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Rukmana A, Gozali C, Erlina L. Mycobacterium tuberculosis Lineage Distribution Using Whole-Genome Sequencing and Bedaquiline, Clofazimine, and Linezolid Phenotypic Profiles among Rifampicin-Resistant Isolates from West Java, Indonesia. Int J Microbiol 2024; 2024:2037961. [PMID: 38469390 PMCID: PMC10927343 DOI: 10.1155/2024/2037961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/03/2024] [Accepted: 02/22/2024] [Indexed: 03/13/2024] Open
Abstract
Tuberculosis (TB) is caused by Mycobacterium tuberculosis infection. Indonesia is ranked second in the world for TB cases. New anti-TB drugs from groups A and B, such as bedaquiline, clofazimine, and linezolid, have been shown to be effective in curing drug resistance in TB patients, and Indonesia is already using these drugs to treat patients. However, studies comparing the TB strain types with anti-TB resistance profiles are still relevant to understanding the prevalent strains in the country and their phenotypic characteristics. This study aimed to determine the association between the TB lineage distribution using whole-genome sequencing and bedaquiline, clofazimine, and linezolid phenotypic profile resistance among M. tuberculosisrifampicin-resistant isolates from West Java. M. tuberculosis isolates stock of the Department of Microbiology, Faculty of Medicine, Universitas Indonesia, was tested against bedaquiline, clofazimine, and linezolid using a mycobacteria growth indicator tube liquid culture. All isolates were tested for M. tuberculosis and rifampicin resistance using Xpert MTB/RIF. The DNA genome of M. tuberculosis was freshly extracted from a Löwenstein-Jensen medium culture and then sequenced. The isolates showed phenotypically resistance to bedaquiline, clofazimine, and linezolid at 5%, 0%, and 0%, respectively. We identified gene mutations on phenotypically bedaquiline-resistant strains (2/3), and other mutations also found in phenotypically drug-sensitive strains. Mykrobe analysis showed that most (88.33%) of the isolates could be classified as rifampicin-resistant TB. Using Mykrobe and TB-Profiler to determine the lineage distribution, the isolates were found to belong to lineage 4 (Euro-American; 48.33%), lineage 2 (East Asian/Beijing; 46.67%), and lineage 1 (Indo-Oceanic; 5%). This work underlines the requirement to increase the representation of genotype-phenotype TB data while also highlighting the importance and efficacy of WGS in predicting medication resistance and inferring disease transmission.
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Affiliation(s)
- Andriansjah Rukmana
- Department of Microbiology, Faculty of Medicine, Universitas Indonesia, Jakarta 10320, Indonesia
| | - Cynthia Gozali
- Master Programme of Biomedical Sciences, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
| | - Linda Erlina
- Department of Medical Chemistry, Faculty of Medicine, Universitas Indonesia, Jakarta 10430, Indonesia
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Holger DJ, Althubyani A, Morrisette T, Rebold N, Tailor M. Updates in pulmonary drug-resistant tuberculosis pharmacotherapy: A focus on BPaL and BPaLM. Pharmacotherapy 2024; 44:268-282. [PMID: 38270468 DOI: 10.1002/phar.2909] [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: 08/08/2023] [Revised: 12/08/2023] [Accepted: 12/11/2023] [Indexed: 01/26/2024]
Abstract
Drug-resistant tuberculosis (TB) is a major public health concern and contributes to high morbidity and mortality. New evidence supports the use of shorter duration, all-oral regimens, which represent an encouraging treatment strategy for drug-resistant TB. As a result, the landscape of drug-resistant TB pharmacotherapy has drastically evolved regarding treatment principles and preferred agents. This narrative review focuses on the key updates of drug-resistant TB treatment, including the use of short-duration all-oral regimens, while calling attention to current gaps in knowledge that may be addressed in future observational studies.
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Affiliation(s)
- Dana J Holger
- Department of Pharmacy Practice, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA
- Department of Pharmacy Services, Memorial Hospital West, Pembroke Pines, Florida, USA
| | - Ali Althubyani
- Department of Pharmacy Services, St. Elizabeth's Medical Center, Boston, Massachusetts, USA
- Department of Pharmacy Practice, College of Pharmacy, University of Tabuk, Tabuk, Saudi Arabia
| | - Taylor Morrisette
- Department of Clinical Pharmacy & Outcomes Sciences, Medical University of South Carolina College of Pharmacy, Charleston, South Carolina, USA
- Department of Pharmacy Services, Medical University of South Carolina Health, Charleston, South Carolina, USA
| | - Nicholas Rebold
- Department of Clinical & Administrative Pharmacy Sciences, College of Pharmacy, Howard University, Washington, DC, USA
| | - Marylee Tailor
- Department of Pharmacy Practice, Barry and Judy Silverman College of Pharmacy, Nova Southeastern University, Fort Lauderdale, Florida, USA
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Negi A, Perveen S, Gupta R, Singh PP, Sharma R. Unraveling Dilemmas and Lacunae in the Escalating Drug Resistance of Mycobacterium tuberculosis to Bedaquiline, Delamanid, and Pretomanid. J Med Chem 2024; 67:2264-2286. [PMID: 38351709 DOI: 10.1021/acs.jmedchem.3c01892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Delamanid, bedaquiline, and pretomanid have been recently added in the anti-tuberculosis (anti-TB) treatment regimens and have emerged as potential solutions for combating drug-resistant TB. These drugs have proven to be effective in treating drug-resistant TB when used in combination. However, concerns have been raised about the eventual loss of these drugs due to evolving resistance mechanisms and certain adverse effects such as prolonged QT period, gastrointestinal problems, hepatotoxicity, and renal disorders. This Perspective emphasizes the properties of these first-in-class drugs, including their mechanism of action, pharmacokinetics/pharmacodynamics profiles, clinical studies, adverse events, and underlying resistance mechanisms. A brief coverage of efforts toward the generation of best-in-class leads in each class is also provided. The ongoing clinical trials of new combinations of these drugs are discussed, thus providing a better insight into the use of these drugs while designing an effective treatment regimen for resistant TB cases.
