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Hlanze H, Mutshembele A, Reva ON. Universal Lineage-Independent Markers of Multidrug Resistance in Mycobacterium tuberculosis. Microorganisms 2024; 12:1340. [PMID: 39065108 PMCID: PMC11278869 DOI: 10.3390/microorganisms12071340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
(1) Background: This study was aimed to identify universal genetic markers of multidrug resistance (MDR) in Mycobacterium tuberculosis (Mtb) and establish statistical associations among identified mutations to enhance understanding of MDR in Mtb and inform diagnostic and treatment development. (2) Methods: GWAS analysis and the statistical evaluation of identified polymorphic sites within protein-coding genes of Mtb were performed. Statistical associations between specific mutations and antibiotic resistance were established using attributable risk statistics. (3) Results: Sixty-four polymorphic sites were identified as universal markers of drug resistance, with forty-seven in PE/PPE regions and seventeen in functional genes. Mutations in genes such as cyp123, fadE36, gidB, and ethA showed significant associations with resistance to various antibiotics. Notably, mutations in cyp123 at codon position 279 were linked to resistance to ten antibiotics. The study highlighted the role of PE/PPE and PE_PGRS genes in Mtb's evolution towards a 'mutator phenotype'. The pathways of acquisition of mutations forming the epistatic landscape of MDR were discussed. (4) Conclusions: This research identifies marker mutations across the Mtb genome associated with MDR. The findings provide new insights into the molecular basis of MDR acquisition in Mtb, aiding in the development of more effective diagnostics and treatments targeting these mutations to combat MDR tuberculosis.
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Affiliation(s)
- Hleliwe Hlanze
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hillcrest, Lynnwood Rd, Pretoria 0002, South Africa;
| | - Awelani Mutshembele
- South African Medical Research Council, TB Platform, 1 Soutpansberg Road, Private Bag X385, Pretoria 0001, South Africa;
| | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Hillcrest, Lynnwood Rd, Pretoria 0002, South Africa;
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2
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Zhang G, Sun X, Fleming J, Ran F, Luo J, Chen H, Ju H, Wang Z, Zhao H, Wang C, Zhang F, Dai X, Yang X, Li C, Liu Y, Wang Y, Zhang X, Jiang Y, Wu Z, Bi L, Zhang H. Genetic factors associated with acquired phenotypic drug resistance and its compensatory evolution during tuberculosis treatment. Clin Microbiol Infect 2024; 30:637-645. [PMID: 38286176 DOI: 10.1016/j.cmi.2024.01.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 01/15/2024] [Accepted: 01/22/2024] [Indexed: 01/31/2024]
Abstract
OBJECTIVES We elucidated the factors, evolution, and compensation of antimicrobial resistance (AMR) in Mycobacterium tuberculosis (MTB) isolates under dual pressure from the intra-host environment and anti-tuberculosis (anti-TB) drugs. METHODS This retrospective case-control study included 337 patients with pulmonary tuberculosis from 15 clinics in Tianjin, China, with phenotypic drug susceptibility testing results available for at least two time points between January 1, 2009 and December 31, 2016. Patients in the case group exhibited acquired AMR to isoniazid (INH) or rifampicin (RIF), while those in the control group lacked acquired AMR. The whole-genome sequencing (WGS) was conducted on 149 serial longitudinal MTB isolates from 46 patients who acquired or reversed phenotypic INH/RIF-resistance during treatment. The genetic basis, associated factors, and intra-host evolution of acquired phenotypic INH/RIF-resistance were elucidated using a combined analysis. RESULTS Anti-TB interruption duration of ≥30 days showed association with acquired phenotypic INH/RIF resistance (aOR = 2·2, 95% CI, 1·0-5·1) and new rpoB mutations (p = 0·024). The MTB evolution was 1·2 (95% CI, 1·02-1·38) single nucleotide polymorphisms per genome per year under dual pressure from the intra-host environment and anti-TB drugs. AMR-associated mutations occurred before phenotypic AMR appearance in cases with acquired phenotypic INH (10 of 16) and RIF (9 of 22) resistances. DISCUSSION Compensatory evolution may promote the fixation of INH/RIF-resistance mutations and affect phenotypic AMR. The TB treatment should be adjusted based on gene sequencing results, especially in persistent culture positivity during treatment, which highlights the clinical importance of WGS in identifying reinfection and AMR acquisition before phenotypic drug susceptibility testing.
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Affiliation(s)
- Guoqin Zhang
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Tianjin Center for Tuberculosis Control, Tianjin, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xianhui Sun
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Joy Fleming
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Fanlei Ran
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Jianjun Luo
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hong Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Hanfang Ju
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Zhirui Wang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Hui Zhao
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Chunhua Wang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Fan Zhang
- Tianjin Center for Tuberculosis Control, Tianjin, China
| | - Xiaowei Dai
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Xinyu Yang
- Beijing Center for Disease Prevention and Control, Beijing, China
| | - Chuanyou Li
- Biobank of Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumour Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Yi Liu
- Biobank of Beijing Chest Hospital, Beijing Tuberculosis and Thoracic Tumour Research Institute/Beijing Chest Hospital, Capital Medical University, Beijing, China
| | | | - Xilin Zhang
- Foshan Fourth People's Hospital, Foshan, China
| | - Yuan Jiang
- Shanghai Municipal Center for Disease Prevention and Control, Beijing, China
| | - Zhilong Wu
- Foshan Fourth People's Hospital, Foshan, China
| | - Lijun Bi
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China; Guangzhou National Laboratory, Guangzhou, China; University of Chinese Academy of Sciences, Beijing, China
| | - Hongtai Zhang
- Beijing Center for Disease Prevention and Control, Beijing, China.
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3
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Dheda K, Mirzayev F, Cirillo DM, Udwadia Z, Dooley KE, Chang KC, Omar SV, Reuter A, Perumal T, Horsburgh CR, Murray M, Lange C. Multidrug-resistant tuberculosis. Nat Rev Dis Primers 2024; 10:22. [PMID: 38523140 DOI: 10.1038/s41572-024-00504-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2024] [Indexed: 03/26/2024]
Abstract
Tuberculosis (TB) remains the foremost cause of death by an infectious disease globally. Multidrug-resistant or rifampicin-resistant TB (MDR/RR-TB; resistance to rifampicin and isoniazid, or rifampicin alone) is a burgeoning public health challenge in several parts of the world, and especially Eastern Europe, Russia, Asia and sub-Saharan Africa. Pre-extensively drug-resistant TB (pre-XDR-TB) refers to MDR/RR-TB that is also resistant to a fluoroquinolone, and extensively drug-resistant TB (XDR-TB) isolates are additionally resistant to other key drugs such as bedaquiline and/or linezolid. Collectively, these subgroups are referred to as drug-resistant TB (DR-TB). All forms of DR-TB can be as transmissible as rifampicin-susceptible TB; however, it is more difficult to diagnose, is associated with higher mortality and morbidity, and higher rates of post-TB lung damage. The various forms of DR-TB often consume >50% of national TB budgets despite comprising <5-10% of the total TB case-load. The past decade has seen a dramatic change in the DR-TB treatment landscape with the introduction of new diagnostics and therapeutic agents. However, there is limited guidance on understanding and managing various aspects of this complex entity, including the pathogenesis, transmission, diagnosis, management and prevention of MDR-TB and XDR-TB, especially at the primary care physician level.
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Affiliation(s)
- Keertan Dheda
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa.
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK.
| | - Fuad Mirzayev
- Global Tuberculosis Programme, WHO, Geneva, Switzerland
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, IRCCS San Raffaele Scientific Institute Milan, Milan, Italy
| | - Zarir Udwadia
- Department of Pulmonology, Hinduja Hospital & Research Center, Mumbai, India
| | - Kelly E Dooley
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kwok-Chiu Chang
- Tuberculosis and Chest Service, Centre for Health Protection, Department of Health, Hong Kong, SAR, China
| | - Shaheed Vally Omar
- Centre for Tuberculosis, National & WHO Supranational TB Reference Laboratory, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Molecular Medicine & Haematology, School of Pathology, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
| | - Anja Reuter
- Sentinel Project on Paediatric Drug-Resistant Tuberculosis, Boston, MA, USA
| | - Tahlia Perumal
- Centre for Lung Infection and Immunity, Division of Pulmonology, Department of Medicine and UCT Lung Institute & South African MRC/UCT Centre for the Study of Antimicrobial Resistance, University of Cape Town, Cape Town, South Africa
- Faculty of Infectious and Tropical Diseases, Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, UK
| | - C Robert Horsburgh
- Department of Epidemiology, Boston University Schools of Public Health and Medicine, Boston, MA, USA
| | - Megan Murray
- Department of Epidemiology, Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Division of Clinical Infectious Diseases, Research Center Borstel, Borstel, Germany
- German Center for Infection Research (DZIF), TTU-TB, Borstel, Germany
- Respiratory Medicine & International Health, University of Lübeck, Lübeck, Germany
- Department of Paediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
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4
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Silcocks M, Chang X, Thuong Thuong NT, Qin Y, Minh Ha DT, Khac Thai PV, Vijay S, Anh Thu DD, Ngoc Ha VT, Ngoc Nhung H, Huu Lan N, Quynh Nhu NT, Edwards D, Nath A, Pham K, Duc Bang N, Hong Chau TT, Thwaites G, Heemskerk AD, Chuen Khor C, Teo YY, Inouye M, Ong RTH, Caws M, Holt KE, Dunstan SJ. Evolution and transmission of antibiotic resistance is driven by Beijing lineage Mycobacterium tuberculosis in Vietnam. Microbiol Spectr 2023; 11:e0256223. [PMID: 37971428 PMCID: PMC10714959 DOI: 10.1128/spectrum.02562-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 10/12/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Drug-resistant tuberculosis (TB) infection is a growing and potent concern, and combating it will be necessary to achieve the WHO's goal of a 95% reduction in TB deaths by 2035. While prior studies have explored the evolution and spread of drug resistance, we still lack a clear understanding of the fitness costs (if any) imposed by resistance-conferring mutations and the role that Mtb genetic lineage plays in determining the likelihood of resistance evolution. This study offers insight into these questions by assessing the dynamics of resistance evolution in a high-burden Southeast Asian setting with a diverse lineage composition. It demonstrates that there are clear lineage-specific differences in the dynamics of resistance acquisition and transmission and shows that different lineages evolve resistance via characteristic mutational pathways.
