, Haryanto B, Nuryastuti T, Gayatri AAAY, Bahrun U, Kusumawati RL, Sugiyono RI, Susanto NH, Diana A, Kosasih H, Naysilla AM, Lokida D, Neal A, Siddiqui S, Lau CY, Karyana M. Performance of Xpert MTB/RIF and sputum microscopy compared to sputum culture for diagnosis of tuberculosis in seven hospitals in Indonesia. Front Med (Lausanne) 2023; 9:909198. [PMID: 36743681 PMCID: PMC9896521 DOI: 10.3389/fmed.2022.909198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 12/07/2022] [Indexed: 01/21/2023] Open
Abstract
Introduction Tuberculosis (TB) is a major public health concern in Indonesia, where the incidence was 301 cases per 100,000 inhabitants in 2020 and the prevalence of multi-drug resistant (MDR) TB is increasing. Diagnostic testing approaches vary across Indonesia due to resource limitations. Acid-fast bacilli (AFB) smear is widely used, though Xpert MTB/RIF has been the preferred assay for detecting TB and rifampicin resistance since 2012 due to higher sensitivity and ability to rapidly identify rifampicin resistance. However, <1,000 Xpert instruments were available in Indonesia as of 2020 and the Xpert supply chain has suffered interruptions. Methods We compared the performance of Xpert MTB/RIF and AFB smear to facilitate optimization of TB case identification. We analyzed baseline data from a cohort study of adults with pulmonary TB conducted at seven hospitals across Indonesia. We evaluated sensitivity and specificity of AFB smear and Xpert MTB/RIF using Mycobacterium tuberculosis (Mtb) culture as the gold standard, factors associated with assay results, and consistency of Xpert MTB/RIF with drug susceptibility test (DST) in detecting rifampicin resistance. Results Sensitivity of AFB smear was significantly lower than Xpert MTB/RIF (86.2 vs. 97.4%, p-value <0.001), but specificity was significantly better (86.7 vs. 73.3%, p-value <0.001). Performance varied by hospital. Positivity rate for AFB smear and Mtb culture was higher in subjects with pulmonary cavities and in morning sputum samples. Consistency of Xpert MTB/RIF with DST was lower in those with rifampicin- sensitive TB by DST. Discussion Additional evaluation using sputa from primary and secondary Indonesian health centers will increase the generalizability of the assessment of AFB smear and Xpert MTB/RIF performance, and better inform health policy. Clinical trial registration [https://clinicaltrials.gov/], identifier [NCT027 58236].
Collapse
Affiliation(s)
- Anis Karuniawati
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Dr. Cipto Mangunkusumo Hospital, Jakarta, Indonesia
| | - Erlina Burhan
- Department of Pulmonary and Respiratory Medicine, Faculty of Medicine, Universitas Indonesia, Persahabatan Hospital, Jakarta, Indonesia
| | - Eko Budi Koendhori
- Department of Medical Microbiology, Faculty of Medicine, Universitas Airlangga, Dr. Soetomo Hospital, Surabaya, Indonesia
| | - Desvita Sari
- Department of Microbiology, Faculty of Medicine, Universitas Diponegoro, Dr. Kariadi Hospital, Semarang, Indonesia
| | - Budi Haryanto
- Microbiology Unit, Persahabatan Hospital, Jakarta, Indonesia
| | - Titik Nuryastuti
- Department of Microbiology, Faculty of Medicine, Public Health and Nursing, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - A. A. A. Yuli Gayatri
- Department of Internal Medicine, Faculty of Medicine, Universitas Udayana, Prof. IGNG. Ngoerah General Hospital, Bali, Indonesia
| | - Uleng Bahrun
- Department of Clinical Pathology, Faculty of Medicine, University of Hasanuddin, Dr. Wahidin Sudirohusodo Hospital, Makassar, Indonesia
| | - R. Lia Kusumawati
- Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara, H. Adam Malik General Hospital, Medan, Indonesia
| | - Retna Indah Sugiyono
- Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia
| | - Nugroho Harry Susanto
- Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia
| | - Aly Diana
- Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia,Department of Public Health, Faculty of Medicine, Universitas Padjadjaran, Sumedang, Indonesia
| | - Herman Kosasih
- Indonesia Research Partnership on Infectious Disease (INA-RESPOND), Jakarta, Indonesia,*Correspondence: Herman Kosasih,
| | | | - Dewi Lokida
- Department of Clinical Pathology, Tangerang District Hospital, Tangerang, Indonesia
| | - Aaron Neal
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Sophia Siddiqui
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, United States
| | - Chuen-Yen Lau
- HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
| | - Muhammad Karyana
- National Institute of Health Research and Development, Ministry of Health, Republic of Indonesia, Jakarta, Indonesia
| |
Collapse
|
15
|
Khan AS, Phelan JE, Khan MT, Ali S, Qasim M, Mohammad N, Napier G, Ahmad S, Alam J, Khattak B, Campino S, Clark TG, Khan TA. Genetic mutations underlying isoniazid-resistant Mycobacterium tuberculosis in Khyber Pakhtunkhwa, Pakistan. Tuberculosis (Edinb) 2023; 138:102286. [PMID: 36463715 DOI: 10.1016/j.tube.2022.102286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 11/16/2022] [Accepted: 11/21/2022] [Indexed: 11/30/2022]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis, is a major public health issue in Pakistan. Isoniazid is a first-line pro-drug that requires activation through an enzyme called catalase peroxidase, but is subject to widespread resistance, driven by mutations in katG and inhA genes and other loci with compensatory effects (e.g., ahpC). Here, we used whole genome sequencing data from 51 M. tuberculosis isolates collected from Khyber Pakhtunkhwa province (years 2016-2019; all isoniazid phenotypically resistant) to investigate the genetic diversity of mutations in isoniazid candidate genes. The most common mutations underlying resistance were katG S315T (37/51), fabG1 -15C>T (13/51; inhA promoter), and inhA -154G>A (7/51). Other less common mutations (n < 5) were also identified in katG (R128Q, V1A, W505*, A109T, D311G) and candidate compensatory genes ahpC (-54C>T, -51G>A) and oxyS (M249T). Using DynaMut2 software, the mutants exhibited various degrees of stability and flexibility on protein structures, with some katG mutations leading to a decrease in KatG protein flexibility. Overall, the characterisation of circulating isoniazid resistant-linked mutations will assist in drug resistant TB management and control activities in a highly endemic area of Pakistan.
Collapse
Affiliation(s)
- Anwar Sheed Khan
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan; Provincial Tuberculosis Reference Laboratory, Hayatabad Medical Complex, Peshawar, Khyber Pakhtunkhwa, Pakistan.
| | - Jody E Phelan
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, 58810, Pakistan.
| | - Sajid Ali
- Department of Microbiology, Bacha Khan University Charsadda, Pakistan.
| | - Muhammad Qasim
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan.
| | - Noor Mohammad
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan; Provincial Tuberculosis Reference Laboratory, Hayatabad Medical Complex, Peshawar, Khyber Pakhtunkhwa, Pakistan.
| | - Gary Napier
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Sajjad Ahmad
- Institute of Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
| | - Jamshed Alam
- Peshawar Institute of Cardiology, Peshawar, Khyber Pakhtunkhwa, Pakistan.
| | - Baharullah Khattak
- Department of Microbiology, Kohat University of Science and Technology, Kohat, Pakistan.
| | - Susana Campino
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK.
| | - Taane G Clark
- Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Faculty of Epidemiology & Population Health, London School of Hygiene & Tropical Medicine, London, UK.
| | - Taj Ali Khan
- Institute of Institute of Pathology and Diagnostic Medicine, Khyber Medical University, Peshawar, Khyber Pakhtunkhwa, Pakistan.
| |
Collapse
|
16
|
Wu SH, Xiao YX, Hsiao HC, Jou R. Development and Assessment of a Novel Whole-Gene-Based Targeted Next-Generation Sequencing Assay for Detecting the Susceptibility of Mycobacterium tuberculosis to 14 Drugs. Microbiol Spectr 2022; 10:e0260522. [PMID: 36255328 PMCID: PMC9769975 DOI: 10.1128/spectrum.02605-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 09/23/2022] [Indexed: 01/07/2023] Open
Abstract
Targeted next-generation sequencing (tNGS) has emerged as an alternative method for detecting drug-resistant tuberculosis (DR-TB). To provide comprehensive drug susceptibility information and to address mutations missed by available commercial molecular diagnostics, we developed and evaluated a tNGS panel with 22 whole-gene targets using the Ion Torrent platform to predict drug resistance to 14 drugs, namely, rifampicin (RIF), isoniazid (INH), ethambutol (EMB), pyrazinamide (PZA), moxifloxacin (MFX), levofloxacin (LFX), amikacin (AMK), capreomycin (CM), kanamycin (KM), streptomycin (SM), bedaquiline (BDQ), clofazimine (CFZ), linezolid (LZD), and delamanid (DLM). We selected 50 and 35 Mycobacterium tuberculosis isolates with various DR profiles as the training set and the challenge set, respectively. Comparative variant analyses of the DR genes were performed using Sanger sequencing and whole-genome sequencing (WGS). Phenotypic drug susceptibility testing (pDST) results were used as gold standards. Regarding the limit of detection, the tNGS assay detected 2.9 to 3.8% minority variants in 4% mutant mixtures. The sensitivity and specificity of tNGS were 97.0% (95% confidence interval [CI] = 93.1 to 98.7%) and 99.1% (95% CI = 97.7 to 99.7%), respectively. The concordance of tNGS with pDST was 98.5% (95% CI = 97.2 to 99.2%), which was comparable to that of WGS (98.7%, 95% CI = 97.4 to 99.3%) and better than that of Sanger sequencing (96.9%, 95% CI = 95.3 to 98.0%). The agreement between tNGS and pDST was almost perfect for RIF, INH, EMB, MFX, LFX, AMK, CM, KM, SM, BDQ, and LZD (kappa value = 0.807 to 1.000) and substantial for PZA (kappa value = 0.791). Our customized novel whole-gene-based tNGS panel is highly consistent with pDST and WGS for comprehensive and accurate prediction of drug resistance in a strengthened and streamlined DR-TB laboratory program. IMPORTANCE We developed and validated a tNGS assay that was the first to target 22 whole genes instead of regions of drug resistance genes and comprehensively detected susceptibility to 14 anti-TB drugs, with great flexibility to include new or repurposed drugs. Notably, we demonstrated that our custom-designed Ion AmpliSeq TB research panel platform had high concordance with pDST and could significantly reduce turnaround time (by approximately 70%) to meet a clinically actionable time frame. Our tNGS assay is a promising DST solution for providing needed clinical information for precision medicine-guided therapies for DR-TB and allows the rollout of active pharmacovigilance.