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Affiliation(s)
- Anjali Negi
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Summaya Perveen
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Ria Gupta
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Parvinder Pal Singh
- Natural Products and Medicinal Chemistry, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR - Indian Institute of Integrative Medicine, Jammu-180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad-201002, India
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Guo Y, Yang J, Wang W, Wu X, Wan B, Wang H, Sha W, Yu F. Bedaquiline, Delamanid, Linezolid, Clofazimine, and Capreomycin MIC Distributions for Drug Resistance Mycobacterium tuberculosis in Shanghai, China. Infect Drug Resist 2023; 16:7587-7595. [PMID: 38107433 PMCID: PMC10723587 DOI: 10.2147/idr.s440711] [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: 10/16/2023] [Accepted: 11/28/2023] [Indexed: 12/19/2023] Open
Abstract
Background New antituberculosis drugs have recently been approved for the treatment of multidrug-resistant tuberculosis TB (MDR-TB). We aimed to describe the distributions of bedaquiline, delamanid, linezolid, clofazimine, and capreomycin MIC values for M. tuberculosis. Methods M. tuberculosis clinical isolates were originally isolated from 2020 to 2021 from 1452 different pulmonary tuberculosis patients of the Shanghai Pulmonary Hospital in China. The drug susceptibility testing was performed using the Sensititre custom plates (SHTBMY) (TREK Diagnostic Systems, Thermo Fisher Scientific In., USA) consisting of a 96-well microtitre plate containing 4 (bedaquiline, delamanid, clofazimine, capreomycin) antimicrobial agents. MICs were determined for linezolid using a microdilution method. Results Based on the latest definitions, 156 (10.74%) were MDR-TB, 93 (6.40%) were pre-XDR-TB, and 27 (1.86%) were XDR-TB. The rate of BDQ resistance in cases of MDR-TB was 7.69%, while it was observed to be 10.75% in cases of pre-XDR-TB, and significantly higher at 37.04% in cases of XDR-TB. The lowest rate of drug resistance against M. tuberculosis was DLM (0.14%). For LZD, 11 (0.76%) clinical isolates were resistant, based on the CLSI breakpoint of 1μg/mL. The five strains with a MIC value of >32 for LZD resistance were XDR-TB isolates. Among all MDR, pre-XDR, and XDR isolates tested, LZD' MIC50 increased from 0.25 and 0.5 to 1μg/mL. The MIC90 value of LZD against XDR-TB isolates was 32μg/mL. For CFZ, six isolates with elevated MICs of ≥2μg/mL. CFZ's MIC50 and MIC90 values in all isolates were 0.12μg/mL and 0.25μg/mL, respectively. Conclusion The study findings indicate that BDQ, DLM, CFZ, and LZD may exhibited excellent in vitro activity against MDR-TB isolates. Detection of resistance to BDQ and LZD was alarming for XDR-TB isolates. It is necessary to perform universal drug sensitivity testing for M. tuberculosis, especially MDR-TB and XDR-TB patients.
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Affiliation(s)
- Yinjuan Guo
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Jinghui Yang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Weiping Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Xiaocui Wu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Baoshan Wan
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Hongxiu Wang
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Wei Sha
- Tuberculosis Center for Diagnosis and Treatment, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory, Shanghai Pulmonary Hospital, School of Medicine, Tongji University, Shanghai, People's Republic of China
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Joshi T, Nain P, Bhamra P, Kaur J. Favorable clinical outcomes and anti-mycobacterial efficacy of pretomanid in patients with highly resistant tuberculosis: A review. Indian J Tuberc 2023; 71 Suppl 1:S130-S135. [PMID: 39067944 DOI: 10.1016/j.ijtb.2023.09.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 07/30/2024]
Abstract
Rising cases of drug resistance of mycobacterium species are one of the biggest concerns when the goal is to eradicate TB (Tuberculosis) from the world by the year 2030. A limited number of treatment options as MTB (Mycobacterium tuberculosis) is getting resistant to anti-mycobacterial drugs either due to a patient's non-compliance towards treatment regimen or if a patient is infected by drug-resistant species of MTB. This review aims to assess the effectiveness of pretomanid, a recently approved drug for the treatment of extensively drug-resistant TB. A thorough search of databases like PubMed, Cochrane library, CDC, Research Gate, and Google scholar was used in order to find case reports and clinical trials providing data on the efficacy of pretomanid in different drug regimens. According to research trials conducted, the drug appears to be efficacious, safe, and well-tolerable. Only headache was the most frequently observed adverse drug event, and a high dose-related increase in serum creatinine level was seen, which came to normal after the drug was discontinued.
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Affiliation(s)
- Tanishq Joshi
- Department of Pharmacy Practice, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India
| | - Parminder Nain
- Department of Pharmacy Practice, CT Institute of Pharmaceutical Sciences, Shahpur, Jalandhar, Punjab 144020, India
| | - Prajwal Bhamra
- Department of Pharmacy Practice, MM College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Ambala 133207, India
| | - Jaspreet Kaur
- Department of Pharmacy Practice, CT Institute of Pharmaceutical Sciences, Shahpur, Jalandhar, Punjab 144020, India.
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An Q, Lin R, Yang Q, Wang C, Wang D. Evaluation of genetic mutations associated with phenotypic resistance to fluoroquinolones, bedaquiline, and linezolid in clinical Mycobacterium tuberculosis: A systematic review and meta-analysis. J Glob Antimicrob Resist 2023; 34:214-226. [PMID: 37172764 DOI: 10.1016/j.jgar.2023.05.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 03/26/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
OBJECTIVES The aim of the study was to update the classification of drugs used in multidrug-resistant tuberculosis (MDR-TB) regimens. Group A drugs (fluoroquinolones, bedaquiline (BDQ), and linezolid (LZD)) are crucial drugs for the control of MDR-TB. Molecular drug resistance assays could facilitate the effective use of Group A drugs. METHODS We summarised the evidence implicating specific genetic mutations in resistance to Group A drugs. We searched PubMed, Embase, MEDLINE, and the Cochrane Library for studies published from the inception of each database until July 1, 2022. Using a random-effects model, we calculated the odds ratios and 95% confidence intervals as our measures of association. RESULTS A total of 5001 clinical isolates were included in 47 studies. Mutations in gyrA A90V, D94G, D94N, and D94Y were significantly associated with an increased risk of a levofloxacin (LFX)-resistant phenotype. In addition, mutations in gyrA G88C, A90V, D94G, D94H, D94N, and D94Y were significantly associated with an increased risk of a moxifloxacin (MFX)-resistant phenotype. In only one study, the majority of gene loci (n = 126, 90.65%) in BDQ-resistant isolates were observed to have unique mutations in atpE, Rv0678, mmpL5, pepQ, and Rv1979c. The most common mutations occurred at four sites in the rrl gene (g2061t, g2270c, g2270t, and g2814t) and at one site in rplC (C154R) in LZD-resistant isolates. Our meta-analysis demonstrated that there were no mutations associated with BDQ- or LZD-resistant phenotypes. CONCLUSION The mutations detected by rapid molecular assay were correlated with phenotypic resistance to LFX and MFX. The absence of mutation-phenotype associations for BDQ and LZD hindered the development of a rapid molecular assay.
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Affiliation(s)
- Qi An
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Rui Lin
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Qing Yang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China
| | - Chuan Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
| | - Dongmei Wang
- Scientific Research and Teaching Department, Public Health Clinical Center of Chengdu, Chengdu, Sichuan, China.