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Affiliation(s)
- Matthew Silcocks
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
| | - Xuling Chang
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
- Department of Paediatrics, Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Khoo Teck Puat–National University Children’s Medical Institute, National University Health System, Singapore
| | - Nguyen Thuy Thuong Thuong
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - Youwen Qin
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Melbourne, Victoria, Australia
| | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Srinivasan Vijay
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
- Theoretical Microbial Ecology, Friedrich Schiller University Jena, Jena, Germany
| | - Do Dang Anh Thu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Hoang Ngoc Nhung
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Nguyen Thi Quynh Nhu
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - David Edwards
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Artika Nath
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Nguyen Duc Bang
- Pham Ngoc Thach Hospital for TB and Lung Disease, District 5, Ho Chi Minh City, Vietnam
| | - Tran Thi Hong Chau
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Hospital for Tropical Diseases, District 5, Ho Chi Minh City, Vietnam
- Nuffield Department of Medicine, Centre for Tropical Medicine and Global Health, University of Oxford, Oxford, United Kingdom
| | - A. Dorothee Heemskerk
- Department of Medical Microbiology and Infection Prevention, Amsterdam University Medical Centre, Amsterdam, Netherlands
| | | | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Michael Inouye
- Cambridge Baker Systems Genomics Initiative, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Public Health and Primary Care, Cambridge Baker Systems Genomics Initiative, University of Cambridge, Cambridge, United Kingdom
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
| | - Maxine Caws
- Liverpool School of Tropical Medicine, Liverpool, United Kingdom
- Birat Nepal Medical Trust, Kathmandu, Nepal
| | - Kathryn E. Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Sarah J. Dunstan
- Department of Infectious Diseases, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Parkville, Victoria, Australia
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5
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Ren W, Mao Y, Li S, Gao B, Fu X, Liu X, Zhu P, Shang Y, Li Y, Ma B, Sun L, Xu J, Pang Y. Rapid Mycobacterium abscessus antimicrobial susceptibility testing based on antibiotic treatment response mapping via Raman Microspectroscopy. Ann Clin Microbiol Antimicrob 2023; 22:94. [PMID: 37904155 PMCID: PMC10617219 DOI: 10.1186/s12941-023-00644-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Accepted: 10/17/2023] [Indexed: 11/01/2023] Open
Abstract
OBJECTIVES Antimicrobial susceptibility tests (ASTs) are pivotal tools for detecting and combating infections caused by multidrug-resistant rapidly growing mycobacteria (RGM) but are time-consuming and labor-intensive. DESIGN We used a Mycobacterium abscessus-based RGM model to develop a rapid (24-h) AST from the beginning of the strain culture, the Clinical Antimicrobials Susceptibility Test Ramanometry for RGM (CAST-R-RGM). The ASTs obtained for 21 clarithromycin (CLA)-treated and 18 linezolid (LZD)-treated RGM isolates. RESULTS CAST-R-RGM employs D2O-probed Raman microspectroscopy to monitor RGM metabolic activity, while also revealing bacterial antimicrobial drug resistance mechanisms. The results of clarithromycin (CLA)-treated and linezolid (LZD)-treated RGM isolates exhibited 90% and 83% categorical agreement, respectively, with conventional AST results of the same isolates. Furthermore, comparisons of time- and concentration-dependent Raman results between CLA- and LZD-treated RGM strains revealed distinct metabolic profiles after 48-h and 72-h drug treatments, despite similar profiles obtained for both drugs after 24-h treatments. CONCLUSIONS Ultimately, the rapid, accurate, and low-cost CAST-R-RGM assay offers advantages over conventional culture-based ASTs that warrant its use as a tool for improving patient treatment outcomes and revealing bacterial drug resistance mechanisms.
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Affiliation(s)
- Weicong Ren
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuli Mao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Shanshan Li
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Bo Gao
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaoting Fu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaolu Liu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pengfei Zhu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- Qingdao Single-Cell Biotech, Co. Ltd, Qingdao, Shandong, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China
| | - Yuandong Li
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Bo Ma
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Luyang Sun
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Jian Xu
- Single-Cell Center, Shandong Key Laboratory of Energy Genetics and Shandong Energy Institute, Qingdao Institute of Bioenergy and Bioprocess Technology, CAS Key Laboratory of Biofuels, Chinese Academy of Sciences, Qingdao, Shandong, China.
- University of Chinese Academy of Sciences, Beijing, China.
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, 101149, China.
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Pant A, Das B, Arimbasseri GA. Host microbiome in tuberculosis: disease, treatment, and immunity perspectives. Front Microbiol 2023; 14:1236348. [PMID: 37808315 PMCID: PMC10559974 DOI: 10.3389/fmicb.2023.1236348] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/29/2023] [Indexed: 10/10/2023] Open
Abstract
Tuberculosis (TB), an airborne pulmonary disease caused by Mycobacterium tuberculosis (M. tb), poses an unprecedented health and economic burden to most of the developing countries. Treatment of TB requires prolonged use of a cocktail of antibiotics, which often manifest several side effects, including stomach upset, nausea, and loss of appetite spurring on treatment non-compliance and the emergence of antibiotic resistant M. tb. The anti-TB treatment regimen causes imbalances in the composition of autochthonous microbiota associated with the human body, which also contributes to major side effects. The microbiota residing in the gastrointestinal tract play an important role in various physiological processes, including resistance against colonization by pathogens, boosting host immunity, and providing key metabolic functions. In TB patients, due to prolonged exposure to anti-tuberculosis drugs, the gut microbiota significantly loses its diversity and several keystone bacterial taxa. This loss may result in a significant reduction in the functional potency of the microbiota, which is a probable reason for poor treatment outcomes. In this review, we discuss the structural and functional changes of the gut microbiota during TB and its treatment. A major focus of the review is oriented to the gut microbial association with micronutrient profiles and immune cell dynamics during TB infection. Furthermore, we summarize the acquisition of anti-microbial resistance in M. tb along with the microbiome-based therapeutics to cure the infections. Understanding the relationship between these components and host susceptibility to TB disease is important to finding potential targets that may be used in TB prevention, progression, and cure.
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Affiliation(s)
- Archana Pant
- Molecular Genetics Lab, National Institute of Immunology, New Delhi, India
| | - Bhabatosh Das
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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7
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Khan MT, Mahmud A, Islam MM, Sumaia MSN, Rahim Z, Islam K, Iqbal A. Multi-epitope vaccine against drug-resistant strains of Mycobacterium tuberculosis: a proteome-wide subtraction and immunoinformatics approach. Genomics Inform 2023; 21:e42. [PMID: 37813638 PMCID: PMC10584640 DOI: 10.5808/gi.23021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 10/11/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis, one of the most deadly infections in humans. The emergence of multidrug-resistant and extensively drug-resistant Mtb strains presents a global challenge. Mtb has shown resistance to many frontline antibiotics, including rifampicin, kanamycin, isoniazid, and capreomycin. The only licensed vaccine, Bacille Calmette-Guerin, does not efficiently protect against adult pulmonary tuberculosis. Therefore, it is urgently necessary to develop new vaccines to prevent infections caused by these strains. We used a subtractive proteomics approach on 23 virulent Mtb strains and identified a conserved membrane protein (MmpL4, NP_214964.1) as both a potential drug target and vaccine candidate. MmpL4 is a non-homologous essential protein in the host and is involved in the pathogen-specific pathway. Furthermore, MmpL4 shows no homology with anti-targets and has limited homology to human gut microflora, potentially reducing the likelihood of adverse effects and cross-reactivity if therapeutics specific to this protein are developed. Subsequently, we constructed a highly soluble, safe, antigenic, and stable multi-subunit vaccine from the MmpL4 protein using immunoinformatics. Molecular dynamics simulations revealed the stability of the vaccine-bound Toll-like receptor-4 complex on a nanosecond scale, and immune simulations indicated strong primary and secondary immune responses in the host. Therefore, our study identifies a new target that could expedite the design of effective therapeutics, and the designed vaccine should be validated. Future directions include an extensive molecular interaction analysis, in silico cloning, wet-lab experiments, and evaluation and comparison of the designed candidate as both a DNA vaccine and protein vaccine.
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Affiliation(s)
- Md Tahsin Khan
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Araf Mahmud
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Md. Muzahidul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Mst. Sayedatun Nessa Sumaia
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Zeaur Rahim
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Mohakhali, Dhaka, Bangladesh
| | - Kamrul Islam
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
| | - Asif Iqbal
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet 3114, Bangladesh
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea
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8
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Dokrungkoon T, Tulyaprawat O, Suwannakarn K, Ngamskulrungroj P. In vitro modeling of isoniazid resistance mechanisms in Mycobacterium tuberculosis H37Rv. Front Microbiol 2023; 14:1171861. [PMID: 37492259 PMCID: PMC10364472 DOI: 10.3389/fmicb.2023.1171861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Accepted: 06/06/2023] [Indexed: 07/27/2023] Open
Abstract
Introduction Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis, has been a global threat to human beings for several decades. Treating tuberculosis has become more difficult as the prevalence of drug-resistant tuberculosis has increased globally. Evidence suggests that the comprehensive landscape of resistance mechanisms in MTB is ambiguous. More importantly, little is known regarding the series of events connected to resistance mechanisms in MTB before exposure to anti-TB drugs, during exposure to the drugs, and finally, when the MTB becomes resistant after exposure, upon analyses of its genome. Methods We used the wild-type strain of MTB (H37Rv) in an in vitro model for generating induced resistance using a sub-inhibitory concentration of isoniazid, and the generated resistance-associated variants (RAVs) were identified using the whole genome sequencing method. Results The detection of an inhA promoter mutation (fabG1-15C>T), which results in increased production of InhA protein, was found to be a major mechanism for developing resistance to isoniazid in the first place. We observed adaptation of MTB resistance mechanisms in high isoniazid stress by alteration and abolishment of KatG due to the detection of katG S315N, the common region of mutation that confers isoniazid resistance, along with katG K414N, katG N138S, and katG A162E. Furthermore, we detected the ahpC-72C>T and ahpC 21C>A mutations, but further investigation is needed to determine their role in compensating for the loss of KatG activity. Discussion This suggests that increased InhA production is the main mechanism where there are low levels of isoniazid, whereas the alteration of KatG was found to be utilized in mycobacterium with a high concentration of isoniazid. Our work demonstrates that this in vitro approach of generating induced resistance could provide clinically relevant information after the fabG1-15C>T mutation, which is the common mutation found in clinical isolates. Moreover, other mutations detected in this work can also be found in clinical isolates. These findings may shed light on the impact of isoniazid in generating RAV and the resistance mechanism scenario that mycobacterium used under various isoniazid-pressuring conditions. More research is needed to understand better the role of RAV and mechanical resistance events within the mycobacterium genome in promoting a promising drug prediction platform that could lead to the right treatment for patients with MDR-TB and XDR-TB.