Collapse
Affiliation(s)
- Sheng-Han Wu
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yu-Xin Xiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Hseuh-Chien Hsiao
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ruwen Jou
- Tuberculosis Research Center, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
- Reference Laboratory of Mycobacteriology, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| |
Collapse
|
17
|
Narang A, Marras SAE, Kurepina N, Chauhan V, Shashkina E, Kreiswirth B, Varma-Basil M, Vinnard C, Subbian S. Ultrasensitive Detection of Multidrug-Resistant Mycobacterium tuberculosis Using SuperSelective Primer-Based Real-Time PCR Assays. Int J Mol Sci 2022; 23:ijms232415752. [PMID: 36555395 PMCID: PMC9779475 DOI: 10.3390/ijms232415752] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/14/2022] Open
Abstract
The emergence of drug-resistant tuberculosis is a significant global health issue. The presence of heteroresistant Mycobacterium tuberculosis is critical to developing fully drug-resistant tuberculosis cases. The currently available molecular techniques may detect one copy of mutant bacterial genomic DNA in the presence of about 1-1000 copies of wild-type M. tuberculosis DNA. To improve the limit of heteroresistance detection, we developed SuperSelective primer-based real-time PCR assays, which, by their unique assay design, enable selective and exponential amplification of selected point mutations in the presence of abundant wild-type DNA. We designed SuperSelective primers to detect genetic mutations associated with M. tuberculosis resistance to the anti-tuberculosis drugs isoniazid and rifampin. We evaluated the efficiency of our assay in detecting heteroresistant M. tuberculosis strains using genomic DNA isolated from laboratory strains and clinical isolates from the sputum of tuberculosis patients. Results show that our assays detected heteroresistant mutations with a specificity of 100% in a background of up to 104 copies of wild-type M. tuberculosis genomic DNA, corresponding to a detection limit of 0.01%. Therefore, the SuperSelective primer-based RT-PCR assay is an ultrasensitive tool that can efficiently diagnose heteroresistant tuberculosis in clinical specimens and contributes to understanding the drug resistance mechanisms. This approach can improve the management of antimicrobial resistance in tuberculosis and other infectious diseases.
Collapse
Affiliation(s)
- Anshika Narang
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
| | - Salvatore A. E. Marras
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
| | | | - Varsha Chauhan
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | | | - Mandira Varma-Basil
- Department of Microbiology, Vallabhbhai Patel Chest Institute, University of Delhi, Delhi 110021, India
| | | | - Selvakumar Subbian
- Public Health Research Institute, New Jersey Medical School, Rutgers University, Newark, NJ 07103, USA
- Correspondence: (S.A.E.M.); (S.S.)
| |
Collapse
|
18
|
Zheng Y, Xia H, Bao X, Zhao B, He P, Zhao Y. Highly Sensitive Detection of Isoniazid Heteroresistance in Mycobacterium Tuberculosis by Droplet Digital PCR. Infect Drug Resist 2022; 15:6245-6254. [PMID: 36329987 PMCID: PMC9624153 DOI: 10.2147/idr.s381097] [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: 07/18/2022] [Accepted: 10/13/2022] [Indexed: 11/05/2022] Open
Abstract
Purpose The drug resistance of Mycobacterium tuberculosis constitutes a major public health threat. Existing approaches make it challenging to detect low levels of drug-resistant TB, also known as heteroresistance (HR), in a population. The recently found droplet digital PCR (ddPCR) is a sensitive method for determining the precise amount of nucleic acid in a sample. We used ddPCR to test the Mycobacterium tuberculosis heteroresistance because it delivers more exact quantitative data without the need for a reference curve. Patients and Methods A TaqMan-MGB probe mutation detection assay was developed in order to determine the mutant and wild-type sequences of the isoniazid resistance katG (315) gene. We produced heteroresistant MTB combinations, which were subsequently identified by ddPCR, qPCR, and MeltPro/INH. In addition, 21 clinical sputum samples with positive smears were used to validate each method’s capacity to determine HR in sputum. Results We discovered that ddPCR can detect mutant sequences in as few as 0.01% of a combination. DeepMelt TB/INH, which is less sensitive in comparison, cannot detect HR with high resolution and requires a mutation rate of 50% to identify. qPCR likewise has a high resolution of 0.02%, but unlike ddPCR, it cannot determine the exact number of mutations. Our assay is applicable to sputum as well. ddPCR found a katG 315 substitution in two sputums with extremely low values of HR (0.26% and 0.14%). In 21 samples of clinical sputum, the HR prevalence of INH was 9.5%. Conclusion This work demonstrates that a well-designed ddPCR HR detection test can detect low levels of HR with high accuracy and consistency and gives new information for the clinical diagnosis of drug resistance.
Collapse
Affiliation(s)
- Yang Zheng
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Hui Xia
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Xundi Bao
- Laboratory Department, Anhui Chest Hospital, Anhui, People’s Republic of China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Ping He
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China,Correspondence: Yanlin Zhao, National Center for TB Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Chang Bai Road, Changping District,Beijing, 102206, People’s Republic of China, Tel +86-10-58900517, Fax +86-10-58900556, Email
| |
Collapse
|
19
|
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.
Collapse
Affiliation(s)
- Zhiyi Li
- Laboratory Medicine, Nanan Hospital, Nanan, Quanzhou 362300, Fujian, China
| |
Collapse
|
20
|
Identification of S315T mutation in katG gene using probe-free exclusive mismatch primers for a rapid diagnosis of isoniazid-resistant Mycobacterium tuberculosis by real-time loop-mediated isothermal amplification. Microchem J 2022. [DOI: 10.1016/j.microc.2021.107108] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
|
21
|
Rimal R, Shrestha D, Pyakurel S, Poudel R, Shrestha P, Rai KR, Ghimire GR, Rai G, Rai SK. Diagnostic performance of GeneXpert MTB/RIF in detecting MTB in smear-negative presumptive TB patients. BMC Infect Dis 2022; 22:321. [PMID: 35365080 PMCID: PMC8973748 DOI: 10.1186/s12879-022-07287-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 03/20/2022] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a leading cause of morbidity and mortality worldwide. Control of TB is lingering by the lack of diagnostic tests that are simple, rapid, yet accurate. Thus, smear-negative pulmonary TB often misses the diagnosis. The study evaluated the performance of GeneXpert MTB/RIF assay for the detection of Mycobacterium tuberculosis (MTB). METHODS The study was carried out from June to December 2016 in Nepal Tuberculosis Center, Bhaktapur, Nepal. A total of 173 sputum samples were collected and processed by microscopy [Auramine-O staining and Ziehl-Neelsen (ZN) staining], followed by GeneXpert MTB/RIF assay and culture in Lowenstein-Jensen (LJ) medium. RESULTS Of 173 sputum samples, 162 (93.6%) were smear-negative. Of 162 smear-negative sputum samples, 35 (21.6%) were confirmed to have MTB by culture, and 31 (19.1%) by GeneXpert MTB/RIF assay. Of 31 GeneXpert-positive samples, 25 (80.6%) were susceptible, 4 (12.9%) were resistant, and 2 (6.45%) were intermediate to rifampicin. The sensitivity, specificity, positive predictive value, and negative predictive value of GeneXpert MTB/RIF assay for smear-negative sputum samples were 74.3%, 96.6%, 86.7%, and 92%, respectively. The GeneXpert MTB/RIF has a substantial diagnostic agreement of 90.91% with culture (Cohen's Kappa coefficient = 0.73). CONCLUSION The diagnostic performance of GeneXpert MTB/RIF assay was almost on par with culture, and thus can be relied upon for MTB detection in smear-negative sputum samples.
Collapse
Affiliation(s)
- Raksha Rimal
- Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Dhiraj Shrestha
- Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Susil Pyakurel
- Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal.
| | - Rashmi Poudel
- Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Prasha Shrestha
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kul Raj Rai
- Key Laboratory of Fujian-Taiwan Animal Pathogen Biology, College of Animal Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | | | - Ganesh Rai
- Department of Microbiology, Shi-Gan International College of Science and Technology, Kathmandu, Nepal
| | - Shiba Kumar Rai
- Department of Microbiology, Nepal Medical College and Teaching Hospital, Kathmandu, Nepal
| |
Collapse
|
22
|
Peñata A, Pérez C, Castaño T, Bustamante J, Ospina S. Distribución y frecuencia de potenciales mutaciones asociadas con la resistencia a rifampicina en el gen rpoB de Mycobacterium tuberculosis detectadas mediante un método molecular automatizado. REVISTA DE LA FACULTAD DE MEDICINA 2022. [DOI: 10.15446/revfacmed.v71n1.98079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Introducción. La tuberculosis continúa siendo un problema de salud pública agravado por la resistencia de Mycobacterium tuberculosis a los fármacos. Más del 95% de cepas de M. tuberculosis resistentes a rifampicina (RIF) poseen mutaciones en una región del gen rpoB. Xpert® MTB/RIF es un sistema de biología molecular que, mediante 5 sondas (A, B, C, D, E) que conforman las secuencias del gen rpoB, permite identificar mutaciones en la región determinante de resistencia a la RIF de este gen.
Objetivo. Describir la distribución y frecuencia de potenciales mutaciones asociadas con la resistencia a RIF en el gen rpoB de M. tuberculosis detectadas en muestras pulmonares y extrapulmonares usando el método Xpert® MTB/RIF.
Materiales y métodos. Estudio retrospectivo. Se analizaron 66 muestras positivas para M. tuberculosis resistente a RIF procesadas por el sistema GeneXpert MTB/RIF entre enero de 2011 y julio de 2019 en un hospital universitario de Medellín, Colombia. De acuerdo con el software Dx System del instrumento GenXpert, se determinó que había una potencial mutación y resistencia a RIF, si la sondas no se unían a su secuencia complementaria natural o si se presentaba un atraso en la unión (delta CT >4) en relación con las otras sondas por presencia de una secuencia anormal. Los datos se analizaron mediante estadística descriptiva.
Resultados. De las 66 muestras (48 pulmonares y 18 extrapulmonares), el 63.64% eran de hombres y la edad media de los participantes fue 39.60 ± 17.69 años. La frecuencia y distribución de mutaciones fue la siguiente: sonda E: 38 mutaciones (57.58%); B: 16 (24.24%), D: 8 (12.12%); A: 3 (4.54%) y D&E: 1 (1.52%). No se detectó ninguna mutación en la sonda C.
Conclusiones. Las mutaciones asociadas a la resistencia a RIF en el gen rpoB de M. tuberculosis detectadas por el método Xpert® MTB/RIF se encontraron principalmente en la sonda E (codones 529–533). Por el contrario, en la sonda C no se no se detectó ninguna mutación.