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Shi J, Liu Y, Wu T, Li L, Han S, Peng X, Shang Y, Guo Y, Pang Y, Gao M, Lu J. Spontaneous mutational patterns and novel mutations for bedaquiline and clofazimine resistance in Mycobacterium tuberculosis. Microbiol Spectr 2023; 11:e0009023. [PMID: 37646524 PMCID: PMC10581187 DOI: 10.1128/spectrum.00090-23] [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: 01/08/2023] [Accepted: 07/17/2023] [Indexed: 09/01/2023] Open
Abstract
The 2022 World Health Organization guidelines recommend use of two core anti-tuberculosis (TB) drugs, bedaquiline (BDQ) and clofazimine (CFZ), for treatment of drug-resistant (DR)-TB. However, several mutated Mycobacterium tuberculosis (MTB) genes, conferring BDQ and CFZ resistance, have been reported that predominantly arose from sporadic mutations that have not been comprehensively characterized. Herein, MTB clinical isolates collected from drug-susceptible (DS)-, multidrug-resistant (MDR)-, and extensively drug-resistant (XDR)-TB patients were cultured in vitro with BDQ or CFZ to generate progeny strains with resistance to these drugs. Progeny strains exposed to CFZ exhibited increased CFZ minimum inhibitory concentrations (MICs) that exceeded MIC increases of BDQ-exposed progeny strains. Notably, mmpR and pepQ mutations accounted for 83% and 17% of BDQ-induced spontaneous gene mutations, respectively, and 86% and 14% of CFZ-induced spontaneous gene mutations, respectively. Analyses of predicted mutation-induced changes in amino acid sequences and structures of MmpR and PepQ mutants revealed several point mutations affected sequence conversation and functionality as an underlying mechanism for observed acquired BDQ/CFZ resistance. Moreover, our results revealed differences in patterns of BDQ- and CFZ-induced acquired spontaneous mutations that may enhance our understanding of MTB BDQ/CFZ-resistance mechanisms. IMPORTANCE This study of MTB drug resistance mechanisms revealed patterns of spontaneous MTB mutations associated with acquired BDQ and CFZ resistance that arose after clinical MTB isolates were cultured in vitro with BDQ or CFZ. Results of protein sequence and structural analyses provided insights into potential mechanisms underlying associations between MTB gene mutations and DR phenotypes. Taken together, these results revealed differences in acquired BDQ and CFZ resistance mechanisms as a new perspective that may enhance our understanding of BDQ/CFZ resistance mechanisms and facilitate the development of new methods for detecting MTB drug resistance genes.
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Affiliation(s)
- Jin Shi
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, China
| | - Yuanyuan Liu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Tuoya Wu
- Department of Tuberculosis Diseases, Tongliao Infectious Disease Hospital, Tongliao, Inner Mongolia, China
| | - Lu Li
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, China
| | - Shujing Han
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Xiao Peng
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yuanyuan Shang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, China
| | - Yongli Guo
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
| | - Yu Pang
- Department of Bacteriology and Immunology, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, China
| | - Mengqiu Gao
- Department of Tuberculosis, Beijing Chest Hospital, Capital Medical University/Beijing Tuberculosis & Thoracic Tumor Research Institute, Beijing, China
| | - Jie Lu
- Beijing Key Laboratory for Pediatric Diseases of Otolaryngology, Head and Neck Surgery, Beijing Pediatric Research Institute, Beijing Children’s Hospital, Capital Medical University, National Center for Children’s Health, Beijing, China
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Sreelatha S, Nagarajan U, Natarajan S. Protein targets in Mycobacterium tuberculosis and their inhibitors for therapeutic implications: A narrative review. Int J Biol Macromol 2023:125022. [PMID: 37244342 DOI: 10.1016/j.ijbiomac.2023.125022] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 05/19/2023] [Accepted: 05/20/2023] [Indexed: 05/29/2023]
Abstract
Advancement in the area of anti-tubercular drug development has been full-fledged, yet, a very less number of drug molecules have reached phase II clinical trials, and therefore "End-TB" is still a global challenge. Inhibitors to specific metabolic pathways of Mycobacterium tuberculosis (Mtb) gain importance in strategizing anti-tuberculosis drug discovery. The lead compounds that target DNA replication, protein synthesis, cell wall biosynthesis, bacterial virulence and energy metabolism are emerging as potential chemotherapeutic options against Mtb growth and survival within the host. In recent times, the in silico approaches have become most promising tools in the identification of suitable inhibitors for specific protein targets of Mtb. An update in the fundamental understanding of these inhibitors and the mechanism of interaction may bring hope to future perspectives in novel drug development and delivery approaches. This review provides a collective impression of the small molecules with potential antimycobacterial activities and their target pathways in Mtb such as cell wall biosynthesis, DNA replication, transcription and translation, efflux pumps, antivirulence pathways and general metabolism. The mechanism of interaction of specific inhibitor with their respective protein targets has been discussed. The comprehensive knowledge of such an impactful area of research would essentially reflect in the discovery of novel drug molecules and effective delivery approaches. This narrative review encompasses the knowledge of emerging targets and promising n that could potentially translate in to the anti-TB-drug discovery.
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Affiliation(s)
- Souparnika Sreelatha
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Usharani Nagarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India
| | - Saravanan Natarajan
- Department of Biochemistry, ICMR-National Institute for Research in Tuberculosis, Chennai 600031, Tamil Nadu, India.
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Rossini NDO, Dias MVB. Mutations and insights into the molecular mechanisms of resistance of Mycobacterium tuberculosis to first-line. Genet Mol Biol 2023; 46:e20220261. [PMID: 36718771 PMCID: PMC9887390 DOI: 10.1590/1678-4685-gmb-2022-0261] [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: 08/25/2022] [Accepted: 12/18/2022] [Indexed: 01/28/2023] Open
Abstract
Genetically antimicrobial resistance in Mycobacterium tuberculosis is currently one of the most important aspects of tuberculosis, considering that there are emerging resistant strains for almost every known drug used for its treatment. There are multiple antimicrobials used for tuberculosis treatment, and the most effective ones are the first-line drugs, which include isoniazid, pyrazinamide, rifampicin, and ethambutol. In this context, understanding the mechanisms of action and resistance of these molecules is essential for proposing new therapies and strategies of treatment. Additionally, understanding how and where mutations arise conferring a resistance profile to the bacteria and their effect on bacterial metabolism is an important requisite to be taken in producing safer and less susceptible drugs to the emergence of resistance. In this review, we summarize the most recent literature regarding novel mutations reported between 2017 and 2022 and the advances in the molecular mechanisms of action and resistance against first-line drugs used in tuberculosis treatment, highlighting recent findings in pyrazinamide resistance involving PanD and, additionally, resistance-conferring mutations for novel drugs such as bedaquiline, pretomanid, delamanid and linezolid.