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Opperman CJ, Wojno J, Goosen W, Warren R. Phages for the treatment of Mycobacterium species. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2023; 201:41-92. [PMID: 37770176 DOI: 10.1016/bs.pmbts.2023.03.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/03/2023]
Abstract
Highly drug-resistant strains are not uncommon among the Mycobacterium genus, with patients requiring lengthy antibiotic treatment regimens with multiple drugs and harmful side effects. This alarming increase in antibiotic resistance globally has renewed the interest in mycobacteriophage therapy for both Mycobacterium tuberculosis complex and non-tuberculosis mycobacteria. With the increasing number of genetically well-characterized mycobacteriophages and robust engineering tools to convert temperate phages to obligate lytic phages, the phage cache against extensive drug-resistant mycobacteria is constantly expanding. Synergistic effects between phages and TB drugs are also a promising avenue to research, with mycobacteriophages having several additional advantages compared to traditional antibiotics due to their different modes of action. These advantages include less side effects, a narrow host spectrum, biofilm penetration, self-replication at the site of infection and the potential to be manufactured on a large scale. In addition, mycobacteriophage enzymes, not yet in clinical use, warrant further studies with their additional benefits for rupturing host bacteria thereby limiting resistance development as well as showing promise in vitro to act synergistically with TB drugs. Before mycobacteriophage therapy can be envisioned as part of routine care, several obstacles must be overcome to translate in vitro work into clinical practice. Strategies to target intracellular bacteria and selecting phage cocktails to limit cross-resistance remain important avenues to explore. However, insight into pathophysiological host-phage interactions on a molecular level and innovative solutions to transcend mycobacteriophage therapy impediments, offer sufficient encouragement to explore phage therapy. Recently, the first successful clinical studies were performed using a mycobacteriophage-constructed cocktail to treat non-tuberculosis mycobacteria, providing substantial insight into lessons learned and potential pitfalls to avoid in order to ensure favorable outcomes. However, due to mycobacterium strain variation, mycobacteriophage therapy remains personalized, only being utilized in compassionate care cases until there is further regulatory approval. Therefore, identifying the determinants that influence clinical outcomes that can expand the repertoire of mycobacteriophages for therapeutic benefit, remains key for their future application.
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Affiliation(s)
- Christoffel Johannes Opperman
- National Health Laboratory Service, Green Point TB-Laboratory, Cape Town, South Africa; DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa; Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa.
| | - Justyna Wojno
- Division of Medical Microbiology, University of Cape Town, Cape Town, South Africa; Lancet Laboratories, Cape Town, South Africa
| | - Wynand Goosen
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
| | - Rob Warren
- DSI-NRF Centre of Excellence for Biomedical Tuberculosis Research, SAMRC Centre for tuberculosis Research, Division of Molecular Biology and Human Genetics, Stellenbosch University, Cape Town, South Africa
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Ejo M, Torrea G, Diro E, Abebe A, Kassa M, Girma Y, Tesfa E, Ejigu K, Uwizeye C, Gehre F, de Jong BC, Rigouts L. Strain diversity and gene mutations associated with presumptive multidrug-resistant Mycobacterium tuberculosis complex isolates in Northwest Ethiopia. J Glob Antimicrob Resist 2023; 32:167-175. [PMID: 36470362 DOI: 10.1016/j.jgar.2022.11.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 08/25/2022] [Accepted: 11/25/2022] [Indexed: 12/07/2022] Open
Abstract
OBJECTIVES In this study, we assessed the genetic diversity and gene mutations that confer resistance to rifampicin (RIF), isoniazid (INH), fluoroquinolone (FQ), and second-line injectable (SLI) drugs in RIF-resistant (RR)/multidrug-resistant tuberculosis (MDR-TB) isolates in Northwest Ethiopia. METHODS Spoligotyping was used to assign isolates to TB lineages (Ls), and Hain line probe assays were used to detect resistance to RIF, INH, and FQs, and SLIs. RESULTS Among 130 analyzed strains, 68.5% were RR, and four major Mycobacterium tuberculosis complex lineages (L1, L3, L4, and L7) were identified with a predominance of the Euro-American L4 (72, 54.7%), while L7 genotypes were less common (3, 2.3%). Overall, the L4-T3-ETH (41, 32.0%), L3-CAS1-Delhi (29, 22.7%), and L3-CAS1-Killi (19, 14.8%) families were most common. Line probe analysis showed that among rpoB mutants, 65.2% were S450L, while 87.8% of katG mutants were S315T. Only three isolates showed mutation (c-15t) at the inhA gene, and no double mutation with katG and inhA genes was found. Six strains, two each of L1, L3, and L4, were resistant to FQs, having gyrA mutations (D94G, S91P), of which three isolates had additional resistance to SLI (rrs A1401G or C1402T mutations) including one isolate with low-level kanamycin (KAN) resistance. CONCLUSIONS This study showed a predominance of L4-T3-ETH, L3-CAS1-Delhi, and L3-CAS1-Killi families, with a high rate of rpoB_S450L and katG_S315T mutations and a low proportion of gyrA and rrs mutations. L7 was less frequently observed in this study. Further investigations are, therefore, needed to understand L7 and other lineages with undefined mutations.
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Affiliation(s)
- Mebrat Ejo
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Gondar, Gondar, Ethiopia; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium.
| | - Gabriela Torrea
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Ermias Diro
- Department of Internal Medicine, University of Gondar, Gondar, Ethiopia; MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Ayenesh Abebe
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Meseret Kassa
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Yilak Girma
- TB culture laboratory, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Eyasu Tesfa
- MDR-TB Treatment and Follow-up Center, University of Gondar Specialized Hospital, Gondar, Ethiopia
| | - Kefialew Ejigu
- TB culture laboratory, Amhara Public Health Institute, Bahir Dar, Ethiopia
| | - Cecile Uwizeye
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Florian Gehre
- Department of Infectious Disease Epidemiology, Bernhard-Nocht-Institute for Tropical Medicine, Hamburg, Germany; East African Community Secretariat, Arusha, Tanzania
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
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Marie V, Gordon M. Understanding the co-evolutionary molecular mechanisms of resistance in the HIV-1 Gag and protease. J Biomol Struct Dyn 2022; 40:10852-10861. [PMID: 34253143 DOI: 10.1080/07391102.2021.1950569] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Due to high human immunodeficiency virus type 1 (HIV-1) subtype C infections coupled with increasing antiretroviral treatment failure, the elucidation of complex drug resistance mutational patterns arising through protein co-evolution is required. Despite the inclusion of potent protease inhibitors Lopinavir (LPV) and Darunavir (DRV) in second- and third-line therapies, many patients still fail treatment due to the accumulation of mutations in protease (PR) and recently, Gag. To understand the co-evolutionary molecular mechanisms of resistance in the HIV-1 PR and Gag, we performed 100 ns molecular dynamic simulations on multidrug resistant PR's when bound to LPV, DRV or a mutated A431V NC|p1 Gag cleavage site (CS). Here we showed that distinct changes in PR's active site, flap and elbow regions due to several PR resistance mutations (L10F, M46I, I54V, L76V, V82A) were found to alter LPV and DRV drug binding. However, binding was significantly exacerbated when the mutant PRs were bound to the NC|p1 Gag CS. Although A431V was shown to coordinate several residues in PR, the L76V PR mutation was found to have a significant role in substrate recognition. Consequently, a greater binding affinity was observed when the mutated substrate was bound to an L76V-inclusive PR mutant (Gbind: -62.46 ± 5.75 kcal/mol) than without (Gbind: -50.34 ± 6.28 kcal/mol). These data showed that the co-selection of resistance mutations in the enzyme and substrate can simultaneously constrict regions in PR's active site whilst flexing the flaps to allow flexible movement of the substrate and multiple, complex mechanisms of resistance to occur. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Veronna Marie
- KwaZulu-Natal Research Innovation & Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, DurbanSouth Africa
| | - Michelle Gordon
- KwaZulu-Natal Research Innovation & Sequencing Platform (KRISP), Nelson R Mandela School of Medicine, University of KwaZulu-Natal, DurbanSouth Africa
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Li S, Chen W, Feng M, Liu Y, Wang F. Drug Resistance and Molecular Characteristics of Mycobacterium tuberculosis: A Single Center Experience. J Pers Med 2022; 12:jpm12122088. [PMID: 36556308 PMCID: PMC9783070 DOI: 10.3390/jpm12122088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 12/11/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
In recent years, the incidence of tuberculosis (TB) and mortality caused by the disease have been decreasing. However, the number of drug-resistant tuberculosis patients is increasing rapidly year by year. Here, a total of 380 Mycobacterium tuberculosis (MTB)-positive formalin-fixed and paraffin-embedded tissue (FFPE) specimens diagnosed in the Department of Pathology of the Eighth Medical Center, Chinese PLA General Hospital were collected. Among 380 cases of MTB, 85 (22.37%) were susceptible to four anti-TB drugs and the remaining 295 (77.63%) were resistant to one or more drugs. The rate of MDR-TB was higher in previously treated cases (52.53%) than in new cases [(36.65%), p < 0.05]. Of previously treated cases, the rate of drug resistance was higher in females than in males (p < 0.05). Among specimens obtained from males, the rate of drug resistance was higher in new cases than in previously treated cases (p < 0.05). Of mutation in drug resistance-related genes, the majority (53/380, 13.95%) of rpoB gene carried the D516V mutation, and 13.42% (51/380) featured mutations in both the katG and inhA genes. Among the total specimens, 18.68% (71/380) carried the 88 M mutation in the rpsL gene, and the embB gene focused on the 306 M2 mutation with a mutation rate of 19.74%. Among the resistant INH, the mutation rate of −15 M was higher in resistance to more than one drug than in monodrug-resistant (p < 0.05). In conclusion, the drug resistance of MTB is still very severe and the timely detection of drug resistance is conducive to the precise treatment of TB.
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13
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Jiang H, Zhu C, Qin L, Wu X, Yin J, Guo Y, Ma H, Jia J, Huo F, Xue Y, Gao M, Li W. Case report: A 9-year systematic treatment failure of a pulmonary tuberculosis patient. Front Public Health 2022; 10:966891. [PMID: 36148360 PMCID: PMC9487995 DOI: 10.3389/fpubh.2022.966891] [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: 06/11/2022] [Accepted: 08/17/2022] [Indexed: 01/24/2023] Open
Abstract
Objective To explore the reasons of failure in a case of pulmonary tuberculosis (PTB) after 9 years systematic treatment. Methods We extracted the patients' treatment history, drug susceptibility testing (DST), Computed tomography (CT) images, and sequenced the isolated strains by whole gene sequencing (WGS). Results Although most results of the phenotypical DSTs were consistent with the genotype DST, the occurrence of gene resistance to amikacin (AMK), capreomycin (CAP), moxifloxacin (MFX) was earlier than the phenotypical DST. Based on the continuously reversed results of phenotypical DSTs, CT images in different stages and WGS, it can be confirmed that the patient was infected with two different strains of Mycobacterium tuberculosis (M.TB). Moreover, severe cavities may be another factor leading to treatment failure. Conclusion Given the suggestive effect of genotype DST is earlier than the phenotypical DST, so genotype DST can play a better guiding role in patients with MDR-TB. Additionally, for patients who have not been cured for a long time, medication should be more cautious and the role of WGS in drug resistance surveillance should be fully utilized.