Collapse
|
23
|
Fan Y, Chen J, Liu M, Xu X, Zhang Y, Yue P, Cao W, Ji Z, Su X, Wen S, Kong J, Zhou G, Li B, Dong Y, Liu A, Bao F. Application of Droplet Digital PCR to Detection of Mycobacterium tuberculosis and Mycobacterium leprae Infections: A Narrative Review. Infect Drug Resist 2022; 15:1067-1076. [PMID: 35313727 PMCID: PMC8934166 DOI: 10.2147/idr.s349607] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 01/25/2022] [Indexed: 12/15/2022] Open
Abstract
Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis (MTB) infection, which has seriously endangered human health for many years. With the emergence of multidrug-resistant and extensively drug-resistant MTB, the prevention and treatment of TB has become a pressing need. Early diagnosis, drug resistance monitoring, and control of disease transmission are critical aspects in the prevention and treatment of TB. However, the currently available diagnostic technologies and drug sensitivity tests are time consuming, and thus, it is difficult to achieve the goal of early diagnosis and detection drug sensitivity, which results in limited control of disease transmission. The development of molecular testing technology has gradually achieved the vision of rapid and accurate diagnosis of TB. Droplet digital PCR (ddPCR) is an excellent nucleic acid quantification method with high sensitivity and no need for a calibration curve. Herein, we review the application of ddPCR in TB diagnosis and drug resistance detection and transmission monitoring.
Collapse
Affiliation(s)
- Yuxin Fan
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jingjing Chen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Meixiao Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xin Xu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yu Zhang
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Peng Yue
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Wenjing Cao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Zhenhua Ji
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Xuan Su
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Shiyuan Wen
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Jing Kong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Guozhong Zhou
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Bingxue Li
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Yan Dong
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
| | - Aihua Liu
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Department of Biochemistry and Molecular Biology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Correspondence: Aihua Liu; Fukai Bao, The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China, Email ;
| | - Fukai Bao
- The Institute for Tropical Medicine, Faculty of Basic Medical Sciences, Kunming Medical University, Kunming, 650500, People’s Republic of China
- Department of Microbiology and Immunology, Kunming Medical University, Kunming, 650030, People’s Republic of China
- Yunnan Province Key Laboratory of Children’s Major Diseases Research, The Affiliated Children Hospital, Kunming Medical University, Kunming, 650030, People’s Republic of China
| |
Collapse
|
24
|
Xia H, Song Y, Zheng Y, Wang S, Zhao B, He W, Liu D, Ou X, Zhou Y, Zhao Y. Detection of Mycobacterium tuberculosis Rifampicin Resistance Conferred by Borderline rpoB Mutations: Xpert MTB/RIF is Superior to Phenotypic Drug Susceptibility Testing. Infect Drug Resist 2022; 15:1345-1352. [PMID: 35378895 PMCID: PMC8976515 DOI: 10.2147/idr.s358301] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/12/2022] [Indexed: 11/23/2022] Open
Affiliation(s)
- Hui Xia
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yuanyuan Song
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zheng
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Shengfen Wang
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Bing Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Wencong He
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Dongxin Liu
- Institute of Hepatology, National Clinical Research Center for Infectious Disease, Shenzhen Third People’s Hospital, Shenzhen, People’s Republic of China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People’s Republic of China
- Correspondence: Yanlin Zhao, National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155, Changbai Road, Changping District, Beijing, People’s Republic of China, Tel +86 10-58900517, Email
| |
Collapse
|
25
|
Innovations in Molecular Identification of Mycobacterium tuberculosis. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.1.76] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Tuberculosis (TB) continues to be a significant public health concern on a global scale. Quick and precise identification of Mycobacterium tuberculosis (MTB) in symptomatic patients is pivotal for worldwide TB eradication initiatives. As an infectious disorder induced by MTB, it remains a critical threat to public health, particularly in poor countries, due to an inadequate diagnostic research laboratory. There is a need for a persistent incentive to reduce response time for effective diagnosis and control of TB infection, which is a benefit that molecular techniques provide over traditional methods. Although there is a tremendous overall prevalence of TB and a relatively poor probability of case identification worldwide. Common screening techniques have focused on tests that have many fundamental shortcomings. Due to the development of antibiotic-resistant Mycobacterium strains, TB is one of the leading contributors to fatalities. It is now possible to examine TB using molecular detection techniques, which are faster and more cost-effective than previous methods, such as standard culture procedures to test and verify antibiotic resistance in patients with TB. Whole genome sequencing (WGS), faster nucleic acid amplification tests, has made it easier to diagnose and treat TB more quickly. This article addresses the genetic approaches for detecting Mycobacterium tuberculosis complex (MTBC) in clinical specimens as well as antibiotic resistance in mycobacterium and discusses the practical limitations of using these methods.
Collapse
|
26
|
Micheni LN, Kassaza K, Kinyi H, Ntulume I, Bazira J. Detection of Mycobacterium tuberculosis multiple strains in sputum samples from patients with pulmonary tuberculosis in south western Uganda using MIRU-VNTR. Sci Rep 2022; 12:1656. [PMID: 35102181 PMCID: PMC8803872 DOI: 10.1038/s41598-022-05591-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/11/2022] [Indexed: 11/25/2022] Open
Abstract
Infections with multiple strains of Mycobacterium tuberculosis are now widely recognized as a common occurrence. Identification of patients infected with multiple strains provides both insight into the disease dynamics and the epidemiology of tuberculosis. Analysis of Mycobacterial Interspersed Repetitive Unit-Variable-Number Tandem Repeats (MIRU-VNTR) has been shown to be highly sensitive in detecting multiple M. tuberculosis strains even in sputum. The goal of this study was to identify cases of multiple M. tuberculosis strain infections among patients diagnosed with pulmonary tuberculosis in Southwestern Uganda and assessment of factors associated with multiple strain infections. DNA extracted directly from 78 sputum samples, each from an individual patient, was analyzed using the standard 24 loci MIRU-VNTR typing. Five (6.4%) of the 78 patients were infected with multiple strains of M. tuberculosis with all of them being the newly diagnosed cases while two-thirds of them were co-infected with HIV. Exact regression analysis projected that the natives were more likely to harbor multiple strains (OR; 0.981, 95% CI 0–7.926) as well as those with a high microbial load (OR; 0.390, 95% CI 0–3.8167). Despite these findings being not statistically significant due to the small sample size, this points to a critical component of disease dynamics that has clinical implications and emphasizes a need for a study using a larger cohort. It is also essential to study the potential factors associated with higher risk of exposure to newly diagnosed and HIV positive patients at the community level. In addition, our ability to detect multiple M. tuberculosis strains using the standard 24 loci MIRU-VNTR typing especially with allelic diversity in loci 2059 and 3171, which are excluded from the 15-locus MIRU-VNTR, lead us to recommend the use of this genotyping technique, especially in areas with tuberculosis endemicity similar to this study.
Collapse
Affiliation(s)
- Lisa Nkatha Micheni
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda. .,Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda.
| | - Kennedy Kassaza
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda
| | - Hellen Kinyi
- Department of Biochemistry, School of Medicine, Kabale University, Box 317, Kabale, Uganda
| | - Ibrahim Ntulume
- Department of Microbiology and Immunology, Kampala International University Western Campus, Box 71, Bushenyi, Uganda
| | - Joel Bazira
- Department of Microbiology, Mbarara University of Science and Technology, Box 1410, Mbarara, Uganda.
| |
Collapse
|
27
|
Gupta NK, Ish P. Tuberculosis with discordant drug resistance patterns- A diagnostic dilemma. Indian J Tuberc 2022; 69:8-11. [PMID: 35074156 DOI: 10.1016/j.ijtb.2021.05.003] [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: 03/27/2021] [Accepted: 05/22/2021] [Indexed: 06/14/2023]
Abstract
Programmatic management of drug-resistant tuberculosis (PMDT) guidelines in India specify the use of cartridge based nucleic acid amplification test (CBNAAT) and Line probe assay (LPA) for early diagnosis of drug-resistant Tuberculosis. However, discrepancy among these genotypic tests (CBNAAT and LPA) or with the phenotypic DST in real practice poses a clinical dilemma. The usual solutions are to rely on methods with short turnaround times like CBNAAT and LPA to start an initial regimen. The culture and DST results, that are typically available after at least a few weeks, are used to modify the regimen if required. This practice is based on the fact that culture and DST based sensitivity patterns are considered the gold standard for diagnosing and drug resistance. DNA sequencing by pyrosequencing, Sanger sequencing and next generation sequencing (NGS) are being evaluated; their future availability may help in early clarifications in discordant drug resistance patterns. Such tests are costly and have limited availability, however, in view of immense benefit to detect TB Drug-resistant phenotypes, national guidelines plan to scale up their use in national and well-performing intermediate TB reference laboratories.
Collapse
Affiliation(s)
- Neeraj Kumar Gupta
- Department of Pulmonary, Critical Care and Sleep Medicine and Nodal Officer for DOTS, VMMC and Safdarjung Hospital, New Delhi, India
| | - Pranav Ish
- Department of Pulmonary, Critical Care and Sleep Medicine, VMMC and Safdarjung Hospital, New Delhi, India.
| |
Collapse
|
28
|
Lozano N, Lanza VF, Suárez-González J, Herranz M, Sola-Campoy PJ, Rodríguez-Grande C, Buenestado-Serrano S, Ruiz-Serrano MJ, Tudó G, Alcaide F, Muñoz P, García de Viedma D, Pérez-Lago L. Detection of Minority Variants and Mixed Infections in Mycobacterium tuberculosis by Direct Whole-Genome Sequencing on Noncultured Specimens Using a Specific-DNA Capture Strategy. mSphere 2021; 6:e0074421. [PMID: 34908457 PMCID: PMC8673255 DOI: 10.1128/msphere.00744-21] [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: 09/02/2021] [Accepted: 11/24/2021] [Indexed: 12/01/2022] Open
Abstract
Detection of mixed Mycobacterium tuberculosis (MTB) infections is essential, particularly when resistance mutations are present in minority bacterial populations that may affect patients' disease evolution and treatment. Whole-genome sequencing (WGS) has extended the amount of key information available for the diagnosis of MTB infection, including the identification of mixed infections. Having genomic information at diagnosis for early intervention requires carrying out WGS directly on the clinical samples. However, few studies have been successful with this approach due to the low representation of MTB DNA in sputa. In this study, we evaluated the ability of a strategy based on specific MTB DNA enrichment by using a newly designed capture platform (MycoCap) to detect minority variants and mixed infections by WGS on controlled mixtures of MTB DNAs in a simulated sputum genetic background. A pilot study was carried out with 12 samples containing 98% of a DNA pool from sputa of patients without MTB infection and 2% of MTB DNA mixtures at different proportions. Our strategy allowed us to generate sequences with a quality equivalent to those obtained from culture: 62.5× depth coverage and 95% breadth coverage (for at least 20× reads). Assessment of minority variant detection was carried out by manual analysis and allowed us to identify heterozygous positions up to a 95:5 ratio. The strategy also automatically distinguished mixed infections up to a 90:10 proportion. Our strategy efficiently captures MTB DNA in a nonspecific genetic background, allows detection of minority variants and mixed infections, and is a promising tool for performing WGS directly on clinical samples. IMPORTANCE We present a new strategy to identify mixed infections and minority variants in Mycobacterium tuberculosis by whole-genome sequencing. The objective of the strategy is the direct detection in patient sputum; in this way, minority populations of resistant strains can be identified at the time of diagnosis, facilitating identification of the most appropriate treatment for the patient from the first moment. For this, a platform for capturing M. tuberculosis-specific DNA was designed to enrich the clinical sample and obtain quality sequences.