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Affiliation(s)
- Nicolas de Oliveira Rossini
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil
| | - Marcio Vinicius Bertacine Dias
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil. Universidade de São PauloInstituto de Ciências BiomédicasDepartamento de MicrobiologiaSão PauloSPBrazil,University of Warwick, Department of Chemistry, Coventry, United Kingdom. University of WarwickDepartment of ChemistryCoventryUnited Kingdom
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Anjos TRD, Castro VS, Machado Filho ES, Suffys PN, Gomes HM, Duarte RS, Figueiredo EEDS, Carvalho RCT. Genomic analysis of Mycobacterium tuberculosis variant bovis strains isolated from bovine in the state of Mato Grosso, Brazil. Front Vet Sci 2022; 9:1006090. [DOI: 10.3389/fvets.2022.1006090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 10/28/2022] [Indexed: 11/18/2022] Open
Abstract
The species Mycobacterium tuberculosis variant bovis (M. tuberculosis var. bovis) is associated with tuberculosis, mainly in cattle and buffaloes. This pathogen has the potential to infect other mammals, including humans. Tuberculosis caused by M. tuberculosis var. bovis is a zoonosis clinically identical to tuberculosis caused by Mycobacterium tuberculosis, and the recommended treatment in humans results in the use of antibiotics. In this study, we used the whole genome sequencing (WGS) methodology Illumina NovaSeq 6000 System platform to characterize the genome of M. tuberculosis var. bovis in cattle circulating in Mato Grosso, identify mutations related to drug resistance genes, compare with other strains of M. tuberculosis var. bovis brazilian and assess potential drug resistance. Four isolates of M. tuberculosis var. bovis of cattle origin representing the main livestock circuits, which had been more prevalent in previous studies in the state of Mato Grosso, were selected for the genomic study. The genome sizes of the sequenced strains ranged from 4,306,423 to 4,332,964 bp, and the GC content was 65.6%. The four strains from Mato Grosso presented resistance genes to pncA (pyrazinamide), characterized as drug-resistant strains. In addition to verifying several point mutations in the pncA, rpsA, rpsL, gid, rpoB, katG, gyrB, gyrA, tlyA, embA, embB, embC, fgd, fbiB, and fbiC genes, these genes were similar to antibiotic resistance in more than 92% of the Brazilian strains. Therefore, our results indicated a high genetic diversity between our isolates and other M. tuberculosis var. bovis isolated in Brazil. Thus, multiple transmission routes of this pathogen may be present in the production chain. So, to achieve a bovine tuberculosis-free health status, the use of the WGS as a control and monitoring tool will be crucial to determine these transmission routes.
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Poulton NC, Azadian ZA, DeJesus MA, Rock JM. Mutations in rv0678 Confer Low-Level Resistance to Benzothiazinone DprE1 Inhibitors in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2022; 66:e0090422. [PMID: 35920665 PMCID: PMC9487612 DOI: 10.1128/aac.00904-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Tuberculosis (TB) is the leading cause of death from any bacterial infection, causing 1.5 million deaths worldwide each year. Due to the emergence of drug-resistant strains of Mycobacterium tuberculosis (Mtb) there have been significant efforts aimed at developing novel drugs to treat TB. One promising drug target in Mtb is the arabinogalactan biosynthetic enzyme DprE1, and there have been over a dozen unique chemical scaffolds identified which inhibit the activity of this protein. Among the most promising lead compounds are the benzothiazinones BTZ043 and PBTZ169, both of which are currently in or have completed phase IIa clinical trials. Due to the potential clinical utility of these drugs, we sought to identify potential synergistic interactions and new mechanisms of resistance using a genome-scale CRISPRi chemical-genetic screen with PBTZ169. We found that knockdown of rv0678, the negative regulator of the mmpS5/L5 drug efflux pump, confers resistance to PBTZ169. Mutations in rv0678 are the most common form of resistance to bedaquiline and there is already abundant evidence of these mutations emerging in bedaquiline-treated patients. We confirmed that rv0678 mutations from clinical isolates confer low level cross-resistance to BTZ043 and PBTZ169. While it is yet unclear whether rv0678 mutations would render benzothiazinones ineffective in treating TB, these results highlight the importance of monitoring for clinically prevalent rv0678 mutations during ongoing BTZ043 and PBTZ169 clinical trials.
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Affiliation(s)
- Nicholas C. Poulton
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Zachary A. Azadian
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Michael A. DeJesus
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
| | - Jeremy M. Rock
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, New York, USA
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12
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Miotto P, Sorrentino R, De Giorgi S, Provvedi R, Cirillo DM, Manganelli R. Transcriptional regulation and drug resistance in Mycobacterium tuberculosis. Front Cell Infect Microbiol 2022; 12:990312. [PMID: 36118045 PMCID: PMC9480834 DOI: 10.3389/fcimb.2022.990312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bacterial drug resistance is one of the major challenges to present and future human health, as the continuous selection of multidrug resistant bacteria poses at serious risk the possibility to treat infectious diseases in the near future. One of the infection at higher risk to become incurable is tuberculosis, due to the few drugs available in the market against Mycobacterium tuberculosis. Drug resistance in this species is usually due to point mutations in the drug target or in proteins required to activate prodrugs. However, another interesting and underexplored aspect of bacterial physiology with important impact on drug susceptibility is represented by the changes in transcriptional regulation following drug exposure. The main regulators involved in this phenomenon in M. tuberculosis are the sigma factors, and regulators belonging to the WhiB, GntR, XRE, Mar and TetR families. Better understanding the impact of these regulators in survival to drug treatment might contribute to identify new drug targets and/or to design new strategies of intervention.