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Affiliation(s)
- Hui Jiang
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Chendi Zhu
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Liyi Qin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Xiaoguang Wu
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Jinfeng Yin
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Yijia Guo
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Huan Ma
- School of Public Health, Wenzhou Medical University, Wenzhou, China
| | - Junnan Jia
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Fengmin Huo
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Yi Xue
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China
| | - Mengqiu Gao
- Beijing Chest Hospital, Capital Medical University, Beijing, China,Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Weimin Li
- Beijing Chest Hospital, Capital Medical University, Beijing, China,National Tuberculosis Clinical Laboratory, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China,Beijing Key Laboratory for Drug Resistant Tuberculosis, Beijing, China,*Correspondence: Weimin Li
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Promising Antimycobacterial Activities of Flavonoids against Mycobacterium sp. Drug Targets: A Comprehensive Review. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165335. [PMID: 36014572 PMCID: PMC9415813 DOI: 10.3390/molecules27165335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 08/03/2022] [Accepted: 08/09/2022] [Indexed: 11/17/2022]
Abstract
Tuberculosis (TB) caused by the bacterial pathogen Mycobacterium tuberculosis (Mtb) remains a threat to mankind, with over a billion of deaths in the last two centuries. Recent advancements in science have contributed to an understanding of Mtb pathogenesis and developed effective control tools, including effective drugs to control the global pandemic. However, the emergence of drug resistant Mtb strains has seriously affected the TB eradication program around the world. There is, therefore, an urgent need to develop new drugs for TB treatment, which has grown researchers’ interest in small molecule-based drug designing and development. The small molecules-based treatments hold significant potential to overcome drug resistance and even provide opportunities for multimodal therapy. In this context, various natural and synthetic flavonoids were reported for the effective treatment of TB. In this review, we have summarized the recent advancement in the understanding of Mtb pathogenesis and the importance of both natural and synthetic flavonoids against Mtb infection studied using in vitro and in silico methods. We have also included flavonoids that are able to inhibit the growth of non-tubercular mycobacterial organisms. Hence, understanding the therapeutic properties of flavonoids can be useful for the future treatment of TB.
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15
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Li H, Yuan J, Duan S, Pang Y. Resistance and tolerance of Mycobacterium tuberculosis to antimicrobial agents-How M. tuberculosis can escape antibiotics. WIREs Mech Dis 2022; 14:e1573. [PMID: 35753313 DOI: 10.1002/wsbm.1573] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 05/22/2022] [Accepted: 05/30/2022] [Indexed: 12/13/2022]
Abstract
Tuberculosis (TB) poses a serious threat to public health worldwide since it was discovered. Until now, TB has been one of the top 10 causes of death from a single infectious disease globally. The treatment of active TB cases majorly relies on various anti-tuberculosis drugs. However, under the selection pressure by drugs, the continuous evolution of Mycobacterium tuberculosis (Mtb) facilitates the emergence of drug-resistant strains, further resulting in the accumulation of tubercle bacilli with multiple drug resistance, especially deadly multidrug-resistant TB and extensively drug-resistant TB. Researches on the mechanism of drug action and drug resistance of Mtb provide a new scheme for clinical management of TB patients, and prevention of drug resistance. In this review, we summarized the molecular mechanisms of drug resistance of existing anti-TB drugs to better understand the evolution of drug resistance of Mtb, which will provide more effective strategies against drug-resistant TB, and accelerate the achievement of the EndTB Strategy by 2035. This article is categorized under: Infectious Diseases > Molecular and Cellular Physiology.
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Affiliation(s)
- Haoran Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Jinfeng Yuan
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
| | - Shujuan Duan
- School of Medical Technology, Guangdong Medical University, Dongguan, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing, China
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Panova AE, Vinokurov AS, Shemetova AA, Burmistrova IA, Shulgina MV, Samoilova AG, Vasilyeva IA, Vakhrusheva DV, Umpeleva TV, Eremeeva NI, Lavrenchuk LS, Golubeva LA, Danilova TI, Vasilyeva TB, Ugol'kova VA, Sosova NV, Lekhlyaider MV, Gorshkova IA, Romanova TA. Molecular characteristics of Mycobacterium tuberculosis drug-resistant isolates from HIV- and HIV+ tuberculosis patients in Russia. BMC Microbiol 2022; 22:138. [PMID: 35590243 PMCID: PMC9118847 DOI: 10.1186/s12866-022-02553-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 05/09/2022] [Indexed: 11/23/2022] Open
Abstract
Background High burden of drug-resistant (DR) tuberculosis (TB) is a significant threat to national TB control programs all over the world and in the Russian Federation. Different Mycobacterium tuberculosis (MTB) genotypes are hypothesized to have specific characteristics affecting TB control programs. For example, Beijing strains are supposed to have higher mutation rates compared to strains of other genotypes and subsequently higher capability to develop drug-resistance. Results Clinical MTB isolates from HIV- and HIV+ patients from four regions of Russia were analyzed for genotypes and mutations conferring resistance to Isoniazid, Rifampicin, Ethambutol, aminoglycosides, and fluoroquinolones. Analysis of genotypes and polymorphism of genomic loci according to the HIV status of the patients – sources of MTB isolates were performed. Studied MTB isolates from HIV- TB patients belonged to 15 genotypes and from HIV + TB patients – to 6 genotypes. Beijing clinical isolates dominated in HIV- (64,7%) and HIV+ (74,4%) groups. Other isolates were of LAM (including LAM1 and LAM9), Ural, and 4 minor groups of genotypes (including 5 subclones T). The spectrum of genotypes in the HIV- group was broader than in the HIV+ group. PR of B0/W148 Beijing was significantly lower than of other Beijing genotypes in susceptible and MDR-XDR isolates. Rates of isolates belonging to non-Beijing genotypes were higher than Beijing in susceptible isolates from HIV- patients. Conclusions Beijing genotype isolates prevailed in clinical isolates of all drug susceptibility profiles both from HIV- and HIV+ patients, although B0/W148 Beijing genotype did not dominate in this study. Genome loci and mutations polymorphisms were more pronounced in clinical isolates from HIV- patients, than from HIV+.
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Affiliation(s)
- Anna E Panova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anatoliy S Vinokurov
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Anastasiya A Shemetova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Burmistrova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Marina V Shulgina
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation.
| | - Anastasiya G Samoilova
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Irina A Vasilyeva
- National Medical Research Center of Phthisiopulmonology and Infectious Diseases, Ministry of Public Heath of the Russian Federation (NMRC PhID), Moscow, Russian Federation
| | - Diana V Vakhrusheva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana V Umpeleva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Nataliya I Eremeeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Leonid S Lavrenchuk
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Lyudmila A Golubeva
- Ural Research Institute of Phthisiopulmonology -Branch of NMRC PhID, Ekaterinburg, Russian Federation
| | - Tatiana I Danilova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Tatiana B Vasilyeva
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Vera A Ugol'kova
- Regional TB dispensary of Leningradskaya oblast, Saint Petersburg, Russian Federation
| | - Nataliya V Sosova
- Regional TB dispensary of Stavropolskiy kray, Stavropol, Russian Federation
| | - Marina V Lekhlyaider
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Irina A Gorshkova
- Regional TB dispensary of Chelyabinskaya oblast, Chelyabinsk, Russian Federation
| | - Tatiana A Romanova
- Regional TB dispensary of Kemerovskaya oblast, Kemerovo, Russian Federation
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Chen J, Chen L, Zhou M, Wu G, Yi F, Jiang C, Duan Q, Zhou M. Transmission of multidrug-resistant tuberculosis within family households by DTM-PCR and MIRU-VNTR genotyping. BMC Infect Dis 2022; 22:192. [PMID: 35219320 PMCID: PMC8881899 DOI: 10.1186/s12879-022-07188-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 02/18/2022] [Indexed: 11/10/2022] Open
Abstract
Background Drug-resistant tuberculosis (TB) continues to be a public health threat. There are few studies on transmission and genotyping of MDR-TB family households in China. This study aimed to investigate transmission of multidrug-resistant tuberculosis (MDR-TB) within family households by deletion-targeted multiplex polymerase chain reaction (DTM-PCR), mycobacterial interspersed repetitive unit variable number tandem repeats (MIRU-VNTR) genotyping.
Methods Among 993 MDR-TB patients registered from Wuhan Institute for Tuberculosis Control, drug resistance and the time interval between the index patients and secondary patients were analyzed in 49 MDR-TB patients from 23 families, in which 22 MDR-TB strains from 11 families who had matched strains were genotyped by DTM-PCR and standard 24-loci MIRU-VNTR genotyping method. Results The time interval between the index patients and the secondary patients ranged from half a month to 110 months. Thirteen secondary patients developed active MDR-TB within two years and accounted for 50% (13/26) of all secondary patients. Among eleven pairs of MDR-TB families, six pairs had identical genotypes, the cluster rate was 54.5% (12/22); three pairs had a single MIRU-VNTR locus variation. If a single MIRU-VNTR locus variation was tolerated in the cluster definition, the cluster rate raised to 81.8% (18/22). Conclusions The family households of MDR-TB patients are at risk for infection of MDR-TB. To reduce transmission, MDR-TB patients should be diagnosed earlier and promptly treated in an effective manner, meanwhile, the close family contacts should be screened for TB infection.
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18
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Experimental confirmation that an uncommon
rrs
gene mutation (g878a) of
Mycobacterium tuberculosis
confers resistance to streptomycin. Antimicrob Agents Chemother 2022; 66:e0191521. [DOI: 10.1128/aac.01915-21] [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
The effective treatment of patients diagnosed with drug resistant tuberculosis is highly dependent upon the ability to rapidly and accurately determine the antibiotic susceptibility profile of the
Mycobacterium tuberculosis
isolate(s) involved. Thus, as more clinical microbiology laboratories advance towards the use of DNA sequence-based diagnostics, it is imperative that their predictive functions extend beyond the well-known resistance mutations, in order to also encompass as many of the lower-frequency mutations as possible. However, in most cases, the fundamental experimental proof that links these uncommon mutations with phenotypic resistance is lacking. One such example is the g878a polymorphism within the
rrs
16s rRNA gene. We, and others, have identified this mutation within a small number of drug-resistant isolates, although a consensus regarding exactly which aminoglycoside antibiotic(s) it confers resistance toward has not previously been reached. Here we have employed oligo-mediated recombineering to introduce the g878a polymorphism into the
rrs
gene of
M. bovis
BCG - a close relative of
M. tuberculosis
- and demonstrate that it confers low-level resistance to streptomycin alone. It does not confer cross-resistance towards amikacin, capreomycin, nor kanamycin. We also demonstrate that the
rrs
g878a
mutation exerts a substantial fitness defect
in vitro
, that may at least in part explain why clinical isolates bearing this mutation appear to be quite rare. Overall, this study provides clarity to the phenotype attributable to the
rrs
g878a
mutation and is relevant to the future implementation of genomics-based diagnostics, as well as the clinical management of patients where this particular polymorphism is encountered.