Collapse
Affiliation(s)
- Nuria Lozano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit IRYCIS, University Hospital Ramón y Cajal, Madrid, Spain
- CIBER Enfermedades Infecciosas, Madrid, Spain
| | - Julia Suárez-González
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Unidad de Genómica, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Marta Herranz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Pedro J. Sola-Campoy
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Cristina Rodríguez-Grande
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Sergio Buenestado-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - María Jesús Ruiz-Serrano
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Griselda Tudó
- Servei de Microbiologia, Hospital Clinic-CDB, Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Fernando Alcaide
- Servicio de Microbiología, Hospital Universitario de Bellvitge-IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
- Department of Pathology and Experimental Therapy, University of Barcelona, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Patricia Muñoz
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
- Departmento de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
- CIBER Enfermedades Respiratorias, CIBERES, Madrid, Spain
| | - Laura Pérez-Lago
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| |
Collapse
|
29
|
Ssengooba W, Komakech K, Namiiro S, Byabajungu H, Nalunjogi J, Katagira W, Kimuli I, Joloba ML, Adakun S, Nakiyingi L, Torrea G, Kirenga BJ. Rifampicin susceptibility discordance between Xpert MTB/RIF G4 and Xpert Ultra before MDRT-TB treatment initiation: A case report from Uganda. J Clin Tuberc Other Mycobact Dis 2021; 25:100286. [PMID: 34816021 PMCID: PMC8592849 DOI: 10.1016/j.jctube.2021.100286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Tuberculosis (TB) resistance to rifampicin, the most powerful drug leads to increase in mortality. Globally, half a million new patients develop such resistant TB each year, coupled with both inappropriate diagnosis and treatment initiation. We report a case of rifampicin resistant Mycobacterium tuberculosis whose rifampicin resistance was missed by Xpert MTB/RIF Assay G4 but detected by the Xpert MTB/RIF Ultra assay at different time points leading to increased delays for MDR-TB treatment initiation at Mulago Hospital, Kampala, Uganda. Our case report compels greater urgency in accelerating the transition to the newer assay, Ultra, to benefit from higher sensitivity of rifampicin resistance detection.
Collapse
Affiliation(s)
- Willy Ssengooba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Kevin Komakech
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Sharon Namiiro
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Henry Byabajungu
- National TB Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Joanitah Nalunjogi
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Winceslaus Katagira
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Ivan Kimuli
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| | - Moses L Joloba
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- Makerere University, Department of Medical Microbiology, Mycobacteriology (BSL-3) Laboratory, P.O.BOX 7072, Kampala, Uganda
| | - Susan Adakun
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
- National Tuberculosis Treatment Unit, Mulago Hospital, Kampala, Uganda
| | - Lydia Nakiyingi
- Infectious Diseases Institute, Makerere University, Kampala, Uganda
| | - Gabriela Torrea
- Unit of Mycobacteriology, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Bruce J Kirenga
- Makerere University Lung Institute, College of Health Sciences, Makerere University, Kampala, Uganda
| |
Collapse
|
30
|
Liu Q, Chen X, Dai X, Liu X, Xu F, Peng P. Comparative analysis of five inspection techniques for the application in the diagnosis and treatment of osteoarticular tuberculosis. Int J Infect Dis 2021; 112:258-263. [PMID: 34536611 DOI: 10.1016/j.ijid.2021.09.019] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 08/27/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022] Open
Abstract
OBJECTIVE To evaluate five examination techniques in the diagnosis and treatment of osteoarticular tuberculosis (TB). METHODS Microbiological samples were collected from a total of 284 patients during the period August 2017 to December 2019 in Wuhan Pulmonary Hospital. The specimens were examined by acid-fast bacillus (AFB) smear microscopy, mycobacterial culture, PCR, T-SPOT.TB, and X-pert MTB/RIF rapid molecular detection. RESULTS The diagnostic sensitivity of the Xpert technology was 96.8% (116/120), specificity was 96.8% (58/60), the Youden index was 0.936, and the area under the receiver operating characteristic (ROC) curve was 0.967. The sensitivity and specificity of PCR were 84.2% (104/128) and 95.2% (76/80), respectively; the area under the ROC curve was 0.881. T-SPOT.TB had a detection sensitivity of 75.0% (12/16) and specificity of 85.0% (17/20). AFB smear microscopy had a sensitivity of 60.0% (75/125) and specificity of 95.8% (152/159). TB culture sensitivity was 58.1% (72/124) and specificity was 96.2% (73/76). The sensitivity and specificity of Xpert MTB/RIF for detecting rifampicin resistance were 100% (2/2) and 97.3% (73/75), respectively. CONCLUSIONS The Xpert MTB/RIF technique was found to have a good diagnostic value. With an additional diagnosis of Rifampicin resistance, it was also useful in tuberculosis therapy.
Collapse
Affiliation(s)
- Qibin Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| | - Xianxiang Chen
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| | - Xiyong Dai
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| | - Xiaoyu Liu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| | - Feng Xu
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| | - Peng Peng
- Wuhan Pulmonary Hospital, Wuhan Institute for Tuberculosis Control, No. 28 Baofeng Road, Qiaokou District, Wuhan City, Hubei Province, China.
| |
Collapse
|
31
|
Detection of Pyrazinamide Heteroresistance in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2021; 65:e0072021. [PMID: 34181476 PMCID: PMC8370246 DOI: 10.1128/aac.00720-21] [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] [Indexed: 01/09/2023] Open
Abstract
Heteroresistance is defined as the coexistence of both susceptible and resistant bacteria in a bacterial population. Previously published data show that it may occur in 9 to 57% of Mycobacterium tuberculosis isolates for various drugs. Pyrazinamide (PZA) is an important first-line drug used for treatment of both drug-susceptible and PZA-susceptible multidrug-resistant TB. Clinical PZA resistance is defined as a proportion of resistant bacteria in the isolate exceeding 10%, when the drug is no longer considered clinically effective. The ability of traditional drug susceptibility testing techniques to detect PZA heteroresistance has not yet been evaluated. The aim of this study was to compare the capacity of Bactec MGIT 960, Wayne's test, and whole-genome sequencing (WGS) to detect PZA-resistant subpopulations in bacterial suspensions prepared with different proportions of mutant strains. Both Bactec MGIT 960 and WGS were able to detect the critical level of 10% PZA heteroresistance, whereas Wayne's test failed to do so, with the latter falsely reporting highly resistant samples as PZA susceptible. Failure to detect drug-resistant subpopulations may lead to inadvertently weak treatment regimens if ineffective drugs are included, with the risk of treatment failure with the selective growth of resistant subpopulations. We need clinical awareness of heteroresistance as well as evaluation of new diagnostic tools for their capacity to detect heteroresistance in TB.
Collapse
|
32
|
GeneXpert on patients with human immunodeficiency virus and smear-negative pulmonary tuberculosis. PLoS One 2021; 16:e0253961. [PMID: 34228759 PMCID: PMC8259960 DOI: 10.1371/journal.pone.0253961] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 06/17/2021] [Indexed: 11/25/2022] Open
Abstract
Objectives Vietnam is a high-prevalence country for tuberculosis (TB). Xpert MTB/RIF is a novel PCR-based diagnostic test that is substantially more sensitive for detecting M. tuberculosis than traditional smear-based techniques. However, locally-derived evidence of Xpert MTB/RIF in HIV-infected people is limited. This study evaluates the performance of the Xpert MTB/RIF in HIV-infected patients with smear-negative pulmonary TB (SNTB). Methods This was a cross-sectional study in 3 hospitals. The performance of Xpert MTB/RIF was compared with the reference standard of liquid culture and phenotypic drug-susceptibility testing for rifampicin (RIF) resistance. Results Out of 123 patients, the median age was 37.0 (IQR: 32.0–41.0) and 81.3% were male. The area under the receiver operating characteristic curve, sensitivity (Se) and specificity (Sp) of Xpert MTB/RIF for pulmonary TB diagnosis were 0.72 (95% confidence interval [CI]: 0.63–0.81), 66.7% (95%CI: 54.8–77.1) and 77.1% (95%CI: 62.7–88.0), respectively, while Se and Sp of Xpert MTB/RIF in detecting RIF resistance were 50.0 (11.8–88.2) and 86.4% (95%CI: 72.7–94.8). Conclusion The performance of Xpert MTB/RIF in HIV-infected patients with SNTB for the diagnosis of TB and RIF-resistance was low. Further studies are required to evaluate the results of Xpert MTB/RIF assay in HIV-infected patients with SNTB and the role of Xpert repetition on the same specimens.
Collapse
|
33
|
Gil H, Margaryan H, Azamat I, Ziba B, Bayram H, Nazirov P, Gomez D, Singh J, Zayniddin S, Parpieva N, Achar J. Accuracy of molecular drug susceptibility testing amongst tuberculosis patients in Karakalpakstan, Uzbekistan. Trop Med Int Health 2021; 26:421-427. [PMID: 33406316 DOI: 10.1111/tmi.13543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
OBJECTIVES In this retrospective study, we evaluated the diagnostic accuracy of molecular tests (MT) for the detection of DR-TB, compared to the gold standard liquid-based drug susceptibility testing (DST) in Karakalpakstan. METHODS A total of 6670 specimens received in the Republican TB No 1 Hospital Laboratory of Karakalpakstan between January and July 2017 from new and retreatment patients were analysed. Samples were tested using Xpert MTB/RIF and line probe assays (LPA) for the detection of mutations associated with resistance. The sensitivity and specificity of MTs were calculated relative to results based on DST. RESULTS The accuracy of MT for detection of rifampicin resistance was high, with sensitivity and specificity over 98%. However, we observed reduced sensitivity of LPA for detection of resistance; 86% for isoniazid (95% CI 82-90%), 86% for fluoroquinolones (95% CI 68-96%), 70% for capreomycin (95% CI 46-88%) and 23% for kanamycin (95% CI 13-35%). CONCLUSIONS We show that MTs are a useful tool for rapid and safe diagnosis of DR-TB; however, clinicians should be aware of their limitations. Although detection of rifampicin resistance was highly accurate, our data suggest that resistance mutations circulating in the Republic of Karakalpakstan for other drugs were not detected by the methods used here. This merits further investigation.