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Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Rita Sorrentino
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Stefano De Giorgi
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | | | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Div. of Immunology, Transplantation and Infectious Diseases IRCCS San Raffaele Scientific Institute, Milano, Italy
| | - Riccardo Manganelli
- Department of Molecular Medicine, University of Padova, Padova, Italy
- *Correspondence: Riccardo Manganelli,
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13
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Azimi T, Khoshnood S, Asadi A, Heidary M, Mahmoudi H, Kaviar VH, Hallajzadeh M, Nasiri MJ. Linezolid resistance in multidrug-resistant mycobacterium tuberculosis: A systematic review and meta-analysis. Front Pharmacol 2022; 13:955050. [PMID: 36110536 PMCID: PMC9468755 DOI: 10.3389/fphar.2022.955050] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 07/15/2022] [Indexed: 11/13/2022] Open
Abstract
Introduction: Linezolid (LNZ) is an effective antibiotic to treat patients with multidrug-resistant tuberculosis (MDR-TB) treatment failure. M. tuberculosis strains resistant to isoniazid and rifampin are defined as MDR-TB. In recent years, resistance to LNZ among MDR-TB cases has been reported in several different countries. In this study, we performed a systematic review and meta-analysis to investigate the prevalence of LNZ resistance among MDR-TB isolates.Methods: The databases of Embase, PubMed/Medline, and Web of Science were searched systematically from January 2000 to April 2021. Statistical analyses were performed by using Comprehensive Meta-Analysis software. Heterogeneity was reported by using the t-squared statistic and Q-statistic. Begg’s rank correlation in combination with the funnel plot were used to evaluate any possible publication bias.Results: In total, 25 studies were selected for meta-analysis from 14 different countries; the majority was from China (n = 5) and Turkey (n = 4). Moreover, 7,366 patients were infected with MDR M. tuberculosis. Among the study population, 98 patients were co-infected with HIV, and 18 patients with hepatitis C virus (HCV). Furthermore, 28 cases had diabetes, and139 cases were alcohol abuser. Overall, 4,956 MDR M. tuberculosis strains were isolated from TB patients. The pooled frequency of LNZ resistance among the clinical isolates of MDR M. tuberculosis was 4.2% (95%). Begg’s (p = 0.72) test showed no evidence of publication bias.Conclusion: LNZ resistance among MDR M. tuberculosis isolates is increasing. On the other hand, long-term treatment of MDR-TB cases with LNZ alone is associated with several adverse effects. Thus, it is recommended that newer anti-TB drugs, including bedaquiline and delamanid, in combination with linezolid could increase its effectiveness and decrease toxicities. However, more studies should be done in this field.
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Affiliation(s)
- Taher Azimi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
- Student Research Committee, Ilam University of Medical Sciences, Ilam, Iran
| | - Arezoo Asadi
- Endocrine Research Center, Institute of Endocrinology and Metabolism, Iran University of Medical Sciences (IUMS), Tehran, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
- *Correspondence: Mohsen Heidary, ; Mohammad Javad Nasiri,
| | - Hassan Mahmoudi
- Department of Microbiology, Faculty of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
- Nahavand School of Allied Medical Sciences, Hamadan University of Medical Sciences, Hamadan, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Masoume Hallajzadeh
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Mohammad Javad Nasiri
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- *Correspondence: Mohsen Heidary, ; Mohammad Javad Nasiri,
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Puyén ZM, Santos-Lázaro D, Vigo AN, Coronel J, Alarcón MJ, Cotrina VV, Moore DAJ. Evaluation of the broth microdilution plate methodology for susceptibility testing of Mycobacterium tuberculosis in Peru. BMC Infect Dis 2022; 22:705. [PMID: 36002805 PMCID: PMC9399989 DOI: 10.1186/s12879-022-07677-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 07/26/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tuberculosis (TB) is a communicable, preventable and curable disease caused by the bacterium Mycobacterium tuberculosis (MTB). Peru is amongst the 30 countries with the highest burden of multidrug-resistant tuberculosis (MDR-TB) worldwide. In the fight against drug-resistant tuberculosis, the UKMYC6 microdilution plate was developed and validated by the CRyPTIC project. The objective of the study was to evaluate the use of the broth microdilution (BMD) plate methodology for susceptibility testing of drug-resistant MTB strains in Peru. METHODS MTB strains isolated between 2015 and 2018 in Peru were used. 496 nationally-representative strains determined as drug-resistant by the routine 7H10 Agar Proportion Method (APM) were included in the present study. The Minimum Inhibitory Concentration (MIC) of 13 antituberculosis drugs were determined for each strain using the UKMYC6 microdilution plates. Diagnostic agreement between APM and BMD plate methodology was determined for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. Phenotypes were set using binary (or ternary) classification based on Epidemiological cut-off values (ECOFF/ECV) proposed by the CRyPTIC project. Whole Genome Sequencing (WGS) was performed on strains with discrepant results between both methods. RESULTS MIC distributions were determined for 13 first- and second-line anti-TB drugs, including new (bedaquiline, delamanid) and repurposed (clofazimine, linezolid) agents. MIC results were available for 80% (397/496) of the strains at 14 days and the remainder at 21 days. The comparative analysis determined a good agreement (0.64 ≤ k ≤ 0.79) for the drugs rifampicin, ethambutol, ethionamide and kanamycin, and the best agreement (k > 0.8) for isoniazid and levofloxacin. Overall, 12% of MIC values were above the UKMYC6 plate dilution ranges, most notably for the drugs rifampicin and rifabutin. No strain presented MICs higher than the ECOFF/ECV values for the new or repurposed drugs. Discrepant analysis using genotypic susceptibility testing by WGS supported half of the results obtained by APM (52%, 93/179) and half of those obtained by BMD plate methodology (48%, 86/179). CONCLUSIONS The BMD methodology using the UKMYC6 plate allows the complete susceptibility characterization, through the determination of MICs, of drug-resistant MTB strains in Peru. This methodology shows good diagnostic performances for rifampicin, isoniazid, ethambutol, ethionamide, kanamycin and levofloxacin. It also allows for the characterization of MICs for other drugs used in previous years against tuberculosis, as well as for new and repurposed drugs recently introduced worldwide.
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Affiliation(s)
- Zully M Puyén
- Instituto Nacional de Salud, Lima, Perú.
- Escuela de Medicina, Universidad Peruana de Ciencias Aplicadas, Lima, Perú.
| | | | | | | | | | | | - David A J Moore
- Universidad Peruana Cayetano Heredia, Lima, Perú
- London School of Hygiene & Tropical Medicine, London, UK
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15
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Linezolid Pharmacokinetics/Pharmacodynamics-Based Optimal Dosing for Multidrug-Resistant Tuberculosis. Int J Antimicrob Agents 2022; 59:106589. [DOI: 10.1016/j.ijantimicag.2022.106589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 02/03/2022] [Accepted: 04/03/2022] [Indexed: 11/05/2022]
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Dookie N, Khan A, Padayatchi N, Naidoo K. Application of Next Generation Sequencing for Diagnosis and Clinical Management of Drug-Resistant Tuberculosis: Updates on Recent Developments in the Field. Front Microbiol 2022; 13:775030. [PMID: 35401475 PMCID: PMC8988194 DOI: 10.3389/fmicb.2022.775030] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 02/17/2022] [Indexed: 11/30/2022] Open
Abstract
The World Health Organization’s End TB Strategy prioritizes universal access to an early diagnosis and comprehensive drug susceptibility testing (DST) for all individuals with tuberculosis (TB) as a key component of integrated, patient-centered TB care. Next generation whole genome sequencing (WGS) and its associated technology has demonstrated exceptional potential for reliable and comprehensive resistance prediction for Mycobacterium tuberculosis isolates, allowing for accurate clinical decisions. This review presents a descriptive analysis of research describing the potential of WGS to accelerate delivery of individualized care, recent advances in sputum-based WGS technology and the role of targeted sequencing for resistance detection. We provide an update on recent research describing the mechanisms of resistance to new and repurposed drugs and the dynamics of mixed infections and its potential implication on TB diagnosis and treatment. Whilst the studies reviewed here have greatly improved our understanding of recent advances in this arena, it highlights significant challenges that remain. The wide-spread introduction of new drugs in the absence of standardized DST has led to rapid emergence of drug resistance. This review highlights apparent gaps in our knowledge of the mechanisms contributing to resistance for these new drugs and challenges that limit the clinical utility of next generation sequencing techniques. It is recommended that a combination of genotypic and phenotypic techniques is warranted to monitor treatment response, curb emerging resistance and further dissemination of drug resistance.