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19
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Abstract
The epidemiological importance of mycobacterial species is indisputable, and the necessity to find new molecules that can inhibit their growth is urgent. The shikimate pathway, required for the synthesis of important bacterial metabolites, represents a set of targets for inhibitors of Mycobacterium tuberculosis growth. The aroA-encoded 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) enzyme catalyzes the sixth step of the shikimate pathway. In this study, we combined gene disruption, gene knockdown, point mutations (D61W, R134A, E321N), and kinetic analysis to evaluate aroA gene essentiality and vulnerability of its protein product, EPSPS, from Mycolicibacterium (Mycobacterium) smegmatis (MsEPSPS). We demonstrate that aroA-deficient cells are auxotrophic for aromatic amino acids (AroAAs) and that the growth impairment observed for aroA-knockdown cells grown on defined medium can be rescued by AroAA supplementation. We also evaluated the essentiality of selected MsEPSPS residues in bacterial cells grown without AroAA supplementation. We found that the catalytic residues R134 and E321 are essential, while D61, presumably important for protein dynamics and suggested to have an indirect role in catalysis, is not essential under the growth conditions evaluated. We have also determined the catalytic efficiencies (Kcat/Km) of recombinant wild-type (WT) and mutated versions of MsEPSPS (D61W, R134A, E321N). Our results suggest that drug development efforts toward EPSPS inhibition may be ineffective if bacilli have access to external sources of AroAAs in the context of infection, which should be evaluated further. In the absence of AroAA supplementation, aroA from M. smegmatis is essential, its essentiality is dependent on MsEPSPS activity, and MsEPSPS is vulnerable. IMPORTANCE We found that cells from Mycobacterium smegmatis, a model organism safer and easier to study than the disease-causing mycobacterial species, when depleted of an enzyme from the shikimate pathway, are auxotrophic for the three aromatic amino acids (AroAAs) that serve as building blocks of cellular proteins: l-tryptophan, l-phenylalanine, and l-tyrosine. That supplementation with only AroAAs is sufficient to rescue viable cells with the shikimate pathway inactivated was unexpected, since this pathway produces an end product, chorismate, that is the starting compound of essential pathways other than the ones that produce AroAAs. The depleted enzyme, the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS), catalyzes the sixth step of shikimate pathway. Depletion of this enzyme inside cells was performed by disrupting or silencing the EPSPS-encoding aroA gene. Finally, we evaluated the essentiality of specific residues from EPSPS that are important for its catalytic activity, determined with experiments of enzyme kinetics using recombinant EPSPS mutants.
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20
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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.
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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.
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21
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Muzondiwa D, Hlanze H, Reva ON. The Epistatic Landscape of Antibiotic Resistance of Different Clades of Mycobacterium tuberculosis. Antibiotics (Basel) 2021; 10:857. [PMID: 34356778 PMCID: PMC8300818 DOI: 10.3390/antibiotics10070857] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 07/08/2021] [Accepted: 07/13/2021] [Indexed: 11/16/2022] Open
Abstract
Drug resistance (DR) remains a global challenge in tuberculosis (TB) control. In order to develop molecular-based diagnostic methods to replace the traditional culture-based diagnostics, there is a need for a thorough understanding of the processes that govern TB drug resistance. The use of whole-genome sequencing coupled with statistical and computational methods has shown great potential in unraveling the complexity of the evolution of DR-TB. In this study, we took an innovative approach that sought to determine nonrandom associations between polymorphic sites in Mycobacterium tuberculosis (Mtb) genomes. Attributable risk statistics were applied to identify the epistatic determinants of DR in different clades of Mtb and the possible evolutionary pathways of DR development. It was found that different lineages of Mtb exploited different evolutionary trajectories towards multidrug resistance and compensatory evolution to reduce the DR-associated fitness cost. Epistasis of DR acquisition is a new area of research that will aid in the better understanding of evolutionary biological processes and allow predicting upcoming multidrug-resistant pathogens before a new outbreak strikes humanity.
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Affiliation(s)
| | | | - Oleg N. Reva
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria 0002, South Africa; (D.M.); (H.H.)
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22
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Abstract
Clinical isolates of drug-resistant (isoniazid and/or rifampicin-resistant) Mycobacterium tuberculosis were obtained from 254 patients diagnosed with drug-resistant tuberculosis in Japan from April 2015 to March 2017 in National Hospital Organization hospitals. The 254 patients were approximately 32% of all 795 patients who were diagnosed with culture-confirmed drug-resistant tuberculosis from 2015 to 2016 nationwide in Japan. The whole-genome sequences of all the isolates from the 254 patients and the lineages of these isolates were determined, and phylogenetic trees were constructed based on single nucleotide polymorphism concatemers. Of these patients, 202 (79.5%) were born in Japan and 52 (20.5%) were born elsewhere. Of the 254 drug-resistant isolates, 54 (21.3%) were multidrug resistant, being resistant to both isoniazid and rifampicin. The percentages of multidrug-resistant isolates were significantly higher in foreign-born (38.5% [20/52]) than Japanese-born patients (16.8% [34/202]). Of the 54 multidrug-resistant isolates, nine were extensively drug resistant, which were all obtained from Japanese-born patients. Five extensively drug-resistant isolates were obtained from patients with incipient tuberculosis. A significant number of multidrug-resistant M. tuberculosis strains were isolated from foreign-born patients from Asian countries that have a high tuberculosis burden. Foreign-derived isolates affect the nationwide genetic diversity of drug-resistant M. tuberculosis in Japan. Extensively drug-resistant M. tuberculosis isolates were transmitted among the Japanese population. IMPORTANCE The incidence rate of tuberculosis (TB) in Japan was 11.5 per 100,000 of the population in 2019. Of TB patients in Japan, 61.1% were aged >70 years, and 10.7% were born outside Japan, mostly in Asian countries with a high burden of tuberculosis. Of the tuberculosis patients in the present study, 5.4% and 1.0% showed resistance to isoniazid and rifampicin, respectively, and 0.7% were multidrug resistant. The objective of this study was to clarify the molecular epidemiological properties of drug-resistant tuberculosis in Japan. Molecular epidemiology provides several clues to inform potential measures to control drug-resistant tuberculosis in Japan.
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23
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Yoshida S, Iwamoto T, Arikawa K, Sekizuka T, Kuroda M, Inoue Y, Mitarai S, Tsuji T, Tsuyuguchi K, Suzuki K. Bacterial population kinetics in heteroresistant Mycobacterium tuberculosis harbouring rare resistance-conferring mutations in gyrA and rpoB imply an epistatic interaction of mutations in a pre-XDR-TB patient. J Antimicrob Chemother 2021; 75:1722-1725. [PMID: 32303065 DOI: 10.1093/jac/dkaa109] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/28/2020] [Accepted: 03/02/2020] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVES Bacterial population kinetics of strains harbouring drug resistance-conferring mutations within a patient often show cryptic resistance in clinical practice. We report a case that showed emergence and dominance of Mycobacterium tuberculosis with uncommon rpoB and gyrA mutations, followed by an rpoC compensatory mutation, during treatment. METHODS A pre-XDR-TB patient showed heteroresistance to rifampicin and levofloxacin during treatment as a result of intermittent self-cessation. WGS was applied to investigate intra-host strain composition using five pairs of isolates from sputum samples. RESULTS The subclone in this study possessed rare mutations conferring resistance to rifampicin (rpoB V170F) and levofloxacin (gyrA S91P) and it rapidly outcompeted other subclones during treatment that included levofloxacin but not rifampicin (<7 days). The high-probability compensatory mutation rpoC V483A also emerged and became dominant subsequent to the rpoB V170F mutation. CONCLUSIONS To the best of our knowledge, this is the first case showing the emergence of such a rare variant that dominated the population within a patient during treatment of TB.
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Affiliation(s)
- Shiomi Yoshida
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Hyogo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshikazu Inoue
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Satoshi Mitarai
- Department of Mycobacterium Reference and Research, Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo, Japan
| | - Taisuke Tsuji
- Department of Respiratory Medicine, Japanese Red Cross Kyoto Daiichi Hospital, Kyoto, Japan
| | - Kazunari Tsuyuguchi
- Clinical Research Center, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
| | - Katsuhiro Suzuki
- Department of Internal Medicine, National Hospital Organization Kinki-chuo Chest Medical Center, Kita-ku, Sakai, Osaka, Japan
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24
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Bogaerts B, Delcourt T, Soetaert K, Boarbi S, Ceyssens PJ, Winand R, Van Braekel J, De Keersmaecker SCJ, Roosens NHC, Marchal K, Mathys V, Vanneste K. A Bioinformatics Whole-Genome Sequencing Workflow for Clinical Mycobacterium tuberculosis Complex Isolate Analysis, Validated Using a Reference Collection Extensively Characterized with Conventional Methods and In Silico Approaches. J Clin Microbiol 2021; 59:e00202-21. [PMID: 33789960 PMCID: PMC8316078 DOI: 10.1128/jcm.00202-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/27/2021] [Indexed: 01/18/2023] Open
Abstract
The use of whole-genome sequencing (WGS) for routine typing of bacterial isolates has increased substantially in recent years. For Mycobacterium tuberculosis (MTB), in particular, WGS has the benefit of drastically reducing the time required to generate results compared to most conventional phenotypic methods. Consequently, a multitude of solutions for analyzing WGS MTB data have been developed, but their successful integration in clinical and national reference laboratories is hindered by the requirement for their validation, for which a consensus framework is still largely absent. We developed a bioinformatics workflow for (Illumina) WGS-based routine typing of MTB complex (MTBC) member isolates allowing complete characterization, including (sub)species confirmation and identification (16S, csb/RD, hsp65), single nucleotide polymorphism (SNP)-based antimicrobial resistance (AMR) prediction, and pathogen typing (spoligotyping, SNP barcoding, and core genome multilocus sequence typing). Workflow performance was validated on a per-assay basis using a collection of 238 in-house-sequenced MTBC isolates, extensively characterized with conventional molecular biology-based approaches supplemented with public data. For SNP-based AMR prediction, results from molecular genotyping methods were supplemented with in silico modified data sets, allowing us to greatly increase the set of evaluated mutations. The workflow demonstrated very high performance with performance metrics of >99% for all assays, except for spoligotyping, where sensitivity dropped to ∼90%. The validation framework for our WGS-based bioinformatics workflow can aid in the standardization of bioinformatics tools by the MTB community and other SNP-based applications regardless of the targeted pathogen(s). The bioinformatics workflow is available for academic and nonprofit use through the Galaxy instance of our institute at https://galaxy.sciensano.be.