Collapse
Affiliation(s)
- Horacio Gil
- Médecins Sans Frontières (MSF), Nukus, Uzbekistan
| | | | | | | | - Halmuratov Bayram
- Republican TB No 1 Hospital Laboratory of Karakalpakstan, Nukus, Uzbekistan
| | - Pirimqul Nazirov
- Republican TB No 1 Hospital of Karakalpakstan, Nukus, Uzbekistan
| | | | | | | | - Nargiza Parpieva
- National Tuberculosis Reference Laboratory, Tashkent, Uzbekistan
| | - Jay Achar
- MSF, London, UK.,Karolinska Institutet, Stockholm, Sweden
| |
Collapse
|
34
|
Byrne AS, Goudreau A, Bissonnette N, Shamputa IC, Tahlan K. Methods for Detecting Mycobacterial Mixed Strain Infections-A Systematic Review. Front Genet 2020; 11:600692. [PMID: 33408740 PMCID: PMC7779811 DOI: 10.3389/fgene.2020.600692] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Accepted: 11/19/2020] [Indexed: 12/22/2022] Open
Abstract
Mixed strain infection (MSI) refers to the concurrent infection of a susceptible host with multiple strains of a single pathogenic species. Known to occur in humans and animals, MSIs deserve special consideration when studying transmission dynamics, evolution, and treatment of mycobacterial diseases, notably tuberculosis in humans and paratuberculosis (or Johne's disease) in ruminants. Therefore, a systematic review was conducted to examine how MSIs are defined in the literature, how widespread the phenomenon is across the host species spectrum, and to document common methods used to detect such infections. Our search strategy identified 121 articles reporting MSIs in both humans and animals, the majority (78.5%) of which involved members of the Mycobacterium tuberculosis complex, while only a few (21.5%) examined non-tuberculous mycobacteria (NTM). In addition, MSIs exist across various host species, but most reports focused on humans due to the extensive amount of work done on tuberculosis. We reviewed the strain typing methods that allowed for MSI detection and found a few that were commonly employed but were associated with specific challenges. Our review notes the need for standardization, as some highly discriminatory methods are not adapted to distinguish between microevolution of one strain and concurrent infection with multiple strains. Further research is also warranted to examine the prevalence of NTM MSIs in both humans and animals. In addition, it is envisioned that the accurate identification and a better understanding of the distribution of MSIs in the future will lead to important information on the epidemiology and pathophysiology of mycobacterial diseases.
Collapse
Affiliation(s)
| | - Alex Goudreau
- Science & Health Sciences Librarian, University of New Brunswick, Saint John, NB, Canada
| | - Nathalie Bissonnette
- Sherbrooke Research and Development Center, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
| | - Isdore Chola Shamputa
- Department of Nursing & Health Sciences, University of New Brunswick, Saint John, NB, Canada
| | - Kapil Tahlan
- Department of Biology, Memorial University of Newfoundland, St. John's, NL, Canada
| |
Collapse
|
35
|
Pediatric Tuberculosis: The Impact of "Omics" on Diagnostics Development. Int J Mol Sci 2020; 21:ijms21196979. [PMID: 32977381 PMCID: PMC7582311 DOI: 10.3390/ijms21196979] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 02/07/2023] Open
Abstract
Tuberculosis (TB) is a major public health concern for all ages. However, the disease presents a larger challenge in pediatric populations, partially owing to the lack of reliable diagnostic standards for the early identification of infection. Currently, there are no biomarkers that have been clinically validated for use in pediatric TB diagnosis. Identification and validation of biomarkers could provide critical information on prognosis of disease, and response to treatment. In this review, we discuss how the “omics” approach has influenced biomarker discovery and the advancement of a next generation rapid point-of-care diagnostic for TB, with special emphasis on pediatric disease. Limitations of current published studies and the barriers to their implementation into the field will be thoroughly reviewed within this article in hopes of highlighting future avenues and needs for combating the problem of pediatric tuberculosis.
Collapse
|
36
|
Mycobacterium tuberculosis polyclonal infections through treatment and recurrence. PLoS One 2020; 15:e0237345. [PMID: 32813724 PMCID: PMC7437862 DOI: 10.1371/journal.pone.0237345] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 07/23/2020] [Indexed: 12/02/2022] Open
Abstract
Background Mixed/polyclonal infections due to different genotypes are reported in Tuberculosis. The current study was designed to understand the fate of mixed infections during the course of treatment and follow-up and its role in disease pathogenesis. Methods Sputum samples were collected on 0,1,2,3,6,12 and 24 months from 157 treatment-naïve patients, cultures subjected to Drug-Susceptibility-testing (MGIT 960), spoligotyping, MIRU-VNTR and SNP genotyping. All isolated colonies on thin layer agar (7H11) were subjected to spoligotyping. Findings One thirty three baseline cultures were positive (133/157, 84.7%), 43(32.3%) had mixture of genotypes. Twenty-four of these patients (55.8%) showed change in genotype while six showed different drug-susceptibility patterns while on treatment. Twenty-three (53.5%) patients with polyclonal infections showed resistance to at least one drug compared to 10/90 (11.1%) monoclonal infections (P<0.0001). Eight patients had recurrent TB, two with a new genotype and two with altered phenotypic DST. Conclusions The coexistence of different genotypes and change of genotypes during the same disease episode, while on treatment, confirms constancy of polyclonal infections. The composition of the mixture of genotypes and the relative predominance may be missed by culture due to its limit of detection. Polyclonal infections in TB could be a rule rather than exception and challenges the age-old dogma of reactivation/reinfection.
Collapse
|
37
|
Kayomo MK, Mbula VN, Aloni M, André E, Rigouts L, Boutachkourt F, de Jong BC, Nkiere NM, Dean AS. Targeted next-generation sequencing of sputum for diagnosis of drug-resistant TB: results of a national survey in Democratic Republic of the Congo. Sci Rep 2020; 10:10786. [PMID: 32612134 PMCID: PMC7329841 DOI: 10.1038/s41598-020-67479-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The surveillance of drug resistance among tuberculosis (TB) patients is central to preventing the spread of antimicrobial resistance. The Democratic Republic of the Congo (DR Congo) is classified by the World Health Organization (WHO) as a country with a high burden of TB and multidrug-resistant TB (MDR-TB), but there are no nationally representative data on drug resistance. In 2016-2017, a national survey of TB patients was conducted in 108 microscopy centres across all 11 provinces of the country using innovative molecular approaches. Sputum samples were collected from 1,545 new and 163 previously treated patients. These were tested by the Xpert MTB/RIF assay, followed by targeted next-generation sequencing performed directly on sputum. The prevalence of rifampicin resistance was low, at 1.8% (95% CI: 1.0-3.2) among new and 17.3% (95% CI: 11.9-24.4) among previously treated patients. Resistance to pyrazinamide, fluoroquinolones and second-line injectables was also low. The prevalence of resistance to isoniazid among rifampicin-susceptible patients was higher, at 6.6% (95% CI: 4.4-9.8) among new and 8.7% (95% : 3.2-21.2) among previously treated patients. Diagnosing and treating isoniazid-resistant patients remains a challenge, given that many will be missed by the current national diagnostic algorithm that is driven by detecting rifampicin resistance by Xpert MTB/RIF. This is the first nationwide survey incorporating targeted sequencing directly on sputum. It serves as a proof-of-concept for other settings that do yet have rapid specimen transport networks or capacity to conduct culture.
Collapse
MESH Headings
- Adolescent
- Adult
- Aged
- Child
- Child, Preschool
- Cross-Sectional Studies
- Democratic Republic of the Congo/epidemiology
- Female
- High-Throughput Nucleotide Sequencing
- Humans
- Infant
- Infant, Newborn
- Male
- Middle Aged
- Mycobacterium tuberculosis/genetics
- Prevalence
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/diagnosis
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/epidemiology
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Pulmonary/diagnosis
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/epidemiology
- Tuberculosis, Pulmonary/genetics
Collapse
Affiliation(s)
- Michel Kaswa Kayomo
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Vital Nkake Mbula
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
| | - Muriel Aloni
- National Tuberculosis Program et Laboratoire National de Référence des Mycobactéries (LNRM), Kinshasa, Democratic Republic of the Congo
- Faculté de Médecine, Université de Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Emmanuel André
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Leen Rigouts
- Institute of Tropical Medicine, Antwerp, Belgium
- Antwerp University, Antwerp, Belgium
| | - Fairouz Boutachkourt
- Pôle de Microbiologie Médicale, Institut de Recherche Expérimental Et Clinique, UC Louvain, Brussels, Belgium
| | | | - Nicolas M Nkiere
- World Health Organization, Kinshasa, Democratic Republic of the Congo
| | - Anna S Dean
- Global TB Programme, World Health Organization, Geneva, Switzerland.
| |
Collapse
|
38
|
Morel F, Jaffré J, Sougakoff W, Aubry A, Véziris N. [Molecular diagnosis of tuberculosis]. Rev Mal Respir 2020; 37:412-416. [PMID: 32334967 DOI: 10.1016/j.rmr.2019.09.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 09/24/2019] [Indexed: 10/24/2022]
Abstract
Tuberculosis is caused by the M. tuberculosis complex. Its slow growth delays the bacteriological diagnosis based on phenotypic tests. Molecular biology has significantly reduced this delay, notably thanks to the deployment of the Xpert® MTB/RIF test (Cepheid), which detects the M. tuberculosis complex and rifampicin resistance in 2hours. Other tests detecting isoniazid and second-line antituberculous drugs resistance have been developed. However, the performances of molecular tests are significantly reduced if the acid-fast bacilli microscopy screening is negative. It is therefore crucial to limit their indication to strong clinical suspicions. Resistance detection tests only explore certain characterized positions; however, not all drug-resistance mutations are known. Moreover, the performances vary for different antituberculous drugs. The advent of genomic sequencing is promising. Its integration into routine workflow still needs to be evaluated and the data analysis remains to be standardized. The rise of molecular biology techniques has revolutionized the diagnosis of tuberculosis and drug resistance. However, they remain screening tests; results still have to be confirmed by phenotypic reference methods.