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Affiliation(s)
- Navisha Dookie
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- *Correspondence: Navisha Dookie,
| | - Azraa Khan
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
| | - Kogieleum Naidoo
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu-Natal, Durban, South Africa
- South African Medical Research Council (SAMRC), CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Durban, South Africa
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17
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MDR Tuberculosis Treatment. Medicina (B Aires) 2022; 58:medicina58020188. [PMID: 35208510 PMCID: PMC8878254 DOI: 10.3390/medicina58020188] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/13/2022] [Accepted: 01/15/2022] [Indexed: 11/17/2022] Open
Abstract
Multidrug-resistant (MDR) tuberculosis (TB), resistant to isoniazid and rifampicin, continues to be one of the most important threats to controlling the TB epidemic. Over the last few years, there have been promising pharmacological advances in the paradigm of MDR TB treatment: new and repurposed drugs have shown excellent bactericidal and sterilizing activity against Mycobacterium tuberculosis and several all-oral short regimens to treat MDR TB have shown promising results. The purpose of this comprehensive review is to summarize the most important drugs currently used to treat MDR TB, the recommended regimens to treat MDR TB, and we also summarize new insights into the treatment of patients with MDR TB.
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Abstract
Given the low treatment success rates of drug-resistant tuberculosis (TB), novel TB drugs are urgently needed. The landscape of TB treatment has changed considerably over the last decade with the approval of three new compounds: bedaquiline, delamanid and pretomanid. Of these, delamanid and pretomanid belong to the same class of drugs, the nitroimidazoles. In order to close the knowledge gap on how delamanid and pretomanid compare with each other, we summarize the main findings from preclinical research on these two compounds. We discuss the compound identification, mechanism of action, drug resistance, in vitro activity, in vivo pharmacokinetic profiles, and preclinical in vivo activity and efficacy. Although delamanid and pretomanid share many similarities, several differences could be identified. One finding of particular interest is that certain Mycobacterium tuberculosis isolates have been described that are resistant to either delamanid or pretomanid, but with preserved susceptibility to the other compound. This might imply that delamanid and pretomanid could replace one another in certain regimens. Regarding bactericidal activity, based on in vitro and preclinical in vivo activity, delamanid has lower MICs and higher mycobacterial load reductions at lower drug concentrations and doses compared with pretomanid. However, when comparing in vivo preclinical bactericidal activity at dose levels equivalent to currently approved clinical doses based on drug exposure, this difference in activity between the two compounds fades. However, it is important to interpret these comparative results with caution knowing the variability inherent in preclinical in vitro and in vivo models.
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Affiliation(s)
- Saskia E. Mudde
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Corresponding author. E-mail:
| | | | - Anne Lenaerts
- Mycobacteria Research Laboratories, Department of Microbiology, Immunology, and Pathology, Colorado State University, Fort Collins, CO, USA
| | - Hannelore I. Bax
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Section of Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jurriaan E. M. De Steenwinkel
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
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19
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Bharadwaj R. Linezolid-resistant Mycobacterium tuberculosis: Will it impact the tuberculosis elimination programme? Indian J Med Res 2021; 154:16-18. [PMID: 34782525 PMCID: PMC8715697 DOI: 10.4103/ijmr.ijmr_3537_20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Renu Bharadwaj
- Department of Microbiology, B.J. Government Medical College, Pune 411 038, Maharashtra, India
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20
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Wastewater-Based Surveillance of Antibiotic Resistance Genes Associated with Tuberculosis Treatment Regimen in KwaZulu Natal, South Africa. Antibiotics (Basel) 2021; 10:antibiotics10111362. [PMID: 34827300 PMCID: PMC8614817 DOI: 10.3390/antibiotics10111362] [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: 08/04/2021] [Revised: 10/15/2021] [Accepted: 10/28/2021] [Indexed: 12/15/2022] Open
Abstract
Essential components of public health include strengthening the surveillance of infectious diseases and developing early detection and prevention policies. This is particularly important for drug-resistant tuberculosis (DR-TB), which can be explored by using wastewater-based surveillance. This study aimed to use molecular techniques to determine the occurrence and concentration of antibiotic-resistance genes (ARGs) associated with tuberculosis (TB) resistance in untreated and treated wastewater. Raw/untreated and treated (post-chlorination) wastewater samples were taken from three wastewater treatment plants (WWTPs) in South Africa. The ARGs were selected to target drugs used for first- and second-line TB treatment. Both conventional polymerase chain reaction (PCR) and the more advanced droplet digital PCR (ddPCR) were evaluated as surveillance strategies to determine the distribution and concentration of the selected ARGs. The most abundant ARG in the untreated wastewater was the rrs gene, associated with resistance to the aminoglycosides, specifically streptomycin, with median concentration ranges of 4.69–5.19 log copies/mL. In contrast, pncA gene, associated with resistance to the TB drug pyrazinamide, was the least detected (1.59 to 2.27 log copies/mL). Resistance genes associated with bedaquiline was detected, which is a significant finding because this is a new drug introduced in South Africa for the treatment of multi-drug resistant TB. This study, therefore, establishes the potential of molecular surveillance of wastewater for monitoring antibiotic resistance to TB treatment in communities.