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Affiliation(s)
- Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Thomas Delcourt
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, Internet Technology and Data Science Lab (IDLab), Interuniversity Microelectronics Centre (IMEC), Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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25
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Xu G, Liu H, Jia X, Wang X, Xu P. Mechanisms and detection methods of Mycobacterium tuberculosis rifampicin resistance: The phenomenon of drug resistance is complex. Tuberculosis (Edinb) 2021; 128:102083. [PMID: 33975262 DOI: 10.1016/j.tube.2021.102083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 03/30/2021] [Accepted: 04/25/2021] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is an infectious disease that poses a serious threat to human health. Rifampin (RIF) is an important first-line anti-TB drug, and rifampin resistance (RIF-R) is a key factor in formulating treatment regimen and evaluating the prognosis of TB. Compared with other drugs resistance, the RIF-R mechanism of Mycobacterium tuberculosis (M. tuberculosis) is one of the clearest, which is mainly caused by RIF resistance-related mutations in the rpoB gene. This provides a convenient condition for developing rapid detection methods, and also an ideal object for studying the general drug resistance mechanisms of M. tuberculosis. This review focuses on the mechanisms that influence the RIF resistance of M. tuberculosis and related detection methods. Besides the mutations in rpoB, M. tuberculosis can decrease the amount of drugs entering the cells, enhance the drugs efflux, and be heterogeneous RIF susceptibility to resist drug pressure. Based on the results of current researches, many genes participate in influencing the susceptibility to RIF, which indicates the phenomenon of M. tuberculosis drug resistance is very complex.
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Affiliation(s)
- Ge Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Hangchi Liu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xudong Jia
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China
| | - Xiaomin Wang
- Department of Microbiology, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
| | - Peng Xu
- Key Laboratory of Characteristic Infectious Disease & Bio-safety Development of Guizhou Province Education Department, Institute of Life Sciences, Zunyi Medical University, No.6 West Xuefu Road, Xinpu District, Zunyi, Guizhou Province, 563000, China.
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26
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Nguyen TVA, Anthony RM, Cao TTH, Bañuls AL, Nguyen VAT, Vu DH, Nguyen NV, Alffenaar JWC. Delamanid Resistance: Update and Clinical Management. Clin Infect Dis 2021; 71:3252-3259. [PMID: 32521000 DOI: 10.1093/cid/ciaa755] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 06/05/2020] [Indexed: 12/29/2022] Open
Abstract
Delamanid, a-first-in-class bicyclic nitroimidazole, was recently approved for multidrug-resistant tuberculosis treatment. Pitted against the hope for improving treatment outcomes is the threat of the rapid resistance emergence. This review provides information on the mechanisms of action, resistance emergence, and drug susceptibility testing (DST) for delamanid. Delamanid resistance has already been reported in both in vitro experiments and clinical settings. Although mutations conferring delamanid resistance have been identified in fbiA, fbiB, fbiC, ddn, and fgd1 genes of Mycobacterium tuberculosis, knowledge about the molecular resistance mechanisms is limited, and there remains no standardized DST method. The rapid acquisition of delamanid resistance emphasizes the need for optimal use of new drugs, the need for drug resistance surveillance, and a comprehensive understanding of drug resistance mechanisms. Further studies are necessary to investigate genetic and phenotypic changes that determine clinically relevant delamanid resistance to help develop a rapid delamanid DST.
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Affiliation(s)
- Thi Van Anh Nguyen
- Department of Life Sciences, University of Science and Technology of Hanoi (USTH), Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam.,LMI Drug Resistance in South East Asia, Hanoi, Vietnam
| | - Richard M Anthony
- Tuberculosis reference laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Thi Thu Huyen Cao
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Hanoi, Vietnam.,MIVEGEC, University of Montpellier-IRD-CNRS, Montpellier, France
| | - Van Anh Thi Nguyen
- Laboratory of Tuberculosis, Department of Bacteriology, National Institute of Hygiene and Epidemiology of Vietnam, Hanoi, Vietnam
| | - Dinh Hoa Vu
- The National Centre of Drug information and Adverse Drug Reaction Monitoring, Hanoi University of Pharmacy, Hanoi, Vietnam
| | | | - Jan-Willem C Alffenaar
- University of Sydney, Faculty of Medicine and Health, School of Pharmacy, Sydney, Australia.,Westmead hospital, Sydney, Australia.,Marie Bashir Institute of Infectious Diseases and Biosecurity, University of Sydney, Sydney, Australia
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27
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Cheng N, Wu S, Luo X, Xu C, Lou Q, Zhu J, You L, Li B. A Comparative Study of Chest Computed Tomography Findings: 1030 Cases of Drug-Sensitive Tuberculosis versus 516 Cases of Drug-Resistant Tuberculosis. Infect Drug Resist 2021; 14:1115-1128. [PMID: 33776457 PMCID: PMC7987723 DOI: 10.2147/idr.s300754] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 03/04/2021] [Indexed: 01/15/2023] Open
Abstract
Purpose To investigate the CT features of drug-resistant pulmonary tuberculosis (DR-PTB) and the diagnostic value of CT in DR-PTB diagnosis to provide imaging evidence for the timely detection of drug-resistant Mycobacterium tuberculosis. Materials and Methods A total of 1546 cases of pulmonary tuberculosis (PTB) with complete clinical data, chest CT images and defined drug sensitivity testing results were consecutively enrolled; 516 cases of DR-PTB were included in the drug-resistant group, and 1030 cases of drug-sensitive pulmonary tuberculosis (DS-PTB) were included in the drug-sensitivity group. Comparative analyses of clinical symptoms and imaging findings were conducted. Univariate and logistic regression analyses were performed, a regression equation model was developed, and the receiver operating characteristic (ROC) curve was constructed. Results In the univariate analysis, some features, including whole-lung involvement, multiple cavities, thick-walled cavities, collapsed lung, disseminated lesions along the bronchi, bronchiectasis, emphysema, atelectasis, calcification, proliferative lesions, encapsulated effusion, etc., were observed more frequently in the DR-PTB group than in the DS-PTB group, and the differences were statistically significant (p<0.05). Exudative lesions and pneumoconiosis were observed more frequently in the drug-sensitivity group than in the drug-resistant group (p<0.05). Logistic regression analysis indicated that whole-lung involvement, multiple cavities, thick-walled cavities, disseminated lesions along the bronchi, bronchiectasis, and emphysema were independent risk factors for DR-PTB, and exudative diseases were protective factors. The total prediction accuracy of the regression model was 80.6%, and the area under the ROC curve (AUC) was 82.6%. Conclusion Chest CT manifestations of DR-PTB had certain characteristics that significantly indicated the possibility of drug resistance in tuberculosis patients, specifically when multifarious imaging findings, including multiple cavities, thick-walled cavities, disseminated lesions along the bronchi, whole-lung involvement, etc., coexisted simultaneously. These results may provide imaging evidence for timely drug resistance detection in suspected drug-resistant cases and contribute to the early diagnosis of DR-PTB.
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Affiliation(s)
- Nianlan Cheng
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Shuo Wu
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Xianli Luo
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Chunyan Xu
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Qin Lou
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Jin Zhu
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Lu You
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
| | - Bangguo Li
- Department of Radiology, Affiliated Hospital of Zunyi Medical University, Zunyi, Guizhou Province, People's Republic of China
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28
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Cheng S, Hide M, Pheng SH, Kerléguer A, Delvallez G, Sam S, Mao TE, Nguyen TVA, Bañuls AL. Resistance to Second-Line Anti-TB Drugs in Cambodia: A Phenotypic and Genetic Study. Infect Drug Resist 2021; 14:1089-1104. [PMID: 33762833 PMCID: PMC7982564 DOI: 10.2147/idr.s289907] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 01/06/2021] [Indexed: 12/25/2022] Open
Abstract
Background Due to the emergence of Mycobacterium tuberculosis (M.tb) clinical isolates resistant to most potent first-line drugs (FLD), second-line drugs (SLD) are being prescribed more frequently. We explore the genetic characteristics and molecular mechanisms of M.tb isolates phenotypically resistant to SLD, including pre-extensively drug-resistant (pre-XDR) and extensively drug-resistant (XDR) isolates. Methods Drug-resistant (DR) M.tb isolates collected from 2012 to 2017 were tested using sequencing and phenotypic drug susceptibility testing. Genotypes were determined to explore their links with SLD resistance patterns. Results Of the 272 DR M.tb isolates, 6 non-multidrug resistant (non-MDR) isolates were fluoroquinolones (FQ)-resistant, 3 were XDR and 16 were pre-XDR (14 resistant to FQ and 2 to second-line injectable drugs). The most frequent mutations in FQ-resistant and second-line injectable drugs resistant isolates were gyrA D94G (15/23) and rrs a1401g (3/5), respectively. Seventy-five percent of pre-XDR isolates and 100% of XDR isolates harbored mutations conferring resistance to pyrazinamide. All XDR isolates belonged to the Beijing genotype, of which one, named XDR+, was resistant to all drugs tested. One cluster including pre-XDR and XDR isolates was observed. Conclusion This is the first description of SLD resistance in Cambodia. The data suggest that the proportion of XDR and pre-XDR isolates remains low but is on the rise compared to previous reports. The characterization of the XDR+ isolate in a patient who refused treatment underlines the risk of transmission in the population. In addition, genotypic results show, as expected, that the Beijing family is the main involved in pre-XDR and XDR isolates and that the spread of the Beijing pre-XDR strain is capable of evolving into XDR strain. This study strongly indicates the need for rapid interventions in terms of diagnostic and treatment to prevent the spread of the pre-XDR and XDR strains and the emergence of more resistant ones.