Collapse
Affiliation(s)
- F Morel
- Sorbonne universités, Inserm, centre d'immunologie et des maladies infectieuses (Cimi-Paris), UMR 1135, laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries, assistance publique-hôpitaux de Paris, Paris
| | - J Jaffré
- Sorbonne universités, Inserm, centre d'immunologie et des maladies infectieuses (Cimi-Paris), UMR 1135, laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries, assistance publique-hôpitaux de Paris, Paris
| | - W Sougakoff
- Sorbonne universités, Inserm, centre d'immunologie et des maladies infectieuses (Cimi-Paris), UMR 1135, laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries, assistance publique-hôpitaux de Paris, Paris
| | - A Aubry
- Sorbonne universités, Inserm, centre d'immunologie et des maladies infectieuses (Cimi-Paris), UMR 1135, laboratoire de bactériologie-hygiène, centre national de référence des mycobactéries, assistance publique-hôpitaux de Paris, Paris
| | - N Véziris
- Sorbonne universités, Inserm, centre d'immunologie et des maladies infectieuses (Cimi-Paris), UMR 1135, département de bactériologie, hôpitaux universitaires de l'Est Parisien, centre national de référence des mycobactéries, assistance publique-hopitaux de Paris, Paris.
| |
Collapse
|
39
|
Jelińska A, Zając M, Dadej A, Tomczak S, Geszke-Moritz M, Muszalska-Kolos I. Tuberculosis - Present Medication and Therapeutic Prospects. Curr Med Chem 2020; 27:630-656. [PMID: 30457045 DOI: 10.2174/0929867325666181120100025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 10/18/2018] [Accepted: 11/08/2018] [Indexed: 12/15/2022]
Abstract
BACKGROUND Tuberculosis (TB) has been present in the history of human civilization since time immemorial and has caused more deaths than any other infectious disease. It is still considered one of the ten most common epidemiologic causes of death in the world. As a transmissible disease, it is initiated by rod-shaped (bacillus) mycobacteria. The management of tuberculosis became possible owing to several discoveries beginning in 1882 with the isolation of the TB bacillus by Robert Koch. The diagnosis of TB was enabled by finding a staining method for TB bacteria identification (1883). It was soon realized that a large-scale policy for the treatment and prevention of tuberculosis was necessary, which resulted in the foundation of International Union against Tuberculosis and Lung Diseases (1902). An antituberculosis vaccine was developed in 1921 and has been in therapeutic use since then. TB treatment regimens have changed over the decades and the latest recommendations are known as Directly Observed Treatment Short-course (DOTS, WHO 1993). METHODS A search of bibliographic databases was performed for peer-reviewed research literature. A focused review question and inclusion criteria were applied. Standard tools were used to assess the quality of retrieved papers. RESULTS A total of 112 papers were included comprising original publications and reviews. The paper overviews anti-TB drugs according to their mechanism of action. The chemical structure, metabolism and unwanted effects of such drugs have been discussed. The most recent treatment regimens and new drugs, including those in clinical trials, are also presented. CONCLUSION Despite a 22% decrease in the tuberculosis fatality rate observed between 2000 and 2015, the disease remains one of the ten prime causes of death worldwide. Increasing bacterial resistance and expensive, prolonged therapies are the main reasons for efforts to find effective drugs or antituberculosis regimens, especially to cure multidrug-resistant tuberculosis.
Collapse
Affiliation(s)
- Anna Jelińska
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| | - Marianna Zając
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| | - Adrianna Dadej
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| | - Szymon Tomczak
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| | - Małgorzata Geszke-Moritz
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| | - Izabela Muszalska-Kolos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Poznan University of Medicinal Sciences, Grunwaldzka Str. 6, 60-780, Poznan, Poland
| |
Collapse
|
40
|
Kargarpour Kamakoli M, Farmanfarmaei G, Masoumi M, Khanipour S, Gharibzadeh S, Sola C, Fateh A, Siadat SD, Refregier G, Vaziri F. Prediction of the hidden genotype of mixed infection strains in Iranian tuberculosis patients. Int J Infect Dis 2020; 95:22-27. [PMID: 32251801 DOI: 10.1016/j.ijid.2020.03.056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/19/2020] [Accepted: 03/24/2020] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Patients with mixed-strain Mycobacterium tuberculosis infections may be at a high risk of poor treatment outcomes. However, the mechanisms through which mixed infections affect the clinical manifestations are not well recognized. Evidence suggests that failure to detect the pathogen diversity within the host can influence the clinical results. We aimed to investigate the effects of different genotypes in mixed infections and determine their relationship with heteroresistance in the treatment of Iranian tuberculosis patients. METHODS One of the genotypes was identified in the culture and another genotype pattern in the mixed infection was predicted by comparing the pattern of MIRU-VNTR between the clinical specimens and their respective cultures in each patient. For all patients, the drug susceptibility testing was carried out on three single colonies from each clinical sample. The follow-up of patients was carried out during six months of treatment. RESULTS Based on MIRU-VNTR profiles of clinical samples, we showed that 55.6% (25/45) of the Iranian patients included in the study had mixed infections. Patients with mixed infections had a higher rate of treatment failure, compared to others (P=0.03). By comparing clinical sample profiles to profiles obtained after culture, we were able to distinguish between major and hidden genotypes. Among hidden genotypes, Haarlem (L4.1.2) and Beijing (L2) were associated to treatment failure (6/8 patients). CONCLUSIONS To conclude, we propose a procedure using the MIRU-VNTR method to identify the different genotypes in mixed infections. The present findings suggest that genotypes with potentially higher pathogenicity may not be detected when performing experimental culture in patients with mixed infections.
Collapse
Affiliation(s)
- Mansour Kargarpour Kamakoli
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Ghazaleh Farmanfarmaei
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Masoumi
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Sharareh Khanipour
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Safoora Gharibzadeh
- Department of Epidemiology and Biostatistics, Research Center for Emerging and Reemerging Infectious Diseases, Pasteur Institute of Iran, Tehran, Iran
| | - Christophe Sola
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Abolfazl Fateh
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Guislaine Refregier
- Institut for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris Sud, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
| |
Collapse
|
41
|
Ginn C, Ateh D, Martin J. The use of point-of-care testing to establish cause of death in the autopsy setting. J Forensic Leg Med 2020; 71:101933. [DOI: 10.1016/j.jflm.2020.101933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
|
42
|
Tsenova L, Fallows D, Kolloli A, Singh P, O'Brien P, Kushner N, Kaplan G, Subbian S. Inoculum size and traits of the infecting clinical strain define the protection level against Mycobacterium tuberculosis infection in a rabbit model. Eur J Immunol 2020; 50:858-872. [PMID: 32130727 DOI: 10.1002/eji.201948448] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 12/27/2019] [Accepted: 03/03/2020] [Indexed: 12/28/2022]
Abstract
Host protective immunity against pathogenic Mycobacterium tuberculosis (Mtb) infection is variable and poorly understood. Both prior Mtb infection and BCG vaccination have been reported to confer some protection against subsequent infection and/or disease. However, the immune correlates of host protection with or without BCG vaccination remain poorly understood. Similarly, the host response to concomitant infection with mixed Mtb strains is unclear. In this study, we used the rabbit model to examine the host response to various infectious doses of virulent Mtb HN878 with and without prior BCG vaccination, as well as simultaneous infection with a mixture of two Mtb clinical isolates HN878 and CDC1551. We demonstrate that both the ability of host immunity to control pulmonary Mtb infection and the protective efficacy of BCG vaccination against the progression of Mtb infection to disease is dependent on the infectious inoculum. The host response to infection with mixed Mtb strains mirrors the differential responses seen during infection with each of the strains alone. The protective response mounted against a hyperimmunogenic Mtb strain has a limited impact on the control of disease caused by a hypervirulent strain. This preclinical study will aid in predicting the success of any vaccination strategy and in optimizing TB vaccines.
Collapse
Affiliation(s)
- Liana Tsenova
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Biological Sciences, NYC College of Technology, Brooklyn, NY, USA
| | - Dorothy Fallows
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Celgene Corporation, Summit, NJ, USA
| | - Afsal Kolloli
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Pooja Singh
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
| | - Paul O'Brien
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Division of Cancer Biology, Department of Radiation Oncology, Rutgers University, Newark, NJ, USA
| | - Nicole Kushner
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Microbiology and Immunology, Cornell University, Ithaca, NY, USA
| | - Gilla Kaplan
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA.,Department of Medicine, University of Cape Town, Cape Town, South Africa
| | - Selvakumar Subbian
- The Public Health Research Institute (PHRI) of New Jersey Medical School, Rutgers University, Newark, NJ, USA
| |
Collapse
|
43
|
Anyansi C, Keo A, Walker BJ, Straub TJ, Manson AL, Earl AM, Abeel T. QuantTB - a method to classify mixed Mycobacterium tuberculosis infections within whole genome sequencing data. BMC Genomics 2020; 21:80. [PMID: 31992201 PMCID: PMC6986090 DOI: 10.1186/s12864-020-6486-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Accepted: 01/13/2020] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Mixed infections of Mycobacterium tuberculosis and antibiotic heteroresistance continue to complicate tuberculosis (TB) diagnosis and treatment. Detection of mixed infections has been limited to molecular genotyping techniques, which lack the sensitivity and resolution to accurately estimate the multiplicity of TB infections. In contrast, whole genome sequencing offers sensitive views of the genetic differences between strains of M. tuberculosis within a sample. Although metagenomic tools exist to classify strains in a metagenomic sample, most tools have been developed for more divergent species, and therefore cannot provide the sensitivity required to disentangle strains within closely related bacterial species such as M. tuberculosis. Here we present QuantTB, a method to identify and quantify individual M. tuberculosis strains in whole genome sequencing data. QuantTB uses SNP markers to determine the combination of strains that best explain the allelic variation observed in a sample. QuantTB outputs a list of identified strains, their corresponding relative abundances, and a list of drugs for which resistance-conferring mutations (or heteroresistance) have been predicted within the sample. RESULTS We show that QuantTB has a high degree of resolution and is capable of differentiating communities differing by less than 25 SNPs and identifying strains down to 1× coverage. Using simulated data, we found QuantTB outperformed other metagenomic strain identification tools at detecting strains and quantifying strain multiplicity. In a real-world scenario, using a dataset of 50 paired clinical isolates from a study of patients with either reinfections or relapses, we found that QuantTB could detect mixed infections and reinfections at rates concordant with a manually curated approach. CONCLUSION QuantTB can determine infection multiplicity, identify hetero-resistance patterns, enable differentiation between relapse and re-infection, and clarify transmission events across seemingly unrelated patients - even in low-coverage (1×) samples. QuantTB outperforms existing tools and promises to serve as a valuable resource for both clinicians and researchers working with clinical TB samples.