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21
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Ismail N, Rivière E, Limberis J, Huo S, Metcalfe JZ, Warren RM, Van Rie A. Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis. THE LANCET MICROBE 2021; 2:e604-e616. [PMID: 34796339 PMCID: PMC8597953 DOI: 10.1016/s2666-5247(21)00175-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background Methods Findings Interpretation Funding
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22
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Bedaquiline Drug Resistance Emergence Assessment in MDR-TB (DREAM): a 5-Year Prospective In-Vitro Surveillance Study of Bedaquiline and Other Second-Line Drug-Susceptibility Testing in MDR-TB Isolates. J Clin Microbiol 2021; 60:e0291920. [PMID: 34705538 PMCID: PMC8769720 DOI: 10.1128/jcm.02919-20] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bedaquiline Drug Resistance Emergence Assessment in Multidrug-resistant-tuberculosis (MDR-TB) (DREAM) was a 5-year (2015-2019) phenotypic drug-resistance surveillance study across 11 countries. DREAM assessed the susceptibility of 5036 MDR-TB isolates of bedaquiline-treatment-naïve patients to bedaquiline and other anti-tuberculosis drugs by the 7H9 broth microdilution (BMD) and 7H10/7H11 agar dilution (AD) minimal inhibitory concentration (MIC) methods. Bedaquiline AD MIC quality control (QC) range for the H37Rv reference strain was unchanged, but the BMD MIC QC range (0.015-0.12 μg/ml) was adjusted compared with ranges from a multilaboratory, multicountry reproducibility study conforming to Clinical and Laboratory Standards Institute Tier-2 criteria. Epidemiological cut-off values of 0.12 μg/ml by BMD and 0.25 μg/ml by AD were consistent with previous bedaquiline breakpoints. An area of technical uncertainty or Intermediate category was set at 0.25 μg/ml and 0.5 μg/ml for BMD and AD, respectively. When applied to the 5036 MDR-TB isolates, bedaquiline-susceptible, intermediate and bedaquiline-resistant rates were 97.9%, 1.5% and 0.6%, respectively, for BMD, and 98.8%, 0.8% and 0.4% for AD. Resistance rates were: ofloxacin 35.1%, levofloxacin 34.2%, moxifloxacin 33.3%, 1.5% linezolid and 2% clofazimine. Phenotypic cross resistance between bedaquiline and clofazimine was 0.4% in MDR-TB and 1% in pre-extensively drug-resistant (pre-XDR-TB)/XDR-TB populations. Co-resistance to bedaquiline and linezolid, and clofazimine and linezolid, were 0.1% and 0.3%, respectively, in MDR-TB, and 0.2% and 0.4% in pre-XDR-TB/XDR-TB populations. Resistance rates to bedaquiline appear to be low in the bedaquiline-treatment-naïve population. No treatment-limiting patterns for cross-resistance and co-resistance have been identified with key TB drugs to date.
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23
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Tietjen AK, Kroemer N, Cattaneo D, Baldelli S, Wicha SG. Population pharmacokinetics and target attainment analysis of linezolid in multidrug-resistant tuberculosis patients. Br J Clin Pharmacol 2021; 88:1835-1844. [PMID: 34622478 DOI: 10.1111/bcp.15102] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 08/31/2021] [Accepted: 09/22/2021] [Indexed: 01/02/2023] Open
Abstract
AIM This study investigates the pharmacokinetic/pharmacodynamic (PK/PD) target attainment of linezolid in patients infected with multidrug-resistant (MDR) tuberculosis (TB). METHODS A pharmacometric model was developed including 244 timed linezolid concentration samples from 39 patients employing NONMEM 7.4. The probability of target attainment (PTA, PK/PD target: unbound (f) area-under-the-concentration-time-curve (AUC)/minimal inhibitory concentration (MIC) of 119) as well as a region-specific cumulative fraction of response (CFR) were estimated for different dosing regimens. RESULTS A one-compartment model with linear elimination with a clearance (CL) of 7.69 L/h (interindividual variability 34.1%), a volume of distribution (Vd) of 45.2 L and an absorption constant (KA) of 0.679 h-1 (interoccasion variability 143.7%) allometric scaled by weight best described the PK of linezolid. The PTA at an MIC of 0.5 mg/L was 55% or 97% if patients receiving 300 or 600 mg twice daily, respectively. CFRs varied greatly among populations and geographic regions. A desirable global CFR of ≥90% was achieved if linezolid was administered at a dose of 600 mg twice daily but not at a dose of 300 mg twice daily. CONCLUSION This study showed that a dose of 300 mg twice daily of linezolid might not be sufficient to treat MDR-TB patients from a PK/PD perspective. Thus, it might be recommendable to start with a higher dose of 600 mg twice daily to ensure PK/PD target attainment. Hereby, therapeutic drug monitoring and MIC determination should be performed to control PK/PD target attainment as linezolid shows high variability in its PK in the TB population.
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Affiliation(s)
- Anna K Tietjen
- Department of Clinical Pharmacy, Institute of Pharmacy, University of Hamburg, Hamburg, Germany.,University of Lübeck, Lübeck, Germany
| | - Niklas Kroemer
- Department of Clinical Pharmacy, Institute of Pharmacy, University of Hamburg, Hamburg, Germany
| | - Dario Cattaneo
- Unit of Clinical Pharmacology, Department of Laboratory Medicine, Luigi Sacco University Hospital, Milan, Italy
| | - Sara Baldelli
- Unit of Clinical Pharmacology, Department of Laboratory Medicine, Luigi Sacco University Hospital, Milan, Italy
| | - Sebastian G Wicha
- Department of Clinical Pharmacy, Institute of Pharmacy, University of Hamburg, Hamburg, Germany
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Khoshnood S, Taki E, Sadeghifard N, Kaviar VH, Haddadi MH, Farshadzadeh Z, Kouhsari E, Goudarzi M, Heidary M. Mechanism of Action, Resistance, Synergism, and Clinical Implications of Delamanid Against Multidrug-Resistant Mycobacterium tuberculosis. Front Microbiol 2021; 12:717045. [PMID: 34690963 PMCID: PMC8529252 DOI: 10.3389/fmicb.2021.717045] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 09/02/2021] [Indexed: 11/21/2022] Open
Abstract
Multidrug-resistant (MDR) isolates of Mycobacterium tuberculosis (MTB) remain a primary global threat to the end of tuberculosis (TB) era. Delamanid (DLM) is a nitro-dihydro-imidazooxazole derivative utilized to treat MDR-TB. DLM has distinct mechanism of action, inhibiting methoxy- and keto-mycolic acid (MA) synthesis through the F420 coenzyme mycobacteria system and generating nitrous oxide. While DLM resistance among MTB strains is uncommon, there are increasing reports in Asia and Europe, and such resistance will prolong the treatment courses of patients infected with MDR-TB. In this review, we address the antimycobacterial properties of DLM, report the global prevalence of DLM resistance, discuss the synergism of DLM with other anti-TB drugs, and evaluate the documented clinical trials to provide new insights into the clinical use of this antibiotic.