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Affiliation(s)
- Sokleaph Cheng
- Institut Pasteur du Cambodge and Ministry of Health, Phnom Penh, Cambodia.,Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Mallorie Hide
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
| | - Sok Heng Pheng
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Alexandra Kerléguer
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Gauthier Delvallez
- Medical Biology Laboratory, Institut Pasteur du Cambodge, Phnom Penh, Cambodia
| | - Sophan Sam
- Cambodian Health Committee, Phnom Penh, Cambodia
| | - Tan Eang Mao
- National Center for Tuberculosis and Leprosy Control, Phnom Penh, Cambodia
| | - Thi Van Anh Nguyen
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,Department of Bacteriology, National Institute of Hygiene and Epidemiology, Hanoi, Martinique, Vietnam
| | - Anne-Laure Bañuls
- LMI Drug Resistance in South East Asia, Institut Pasteur du Cambodge, Phnom Penh, Cambodia.,MIVEGEC, University of Montpellier, Institute of Research for Development, Centre National de la Recherche Scientifique, Montpellier, France.,CREES (Centre de Recherche En Écologie Et Évolution de la Santé), Montpellier, France
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Allué-Guardia A, García JI, Torrelles JB. Evolution of Drug-Resistant Mycobacterium tuberculosis Strains and Their Adaptation to the Human Lung Environment. Front Microbiol 2021; 12:612675. [PMID: 33613483 PMCID: PMC7889510 DOI: 10.3389/fmicb.2021.612675] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
In the last two decades, multi (MDR), extensively (XDR), extremely (XXDR) and total (TDR) drug-resistant Mycobacterium tuberculosis (M.tb) strains have emerged as a threat to public health worldwide, stressing the need to develop new tuberculosis (TB) prevention and treatment strategies. It is estimated that in the next 35 years, drug-resistant TB will kill around 75 million people and cost the global economy $16.7 trillion. Indeed, the COVID-19 pandemic alone may contribute with the development of 6.3 million new TB cases due to lack of resources and enforced confinement in TB endemic areas. Evolution of drug-resistant M.tb depends on numerous factors, such as bacterial fitness, strain's genetic background and its capacity to adapt to the surrounding environment, as well as host-specific and environmental factors. Whole-genome transcriptomics and genome-wide association studies in recent years have shed some insights into the complexity of M.tb drug resistance and have provided a better understanding of its underlying molecular mechanisms. In this review, we will discuss M.tb phenotypic and genotypic changes driving resistance, including changes in cell envelope components, as well as recently described intrinsic and extrinsic factors promoting resistance emergence and transmission. We will further explore how drug-resistant M.tb adapts differently than drug-susceptible strains to the lung environment at the cellular level, modulating M.tb-host interactions and disease outcome, and novel next generation sequencing (NGS) strategies to study drug-resistant TB.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
| | | | - Jordi B. Torrelles
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX, United States
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Minias A, Żukowska L, Lechowicz E, Gąsior F, Knast A, Podlewska S, Zygała D, Dziadek J. Early Drug Development and Evaluation of Putative Antitubercular Compounds in the -Omics Era. Front Microbiol 2021; 11:618168. [PMID: 33603720 PMCID: PMC7884339 DOI: 10.3389/fmicb.2020.618168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 12/30/2020] [Indexed: 12/14/2022] Open
Abstract
Tuberculosis (TB) is an infectious disease caused by the bacterium Mycobacterium tuberculosis. According to the WHO, the disease is one of the top 10 causes of death of people worldwide. Mycobacterium tuberculosis is an intracellular pathogen with an unusually thick, waxy cell wall and a complex life cycle. These factors, combined with M. tuberculosis ability to enter prolonged periods of latency, make the bacterium very difficult to eradicate. The standard treatment of TB requires 6-20months, depending on the drug susceptibility of the infecting strain. The need to take cocktails of antibiotics to treat tuberculosis effectively and the emergence of drug-resistant strains prompts the need to search for new antitubercular compounds. This review provides a perspective on how modern -omic technologies facilitate the drug discovery process for tuberculosis treatment. We discuss how methods of DNA and RNA sequencing, proteomics, and genetic manipulation of organisms increase our understanding of mechanisms of action of antibiotics and allow the evaluation of drugs. We explore the utility of mathematical modeling and modern computational analysis for the drug discovery process. Finally, we summarize how -omic technologies contribute to our understanding of the emergence of drug resistance.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
| | - Lidia Żukowska
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Ewelina Lechowicz
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Filip Gąsior
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- BioMedChem Doctoral School of the University of Lodz and the Institutes of the Polish Academy of Sciences in Lodz, Lodz, Poland
| | - Agnieszka Knast
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Molecular and Industrial Biotechnology, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Lodz, Poland
| | - Sabina Podlewska
- Department of Technology and Biotechnology of Drugs, Jagiellonian University Medical College, Krakow, Poland
- Maj Institute of Pharmacology, Polish Academy of Sciences, Krakow, Poland
| | - Daria Zygała
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
- Institute of Microbiology, Biotechnology and Immunology, Faculty of Biology and Environmental Protection, University of Lodz, Lodz, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Lodz, Poland
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31
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Allué-Guardia A, Saranathan R, Chan J, Torrelles JB. Mycobacteriophages as Potential Therapeutic Agents against Drug-Resistant Tuberculosis. Int J Mol Sci 2021; 22:ijms22020735. [PMID: 33450990 PMCID: PMC7828454 DOI: 10.3390/ijms22020735] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/08/2021] [Indexed: 01/21/2023] Open
Abstract
The current emergence of multi-, extensively-, extremely-, and total-drug resistant strains of Mycobacterium tuberculosis poses a major health, social, and economic threat, and stresses the need to develop new therapeutic strategies. The notion of phage therapy against bacteria has been around for more than a century and, although its implementation was abandoned after the introduction of drugs, it is now making a comeback and gaining renewed interest in Western medicine as an alternative to treat drug-resistant pathogens. Mycobacteriophages are genetically diverse viruses that specifically infect mycobacterial hosts, including members of the M. tuberculosis complex. This review describes general features of mycobacteriophages and their mechanisms of killing M. tuberculosis, as well as their advantages and limitations as therapeutic and prophylactic agents against drug-resistant M. tuberculosis strains. This review also discusses the role of human lung micro-environments in shaping the availability of mycobacteriophage receptors on the M. tuberculosis cell envelope surface, the risk of potential development of bacterial resistance to mycobacteriophages, and the interactions with the mammalian host immune system. Finally, it summarizes the knowledge gaps and defines key questions to be addressed regarding the clinical application of phage therapy for the treatment of drug-resistant tuberculosis.
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Affiliation(s)
- Anna Allué-Guardia
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
| | - Rajagopalan Saranathan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - John Chan
- Department of Microbiology and Immunology, Albert Einstein College of Medicine, New York, NY 10461, USA; (R.S.); (J.C.)
| | - Jordi B. Torrelles
- Population Health Program, Tuberculosis Group, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
- Correspondence: (A.A.-G.); (J.B.T.)
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32
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Srilohasin P, Prammananan T, Faksri K, Phelan JE, Suriyaphol P, Kamolwat P, Smithtikarn S, Disratthakit A, Regmi SM, Leechawengwongs M, Twee-Hee Ong R, Teo YY, Tongsima S, Clark TG, Chaiprasert A. Genomic evidence supporting the clonal expansion of extensively drug-resistant tuberculosis bacteria belonging to a rare proto -Beijing genotype. Emerg Microbes Infect 2020; 9:2632-2641. [PMID: 33205698 PMCID: PMC7738298 DOI: 10.1080/22221751.2020.1852891] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Accepted: 11/15/2020] [Indexed: 01/21/2023]
Abstract
Tuberculosis disease (TB), caused by Mycobacterium tuberculosis, is a major public health issue in Thailand. The high prevalence of modern Beijing (Lineage 2.2.1) strains has been associated with multi- and extensively drug-resistant infections (MDR-, XDR-TB), complicating disease control. The impact of rarer proto-Beijing (L2.1) strains is less clear. In our study of thirty-seven L2.1 clinical isolates spanning thirteen years, we found a high prevalence of XDR-TB cases (32.4%). With ≤ 12 pairwise SNP distances, 43.2% of L2.1 patients belong to MDR-TB or XDR-TB transmission clusters suggesting a high level of clonal expansion across four Thai provinces. All XDR-TB (100%) were likely due to transmission rather than inadequate treatment. We found a 47 mutation signature and a partial deletion of the fadD14 gene in the circulating XDR-TB cluster, which can be used for surveillance of this rare and resilient M. tuberculosis strain-type that is causing increasing health burden. We also detected three novel deletion positions, a deletion of 1285 bp within desA3 (Rv3230c), large deletions in the plcB, plcA, and ppe38 gene which may play a role in the virulence, pathogenesis or evolution of the L2.1 strain-type.
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Affiliation(s)
- Prapaporn Srilohasin
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
| | - Therdsak Prammananan
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Jody E. Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Prapat Suriyaphol
- Division of Bioinformatics and Data Management for Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Research Group and Research Network Division, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Phalin Kamolwat
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Saijai Smithtikarn
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Areeya Disratthakit
- Bureau of Tuberculosis, Department of Disease Control, Ministry of Public Health, Bangkok, Thailand
| | - Sanjib Mani Regmi
- Department of Microbiology, Gandaki Medical College Teaching Hospital, Pokhara, Nepal
| | - Manoon Leechawengwongs
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
- Vichaiyut Hospital, Bangkok, Thailand
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Yik Ying Teo
- Saw Swee Hock School of Public Health, National University of Singapore and National University Health System, Singapore, Singapore
| | - Sissades Tongsima
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani, Thailand
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani, Thailand
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Angkana Chaiprasert
- Office for Research and Development, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
- Drug Resistant Tuberculosis Research Fund, Siriraj Foundation, Bangkok, Thailand
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33
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Hjort K, Jurén P, Toro JC, Hoffner S, Andersson DI, Sandegren L. Dynamics of Extensive Drug Resistance Evolution of Mycobacterium tuberculosis in a Single Patient During 9 Years of Disease and Treatment. J Infect Dis 2020; 225:1011-1020. [PMID: 33045067 PMCID: PMC8921999 DOI: 10.1093/infdis/jiaa625] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/08/2020] [Indexed: 11/15/2022] Open
Abstract
Abstract
Mycobacterium tuberculosis is one of the hardest to treat bacterial pathogens with a high capacity to develop antibiotic resistance by mutations. Here we have performed whole-genome sequencing of consecutive M. tuberculosis isolates obtained during 9 years from a patient with pulmonary tuberculosis. The infecting strain was isoniazid resistant and during treatment it stepwise accumulated resistance mutations to 8 additional antibiotics. Heteroresistance was common and subpopulations with up to 3 different resistance mutations to the same drug coexisted. Sweeps of different resistant clones dominated the population at different time points, always coupled to resistance mutations coinciding with changes in the treatment regimens. Resistance mutations were predominant and no hitch-hiking, compensatory, or virulence-increasing mutations were detected, showing that the dominant selection pressure was antibiotic treatment. The results highlight the dynamic nature of M. tuberculosis infection, population structure, and resistance evolution and the importance of rapid antibiotic susceptibility tests to battle this pathogen.
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Affiliation(s)
- Karin Hjort
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | | | | | - Sven Hoffner
- Department of Global Public Health, Karolinska Institutet, Stockholm, Sweden
| | - Dan I Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Linus Sandegren
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
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Prakash C, Pandey M, Talwar S, Singh Y, Kanojiya S, Pandey AK, Kumar N. Extra-ribosomal functions of Mtb RpsB in imparting stress resilience and drug tolerance to mycobacteria. Biochimie 2020; 177:87-97. [PMID: 32828823 DOI: 10.1016/j.biochi.2020.08.007] [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: 05/22/2020] [Revised: 07/31/2020] [Accepted: 08/09/2020] [Indexed: 01/21/2023]
Abstract
Emerging observations suggest that ribosomal proteins (RPs) play important extra-ribosomal roles in maintenance of cellular homeostasis. However, the mechanistic insights into these processes have not been extensively explored, especially in pathogenic bacteria. Here, we present our findings on potential extra-ribosomal functions of Mycobacterium tuberculosis (Mtb) RPs. We observed that Mtb RpsB and RpsQ are differentially localized to cell wall fraction in M. tuberculosis (H37Rv), while their M. smegmatis (Msm) homologs are primarily cytosolic. Cellular fractionation of ectopically expressed Mtb RPs in surrogate host (M. smegmatis) also shows their association with cell membrane/cell wall without any gross changes in cell morphology. M. smegmatis expressing Mtb RpsB exhibited altered redox homeostasis, decreased drug-induced ROS, reduced cell wall permeability and increased tolerance to various proteotoxic stress (oxidative stress, SDS and starvation). Mtb RpsB expression was also associated with increased resistance specifically towards Isoniazid, Ethionamide and Streptomycin. The enhanced drug tolerance was specific to Mtb RpsB and not observed upon ectopic expression of M. smegmatis homolog (Msm RpsB). Interestingly, C-terminus deletion in Mtb RpsB affected its localization and reversed the stress-resilient phenotypes. We also observed that M. tuberculosis (H37Rv) with upregulated RpsB levels had higher intracellular survival in macrophage. All these observations hint towards existence of moonlighting roles of Mtb RpsB in imparting stress resilience to mycobacteria. This work open avenues for further exploration of alternative pathways associated with fitness and drug tolerance in mycobacteria.