Collapse
Affiliation(s)
- Christine Anyansi
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Arlin Keo
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands
| | - Bruce J Walker
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Applied Invention, LLC, 486 Green Street, Cambridge, MA, 02139, USA
| | - Timothy J Straub
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.,Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, 677 Huntington Avenue, Boston, MA, 02115, USA
| | - Abigail L Manson
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Ashlee M Earl
- Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA
| | - Thomas Abeel
- Delft Bioinformatics Lab, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628XE, The Netherlands. .,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
| |
Collapse
|
44
|
Mechal Y, Benaissa E, El Mrimar N, Benlahlou Y, Bssaibis F, Zegmout A, Chadli M, Malik YS, Touil N, Abid A, Maleb A, Elouennass M. Evaluation of GeneXpert MTB/RIF system performances in the diagnosis of extrapulmonary tuberculosis. BMC Infect Dis 2019; 19:1069. [PMID: 31856744 PMCID: PMC6924055 DOI: 10.1186/s12879-019-4687-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 12/08/2019] [Indexed: 02/08/2023] Open
Abstract
Background Tuberculosis represents a serious public health problem and a significant diagnostic and therapeutic challenge worldwide. Molecular diagnostic techniques are crucial in the World Health Organization’s new tuberculosis control strategy. This study aims to evaluate the performance of GeneXpert MTB/RIF (Cepheid Sunnyvale, CA, United States) in diagnosis of extra-pulmonary tuberculosis then compare it’s performance in detecting Rifampicin resistance to GenoType MTBDRplus (HAIN Life Sciences, Nehren, Germany). Methods Samples from pulmonary and/or extra-pulmonary origins were analysed in a 21 months retrospective study. Samples were sent to the bacteriology laboratory for Mycobacterium tuberculosis detection using conventional bacteriological and molecular methods (GeneXpert MTB/RIF and MTBDRplus). Sensitivity and specificity were calculated for the stained smear and GeneXpert according to culture (Gold Standard) as well as for GeneXpert MTB/RIF in both negative and positive microscopy tuberculosis cases. Data’s statistical analysis was performed with SPSS13.0 software. Results Seven hundred fourteen patients’ samples were analysed; the average age was 47.21 ± 19.98 years with a male predominance (66.4%). Out of 714 samples: 285 were from pulmonary and 429 were from extra-pulmonary origins. The positivity rates for microscopy, GeneXpert MTB/RIF and culture were 12.88, 20.59 and 15.82%, respectively. These rates were 18.9, 23.85 and 20.35% for pulmonary samples and 9.71, 18.41 and 12.82% for extra-pulmonary samples, respectively. The sensitivity and specificity of GeneXpert MTB/RIF were almost the same in both pulmonary and extra-pulmonary samples (78.2 and 90.4%) and (79,3 and 90.3%) respectively. Rifampicin resistance rate found by GeneXpert MTB/RIF was 0.84%. Comparison of Rifampicin resistance obtained by GeneXpert MTB/RIF and Genotype MTBDRplus, showed 100% agreement between the two techniques for studied samples. Conclusions This confirms GeneXpert MTB/RIF advantage for tuberculosis diagnosis, particularly extra-pulmonary tuberculosis with negatively stained smear. The performance of GeneXpert and Genotype MTBDRplus are similar in detection of Rifampicin resistance. However, variability of detection performance according to tuberculosis endemicity deserves more attention in the choice of screening techniques of Rifampicin resistance, hence the interest of conducting comparative studies of detection performance under low and medium endemicity on large samples of tuberculosis populations.
Collapse
Affiliation(s)
- Youness Mechal
- Epidemiology and bacterial resistance research team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco. .,Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco.
| | - Elmostafa Benaissa
- Epidemiology and bacterial resistance research team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Nadia El Mrimar
- Epidemiology and bacterial resistance research team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Yassine Benlahlou
- Epidemiology and bacterial resistance research team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Fatna Bssaibis
- Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Adil Zegmout
- Pneumology Department, Mohammed V University Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Mariama Chadli
- Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Yashpal S Malik
- Indian Veterinary Research Institute (IVRI), Bareilly, Uttar Pradesh, India
| | - Nadia Touil
- Research and Biosafety Laboratory, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Ahmed Abid
- Pneumology Department, Mohammed V University Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| | - Adil Maleb
- Laboratory of Microbiology, Mohammed VI University Hospital / Faculty of Medicine and Pharmacy (University Mohammed the first), Oujda, Morocco
| | - Mostafa Elouennass
- Epidemiology and bacterial resistance research team/BIO-INOVA Centre, Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco.,Department of Bacteriology, Mohammed V Military Teaching Hospital / Faculty of Medicine and Pharmacy (University Mohammed V), Rabat, Morocco
| |
Collapse
|
45
|
How Well Do Routine Molecular Diagnostics Detect Rifampin Heteroresistance in Mycobacterium tuberculosis? J Clin Microbiol 2019; 57:JCM.00717-19. [PMID: 31413081 PMCID: PMC6812990 DOI: 10.1128/jcm.00717-19] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/09/2019] [Indexed: 11/20/2022] Open
Abstract
Rifampin heteroresistance—where rifampin-resistant and -susceptible tuberculosis (TB) bacilli coexist—may result in failed standard TB treatment and potential spread of rifampin-resistant strains. The detection of rifampin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment and may improve rifampin-resistant TB control. Rifampin heteroresistance—where rifampin-resistant and -susceptible tuberculosis (TB) bacilli coexist—may result in failed standard TB treatment and potential spread of rifampin-resistant strains. The detection of rifampin heteroresistance in routine rapid diagnostic tests (RDTs) allows for patients to receive prompt and effective multidrug-resistant-TB treatment and may improve rifampin-resistant TB control. The limit of detection (LOD) of rifampin heteroresistance for phenotypic drug susceptibility testing by the proportion method is 1% and, yet, is insufficiently documented for RDTs. We, therefore, aimed to determine, for the four RDTs (XpertMTB/RIF, XpertMTB/RIF Ultra, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII), the LOD per probe and mutation, validated by CFU counting and targeted deep sequencing (Deeplex-MycTB). We selected one rifampin-susceptible and four rifampin-resistant strains, with mutations D435V, H445D, H445Y, and S450L, respectively, mixed them in various proportions in triplicate, tested them with each RDT, and determined the LODs per mutation type. Deeplex-MycTB revealed concordant proportions of the minority resistant variants in the mixtures. The Deeplex-MycTB-validated LODs ranged from 20% to 80% for XpertMTB/RIF, 20% to 70% for Xpert Ultra, 5% to 10% for GenoTypeMTBDRplusv2.0, and 1% to 10% for GenoscholarNTM+MDRTBII for the different mutations. Deeplex-MycTB, GenoTypeMTBDRplusv2.0, and GenoscholarNTM+MDRTBII provide explicit information on rifampin heteroresistance for the most frequently detected mutations. Classic Xpert and Ultra report rifampin heteroresistance as rifampin resistance, while Ultra may denote rifampin heteroresistance through “mixed patterns” of wild-type and mutant melt probe, melt peak temperatures. Overall, our findings inform end users that the threshold for reporting resistance in the case of rifampin heteroresistance is the highest for Classic Xpert and Ultra to resolve phenotypic and genotypic discordant rifampin-resistant TB results.
Collapse
|
46
|
Berhanu RH, Schnippel K, Kularatne R, Firnhaber C, Jacobson KR, Horsburgh CR, Lippincott CK. Can patients afford the cost of treatment for multidrug-resistant tuberculosis in Ethiopia? Int J Tuberc Lung Dis 2019; 22:358-362. [PMID: 29991400 DOI: 10.5588/ijtld.17.0837] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
SETTING Ethiopia has a high prevalence of tuberculosis (TB) and is one of the countries with the highest burden of multidrug-resistant TB (MDR-TB). OBJECTIVE To understand the costs that patients incur in obtaining diagnosis and treatment for MDR-TB. DESIGN In March 2013, interviews were conducted with 169 MDR-TB patients at three hospitals in Ethiopia to identify the cost to patients and the impact on employment and family income. RESULTS The average MDR-TB patient incurred a total cost of US$1378, which represented 25 months of a mid-treatment household income of US$54. The impact on the patient's employment and on overall patient and family income was generally catastrophic: 74% of all respondents reported losing their jobs, 66% of patients lost household income, and household income was reduced by 38%. To help cover the costs, 38% of patients sold some type of property, while 7% leased out property and 41% took out loans, any of which could jeopardize their future financial situation even further. CONCLUSION Despite services being officially free of charge, most patients incurred catastrophic costs and suffered significant income loss as a result of obtaining diagnosis and treatment for MDR-TB.
Collapse
Affiliation(s)
- R H Berhanu
- Division of Infectious Diseases, University of North Carolina at Chapel Hill, North Carolina, USA, Department of Medicine, Faculty of Health Sciences, Health Economics and Epidemiology Research Office, University of the Witwatersrand, Johannesburg, Right to Care, Johannesburg
| | - K Schnippel
- Right to Care, Johannesburg, Clinical HIV Research Unit, Department of Medicine, Faculty of Health Sciences
| | - R Kularatne
- National Institute for Communicable Diseases/National Health Laboratory Service and Department of Clinical Microbiology and Infectious Diseases, University of the Witwatersrand, Johannesburg, South Africa
| | - C Firnhaber
- Clinical HIV Research Unit, Department of Medicine, Faculty of Health Sciences, Department of Medicine, Infectious Disease Division, University of Colorado, Denver, Colorado
| | - K R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
| | - C R Horsburgh
- Department of Epidemiology, Boston University School of Public Health, Boston, Massachusetts
| | - C K Lippincott
- Department of Medicine, Division of Infectious Diseases, Johns Hopkins University, Baltimore, Maryland, USA
| |
Collapse
|
47
|
Rigouts L, Miotto P, Schats M, Lempens P, Cabibbe AM, Galbiati S, Lampasona V, de Rijk P, Cirillo DM, de Jong BC. Fluoroquinolone heteroresistance in Mycobacterium tuberculosis: detection by genotypic and phenotypic assays in experimentally mixed populations. Sci Rep 2019; 9:11760. [PMID: 31409849 PMCID: PMC6692311 DOI: 10.1038/s41598-019-48289-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/01/2019] [Indexed: 12/19/2022] Open
Abstract
Heteroresistance - the simultaneous presence of drug-susceptible and -resistant organisms - is common in Mycobacterium tuberculosis. In this study, we aimed to determine the limit of detection (LOD) of genotypic assays to detect gatifloxacin-resistant mutants in experimentally mixed populations. A fluoroquinolone-susceptible M. tuberculosis mother strain (S) and its in vitro selected resistant daughter strain harbouring the D94G mutation in gyrA (R) were mixed at different ratio’s. Minimum inhibitory concentrations (MICs) against gatifloxacin were determined, while PCR-based techniques included: line probe assays (Genotype MTBDRsl and GenoScholar-FQ + KM TB II), Sanger sequencing and targeted deep sequencing. Droplet digital PCR was used as molecular reference method. A breakpoint concentration of 0.25 mg/L allows the phenotypic detection of ≥1% resistant bacilli, whereas at 0.5 mg/L ≥ 5% resistant bacilli are detected. Line probe assays detected ≥5% mutants. Sanger sequencing required the presence of around 15% mutant bacilli to be detected as (hetero) resistant, while targeted deep sequencing detected ≤1% mutants. Deep sequencing and phenotypic testing are the most sensitive methods for detection of fluoroquinolone-resistant minority populations, followed by line probe assays (provided that the mutation is confirmed by a mutation band), while Sanger sequencing proved to be the least sensitive method.