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Affiliation(s)
- Chetan Prakash
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Manitosh Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India; Department of Life Sciences, ITM University, Gwalior 475001, Madhya Pradesh, India
| | - Sakshi Talwar
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Yatendra Singh
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India
| | - Sanjeev Kanojiya
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India
| | - Amit Kumar Pandey
- Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad, Gurgaon Expressway, Faridabad, 121001, Haryana, India
| | - Niti Kumar
- CSIR-Central Drug Research Institute (CSIR-CDRI), Jankipuram Ext, Sector 10, Lucknow, 226031, Uttar Pradesh, India; Academy of Scientific and Innovative Research (AcSIR), Delhi, India.
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35
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Sathoff AE, Lewenza S, Samac DA. Plant defensin antibacterial mode of action against Pseudomonas species. BMC Microbiol 2020; 20:173. [PMID: 32560676 PMCID: PMC7304088 DOI: 10.1186/s12866-020-01852-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 06/12/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Though many plant defensins exhibit antibacterial activity, little is known about their antibacterial mode of action (MOA). Antimicrobial peptides with a characterized MOA induce the expression of multiple bacterial outer membrane modifications, which are required for resistance to these membrane-targeting peptides. Mini-Tn5-lux mutant strains of Pseudomonas aeruginosa with Tn insertions disrupting outer membrane protective modifications were assessed for sensitivity against plant defensin peptides. These transcriptional lux reporter strains were also evaluated for lux gene expression in response to sublethal plant defensin exposure. Also, a plant pathogen, Pseudomonas syringae pv. syringae was modified through transposon mutagenesis to create mutants that are resistant to in vitro MtDef4 treatments. RESULTS Plant defensins displayed specific and potent antibacterial activity against strains of P. aeruginosa. A defensin from Medicago truncatula, MtDef4, induced dose-dependent gene expression of the aminoarabinose modification of LPS and surface polycation spermidine production operons. The ability for MtDef4 to damage bacterial outer membranes was also verified visually through fluorescent microscopy. Another defensin from M. truncatula, MtDef5, failed to induce lux gene expression and limited outer membrane damage was detected with fluorescent microscopy. The transposon insertion site on MtDef4 resistant P. syringae pv. syringae mutants was sequenced, and modifications of ribosomal genes were identified to contribute to enhanced resistance to plant defensin treatments. CONCLUSIONS MtDef4 damages the outer membrane similar to polymyxin B, which stimulates antimicrobial peptide resistance mechanisms to plant defensins. MtDef5, appears to have a different antibacterial MOA. Additionally, the MtDef4 antibacterial mode of action may also involve inhibition of translation.
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Affiliation(s)
- Andrew E Sathoff
- Department of Plant Pathology, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN, 55108, USA.
- Department of Biology, Dakota State University, 820 N Washington Ave, Madison, SD, 57042, USA.
| | - Shawn Lewenza
- Department of Microbiology and Infectious Disease, 3330 Hospital Dr. N.W., University of Calgary, Calgary, AB, T2N 4Z6, Canada
- Faculty of Science and Technology, 1 University Dr., Athabasca University, Athabasca, AB, T9S 3A3, Canada
| | - Deborah A Samac
- Department of Plant Pathology, 1991 Upper Buford Circle, University of Minnesota, St. Paul, MN, 55108, USA
- USDA-ARS, Plant Science Research Unit, 1991 Upper Buford Circle, St. Paul, MN, 55108, USA
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36
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Nimmo C, Brien K, Millard J, Grant AD, Padayatchi N, Pym AS, O'Donnell M, Goldstein R, Breuer J, Balloux F. Dynamics of within-host Mycobacterium tuberculosis diversity and heteroresistance during treatment. EBioMedicine 2020; 55:102747. [PMID: 32361247 PMCID: PMC7195533 DOI: 10.1016/j.ebiom.2020.102747] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 03/02/2020] [Accepted: 03/19/2020] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Studying within-host genetic diversity of Mycobacterium tuberculosis (Mtb) in patients during treatment may identify adaptations to antibiotic and immune pressure. Understanding the significance of genetic heteroresistance, and more specifically heterozygous resistance-associated variants (RAVs), is clinically important given increasing use of rapid molecular tests and whole genome sequencing (WGS). METHODS We analyse data from six studies in KwaZulu-Natal, South Africa. Most patients (>75%) had baseline rifampicin resistance. Sputum was collected for culture at baseline and at between two and nine intervals until month six. Positive cultures underwent WGS. Mixed infections and reinfections were excluded from analysis. FINDINGS Baseline Mtb overall genetic diversity (at treatment initiation or major change to regimen) was associated with cavitary disease, not taking antiretroviral therapy if HIV infected, infection with lineage 2 strains and absence of second-line drug resistance on univariate analyses. Baseline genetic diversity was not associated with six-month outcome. Genetic diversity increased from baseline to weeks one and two before returning to previous levels. Baseline genetic heteroresistance was most common for bedaquiline (6/10 [60%] of isolates with RAVs) and fluoroquinolones (9/62 [13%]). Most patients with heterozygous RAVs on WGS with sequential isolates available demonstrated RAV persistence or fixation (17/20, 85%). New RAVs emerged in 9/286 (3%) patients during treatment. We could detect low-frequency RAVs preceding emergent resistance in only one case, although validation of deep sequencing to detect rare variants is required. INTERPRETATION In this study of single-strain Mtb infections, baseline within-host bacterial genetic diversity did not predict outcome but may reveal adaptations to host and drug pressures. Predicting emergent resistance from low-frequency RAVs requires further work to separate transient from consequential mutations. FUNDING Wellcome Trust, NIH/NIAID.
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MESH Headings
- Adult
- Antitubercular Agents/therapeutic use
- Cohort Studies
- Diarylquinolines/therapeutic use
- Drug Resistance, Multiple, Bacterial/genetics
- Female
- Fluoroquinolones/therapeutic use
- Gene Expression Regulation, Bacterial
- Genes, Bacterial
- Genetic Variation
- Host-Pathogen Interactions/genetics
- Humans
- Male
- Metabolic Networks and Pathways/genetics
- Microbial Sensitivity Tests
- Middle Aged
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/metabolism
- Rifampin/therapeutic use
- South Africa
- Sputum/microbiology
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/microbiology
- Tuberculosis, Multidrug-Resistant/pathology
- Tuberculosis, Pulmonary/drug therapy
- Tuberculosis, Pulmonary/microbiology
- Tuberculosis, Pulmonary/pathology
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Affiliation(s)
- Camus Nimmo
- Division of Infection and Immunity, University College London, London, UK; UCL Genetics Institute, University College London, London, UK; Africa Health Research Institute, Durban, South Africa.
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | - James Millard
- Africa Health Research Institute, Durban, South Africa; Wellcome Trust Liverpool Glasgow Centre for Global Health Research, Liverpool, UK; Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa; London School of Hygiene & Tropical Medicine, London, UK
| | - Nesri Padayatchi
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | | | - Max O'Donnell
- CAPRISA MRC-HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa; Department of Medicine & Epidemiology, Columbia University Medical Center, New York, NY, USA
| | - Richard Goldstein
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
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37
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Mittal P, Sinha R, Kumar A, Singh P, Ngasainao MR, Singh A, Singh IK. Focusing on DNA Repair and Damage Tolerance Mechanisms in Mycobacterium tuberculosis: An Emerging Therapeutic Theme. Curr Top Med Chem 2020; 20:390-408. [PMID: 31924156 DOI: 10.2174/1568026620666200110114322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 09/02/2019] [Accepted: 10/10/2019] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is one such disease that has become a nuisance in the world scenario and one of the most deadly diseases of the current times. The etiological agent of tuberculosis, Mycobacterium tuberculosis (M. tb) kills millions of people each year. Not only 1.7 million people worldwide are estimated to harbor M. tb in the latent form but also 5 to 15 percent of which are expected to acquire an infection during a lifetime. Though curable, a long duration of drug regimen and expense leads to low patient adherence. The emergence of multi-, extensive- and total- drug-resistant strains of M. tb further complicates the situation. Owing to high TB burden, scientists worldwide are trying to design novel therapeutics to combat this disease. Therefore, to identify new drug targets, there is a growing interest in targeting DNA repair pathways to fight this infection. Thus, this review aims to explore DNA repair and damage tolerance as an efficient target for drug development by understanding M. tb DNA repair and tolerance machinery and its regulation, its role in pathogenesis and survival, mutagenesis, and consequently, in the development of drug resistance.
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Affiliation(s)
- Pooja Mittal
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Rajesh Sinha
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Amit Kumar
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India
| | - Pooja Singh
- Public Health Research Institute, NJMS-Rutgers University, New Jersey, United States
| | - Moses Rinchui Ngasainao
- Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, 110007, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
| | - Indrakant K Singh
- Molecular Biology Research Lab, Department of Zoology, Deshbandhu College, University of Delhi, Kalkaji, New Delhi, 110019, India.,Department of Molecular Ecology, Max-Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, D-07745 Jena, Germany
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Drug-resistant spinal tuberculosis - Current concepts, challenges, and controversies. J Clin Orthop Trauma 2020; 11:863-870. [PMID: 32904104 PMCID: PMC7452346 DOI: 10.1016/j.jcot.2020.07.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 07/08/2020] [Accepted: 07/24/2020] [Indexed: 12/12/2022] Open
Abstract
The alarming global increase in drug-resistant strains plagues the global fight to end tuberculosis (TB), especially in developing countries. The often reported poor treatment outcomes, sequelae, and lack of best practice guidelines in drug-resistant spinal TB poses a significant challenge in its efficient management. While multi-drug chemotherapy is still the primary modality of treatment, surgical intervention is essential in specific scenarios. With limited data on management and outcomes in drug-resistant spinal TB, there is no consensus on the appropriate therapy regarding the number and duration of drugs and therapeutic endpoints of this conundrum. In this light of limited evidence, we have performed a systematic computerized search using the Cochrane Database of Systematic Reviews, Scopus, Embase, Web of Science, and PubMed databases and studies published over the past 30 years on drug-resistance in spinal TB have been analyzed. This systematic review aims to review the current epidemiology, clinical features, updates in clinical diagnostics and chemotherapy, surgical management, and outcomes in drug-resistant spinal TB. We also consolidate potential areas of action and emphasize the need for research and large scale trials in the management of drug-resistant spinal TB.
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