Collapse
Affiliation(s)
- L Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - P Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - M Schats
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - P Lempens
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - A M Cabibbe
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - S Galbiati
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - V Lampasona
- Unit of Genomic for the Diagnosis of Human Pathologies, Division of Genetics and Cell Biology, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - P de Rijk
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - D M Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - B C de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| |
Collapse
|
48
|
Zong K, Luo C, Zhou H, Jiang Y, Li S. Xpert MTB/RIF assay for the diagnosis of rifampicin resistance in different regions: a meta-analysis. BMC Microbiol 2019; 19:177. [PMID: 31382894 PMCID: PMC6683411 DOI: 10.1186/s12866-019-1516-5] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 06/17/2019] [Indexed: 01/08/2023] Open
Abstract
Background To estimate the diagnostic accuracy of Xpert MTB/RIF for rifampicin resistance in different regions, a meta-analysis was carried out. Methods Several databases were searched for relevant studies up to March 3, 2019. A bivariate random-effects model was used to estimate the diagnostic accuracy. Results We identified 97 studies involving 26,037 samples for the diagnosis of rifampicin resistance. The pooled sensitivity, specificity and AUC of Xpert MTB/RIF for rifampicin resistance detection were 0.93 (95% CI 0.90–0.95), 0.98 (95% CI 0.96–0.98) and 0.99 (95% CI 0.97–0.99), respectively. For different regions, the pooled sensitivity were 0.94(95% CI 0.89–0.97) and 0.92 (95% CI 0.88–0.94), the pooled specificity were 0.98 (95% CI 0.94–1.00) and 0.98 (95% CI 0.96–0.99), and the AUC were 0.99 (95% CI 0.98–1.00) and 0.99 (95% CI 0.97–0.99) in high and middle/low income countries, respectively. The pooled sensitivity were 0.91 (95% CI 0.87–0.94) and 0.91 (95% CI 0.86–0.94), the pooled specificity were 0.98 (95% CI 0.96–0.99) and 0.98 (95% CI 0.96–0.99), and the AUC were 0.98 (95% CI 0.97–0.99) and 0.99 (95% CI 0.97–0.99) in high TB burden and middle/low prevalence countries, respectively. Conclusions The diagnostic accuracy of Xpert MTB/RIF for rifampicin resistance detection was excellent.
Collapse
Affiliation(s)
- Kaican Zong
- Department of Respiratory Medicine, The Seventh People's Hospital of Chongqing, Chongqing, People's Republic of China
| | - Chen Luo
- Department of Respiratory Medicine, The Seventh People's Hospital of Chongqing, Chongqing, People's Republic of China
| | - Hui Zhou
- Department of Respiratory Medicine, The Seventh People's Hospital of Chongqing, Chongqing, People's Republic of China
| | - Yangzhi Jiang
- Department of Respiratory Medicine, The Seventh People's Hospital of Chongqing, Chongqing, People's Republic of China
| | - Shiying Li
- Department of Infectious Disease, The Second Affiliated Hospital, Chongqing Medical University, 74# Linjiang Road, Chongqing, 400010, People's Republic of China.
| |
Collapse
|
49
|
Mechanisms and clinical relevance of bacterial heteroresistance. Nat Rev Microbiol 2019; 17:479-496. [DOI: 10.1038/s41579-019-0218-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/09/2019] [Indexed: 02/08/2023]
|
50
|
Horne DJ, Kohli M, Zifodya JS, Schiller I, Dendukuri N, Tollefson D, Schumacher SG, Ochodo EA, Pai M, Steingart KR. Xpert MTB/RIF and Xpert MTB/RIF Ultra for pulmonary tuberculosis and rifampicin resistance in adults. Cochrane Database Syst Rev 2019; 6:CD009593. [PMID: 31173647 PMCID: PMC6555588 DOI: 10.1002/14651858.cd009593.pub4] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
BACKGROUND Xpert MTB/RIF (Xpert MTB/RIF) and Xpert MTB/RIF Ultra (Xpert Ultra), the newest version, are the only World Health Organization (WHO)-recommended rapid tests that simultaneously detect tuberculosis and rifampicin resistance in persons with signs and symptoms of tuberculosis, at lower health system levels. A previous Cochrane Review found Xpert MTB/RIF sensitive and specific for tuberculosis (Steingart 2014). Since the previous review, new studies have been published. We performed a review update for an upcoming WHO policy review. OBJECTIVES To determine diagnostic accuracy of Xpert MTB/RIF and Xpert Ultra for tuberculosis in adults with presumptive pulmonary tuberculosis (PTB) and for rifampicin resistance in adults with presumptive rifampicin-resistant tuberculosis. SEARCH METHODS We searched the Cochrane Infectious Diseases Group Specialized Register, MEDLINE, Embase, Science Citation Index, Web of Science, Latin American Caribbean Health Sciences Literature, Scopus, the WHO International Clinical Trials Registry Platform, the International Standard Randomized Controlled Trial Number Registry, and ProQuest, to 11 October 2018, without language restriction. SELECTION CRITERIA Randomized trials, cross-sectional, and cohort studies using respiratory specimens that evaluated Xpert MTB/RIF, Xpert Ultra, or both against the reference standard, culture for tuberculosis and culture-based drug susceptibility testing or MTBDRplus for rifampicin resistance. DATA COLLECTION AND ANALYSIS Four review authors independently extracted data using a standardized form. When possible, we also extracted data by smear and HIV status. We assessed study quality using QUADAS-2 and performed meta-analyses to estimate pooled sensitivity and specificity separately for tuberculosis and rifampicin resistance. We investigated potential sources of heterogeneity. Most analyses used a bivariate random-effects model. For tuberculosis detection, we first estimated accuracy using all included studies and then only the subset of studies where participants were unselected, i.e. not selected based on prior microscopy testing. MAIN RESULTS We identified in total 95 studies (77 new studies since the previous review): 86 studies (42,091 participants) evaluated Xpert MTB/RIF for tuberculosis and 57 studies (8287 participants) for rifampicin resistance. One study compared Xpert MTB/RIF and Xpert Ultra on the same participant specimen.Tuberculosis detectionOf the total 86 studies, 45 took place in high tuberculosis burden and 50 in high TB/HIV burden countries. Most studies had low risk of bias.Xpert MTB/RIF pooled sensitivity and specificity (95% credible Interval (CrI)) were 85% (82% to 88%) and 98% (97% to 98%), (70 studies, 37,237 unselected participants; high-certainty evidence). We found similar accuracy when we included all studies.For a population of 1000 people where 100 have tuberculosis on culture, 103 would be Xpert MTB/RIF-positive and 18 (17%) would not have tuberculosis (false-positives); 897 would be Xpert MTB/RIF-negative and 15 (2%) would have tuberculosis (false-negatives).Xpert Ultra sensitivity (95% confidence interval (CI)) was 88% (85% to 91%) versus Xpert MTB/RIF 83% (79% to 86%); Xpert Ultra specificity was 96% (94% to 97%) versus Xpert MTB/RIF 98% (97% to 99%), (1 study, 1439 participants; moderate-certainty evidence).Xpert MTB/RIF pooled sensitivity was 98% (97% to 98%) in smear-positive and 67% (62% to 72%) in smear-negative, culture-positive participants, (45 studies). Xpert MTB/RIF pooled sensitivity was 88% (83% to 92%) in HIV-negative and 81% (75% to 86%) in HIV-positive participants; specificities were similar 98% (97% to 99%), (14 studies).Rifampicin resistance detectionXpert MTB/RIF pooled sensitivity and specificity (95% Crl) were 96% (94% to 97%) and 98% (98% to 99%), (48 studies, 8020 participants; high-certainty evidence).For a population of 1000 people where 100 have rifampicin-resistant tuberculosis, 114 would be positive for rifampicin-resistant tuberculosis and 18 (16%) would not have rifampicin resistance (false-positives); 886 would be would be negative for rifampicin-resistant tuberculosis and four (0.4%) would have rifampicin resistance (false-negatives).Xpert Ultra sensitivity (95% CI) was 95% (90% to 98%) versus Xpert MTB/RIF 95% (91% to 98%); Xpert Ultra specificity was 98% (97% to 99%) versus Xpert MTB/RIF 98% (96% to 99%), (1 study, 551 participants; moderate-certainty evidence). AUTHORS' CONCLUSIONS We found Xpert MTB/RIF to be sensitive and specific for diagnosing PTB and rifampicin resistance, consistent with findings reported previously. Xpert MTB/RIF was more sensitive for tuberculosis in smear-positive than smear-negative participants and HIV-negative than HIV-positive participants. Compared with Xpert MTB/RIF, Xpert Ultra had higher sensitivity and lower specificity for tuberculosis and similar sensitivity and specificity for rifampicin resistance (1 study). Xpert MTB/RIF and Xpert Ultra provide accurate results and can allow rapid initiation of treatment for multidrug-resistant tuberculosis.
Collapse
Affiliation(s)
- David J Horne
- University of WashingtonDepartment of Medicine, Division of Pulmonary and Critical Care Medicine, and Firland Northwest TB CenterSeattleUSA
| | - Mikashmi Kohli
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthMontrealCanada
| | - Jerry S Zifodya
- University of WashingtonPulmonary and Critical Care Medicine325 9th Avenue – Campus Box 359762SeattleUSA98104
| | - Ian Schiller
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | - Nandini Dendukuri
- McGill University Health Centre ‐ Research InstituteDivision of Clinical EpidemiologyMontrealCanada
| | | | | | - Eleanor A Ochodo
- Stellenbosch UniversityCentre for Evidence‐based Health Care, Faculty of Medicine and Health SciencesPO Box 241Cape TownSouth Africa8000
| | - Madhukar Pai
- McGill UniversityDepartment of Epidemiology, Biostatistics and Occupational HealthMontrealCanada
| | - Karen R Steingart
- Department of Clinical Sciences, Liverpool School of Tropical MedicineHonorary Research FellowPembroke PlaceLiverpoolUK
| |
Collapse
|