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Affiliation(s)
- Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Elahe Taki
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Nourkhoda Sadeghifard
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | - Vahab Hassan Kaviar
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam, Iran
| | | | - Zahra Farshadzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Ebrahim Kouhsari
- Laboratory Sciences Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar, Iran
- Cellular and Molecular Research Center, Sabzevar University of Medical Sciences, Sabzevar, Iran
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25
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Grinter R, Greening C. Cofactor F420: an expanded view of its distribution, biosynthesis and roles in bacteria and archaea. FEMS Microbiol Rev 2021; 45:fuab021. [PMID: 33851978 PMCID: PMC8498797 DOI: 10.1093/femsre/fuab021] [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: 01/05/2021] [Accepted: 04/11/2021] [Indexed: 12/11/2022] Open
Abstract
Many bacteria and archaea produce the redox cofactor F420. F420 is structurally similar to the cofactors FAD and FMN but is catalytically more similar to NAD and NADP. These properties allow F420 to catalyze challenging redox reactions, including key steps in methanogenesis, antibiotic biosynthesis and xenobiotic biodegradation. In the last 5 years, there has been much progress in understanding its distribution, biosynthesis, role and applications. Whereas F420 was previously thought to be confined to Actinobacteria and Euryarchaeota, new evidence indicates it is synthesized across the bacterial and archaeal domains, as a result of extensive horizontal and vertical biosynthetic gene transfer. F420 was thought to be synthesized through one biosynthetic pathway; however, recent advances have revealed variants of this pathway and have resolved their key biosynthetic steps. In parallel, new F420-dependent biosynthetic and metabolic processes have been discovered. These advances have enabled the heterologous production of F420 and identified enantioselective F420H2-dependent reductases for biocatalysis. New research has also helped resolve how microorganisms use F420 to influence human and environmental health, providing opportunities for tuberculosis treatment and methane mitigation. A total of 50 years since its discovery, multiple paradigms associated with F420 have shifted, and new F420-dependent organisms and processes continue to be discovered.
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Affiliation(s)
- Rhys Grinter
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
| | - Chris Greening
- Department of Microbiology, Monash Biomedicine Discovery Institute, Monash University, Clayton, VIC 3800, Australia
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Lee T, Lee SJ, Jeon D, Lee HY, Kim HJ, Kang BH, Mok J. Additional Drug Resistance in Patients with Multidrug-resistant Tuberculosis in Korea: a Multicenter Study from 2010 to 2019. J Korean Med Sci 2021; 36:e174. [PMID: 34227261 PMCID: PMC8258238 DOI: 10.3346/jkms.2021.36.e174] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/02/2021] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Drug-resistance surveillance (DRS) data provide key information for building an effective treatment regimen in patients with multidrug-resistant tuberculosis (MDR-TB). This study was conducted to investigate the patterns and trends of additional drug resistance in MDR-TB patients in South Korea. METHODS Phenotypic drug susceptibility test (DST) results of MDR-TB patients collected from seven hospitals in South Korea from 2010 to 2019 were retrospectively analyzed. RESULTS In total, 633 patients with MDR-TB were included in the analysis. Of all patients, 361 (57.0%) were new patients. All patients had additional resistance to a median of three anti-TB drugs. The resistance rates of any fluoroquinolone (FQ), linezolid, and cycloserine were 26.2%, 0.0%, and 6.3%, respectively. The proportions of new patients and resistance rates of most anti-TB drugs did not decrease during the study period. The number of additional resistant drugs was significantly higher in FQ-resistant MDR-TB than in FQ-susceptible MDR-TB (median of 9.0 vs. 2.0). Among 26 patients with results of minimum inhibitory concentrations for bedaquiline (BDQ) and delamanid (DLM), one (3.8%) and three (11.5%) patients were considered resistant to BDQ and DLM with interim critical concentrations, respectively. Based on the DST results, 72.4% and 24.8% of patients were eligible for the World Health Organization's longer and shorter MDR-TB treatment regimen, respectively. CONCLUSION The proportions of new patients and rates of additional drug resistance in patients with MDR-TB were high and remain stable in South Korea. A nationwide analysis of DRS data is required to provide effective treatment for MDR-TB patients in South Korea.
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Affiliation(s)
- Taehoon Lee
- Department of Internal Medicine, Ulsan University Hospital, University of Ulsan College of Medicine, Ulsan, Korea
| | - Seung Jun Lee
- Department of Internal Medicine, Gyeongsang National University Hospital, Gyeongsang National University College of Medicine, Jinju, Korea
| | - Doosoo Jeon
- Department of Internal Medicine, Pusan National University Yangsan Hospital, Pusan National University School of Medicine, Yangsan, Korea
| | - Ho Young Lee
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Hyo Jung Kim
- Division of Pulmonary, Department of Internal Medicine, Inje University Haeundae Paik Hospital, Busan, Korea
| | - Bo Hyoung Kang
- Department of Internal Medicine, Dong-A University Hospital, Busan, Korea
| | - Jeongha Mok
- Department of Internal Medicine, Pusan National University Hospital, Pusan National University School of Medicine, Busan, Korea
- Biomedical Research Institute, Pusan National University Hospital, Busan, Korea.
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He W, Liu C, Liu D, Ma A, Song Y, He P, Bao J, Li Y, Zhao B, Fan J, Cheng Q, Zhao Y. Prevalence of Mycobacterium tuberculosis resistant to bedaquiline and delamanid in China. J Glob Antimicrob Resist 2021; 26:241-248. [PMID: 34214699 DOI: 10.1016/j.jgar.2021.06.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/06/2021] [Accepted: 06/15/2021] [Indexed: 11/28/2022] Open
Abstract
OBJECTIVES The new antituberculous drugs delamanid and bedaquiline form the last line of defence against drug-resistant tuberculosis (TB). Understanding the background prevalence of resistance to new drugs can help predict the lifetime of these drugs' effectiveness and inform regimen design. METHODS Mycobacterium tuberculosis without prior exposure to novel anti-TB drugs were analysed retrospectively. Drug susceptibility testing for bedaquiline, delamanid, linezolid, clofazimine and widely used first- and second-line anti-TB drugs was performed. All TB isolates with resistance to new or repurposed drugs were subjected to whole-genome sequencing to explore the molecular characteristics of resistance and to perform phylogenetic analysis. RESULTS Overall, resistance to delamanid, bedaquiline, linezolid and clofazimine was observed in 0.7% (11/1603), 0.4% (6/1603), 0.4% (7/1603) and 0.4% (6/1603) of TB isolates, respectively. Moreover, 1.0% (1/102), 2.9% (3/102), 3.9% (4/102) and 1.0% (1/102) of multidrug-resistant TB (MDR-TB) were resistant to bedaquiline, delamanid, linezolid and clofazimine, respectively. Whereas 22.2% (2/9) of extensively-drug resistant tuberculosis (XDR-TB) isolates were resistant to both delamanid and linezolid, and none was resistant to bedaquiline or clofazimine. Phylogenetic analysis showed that recent transmission occurred in two XDR-TB with additional resistance to delamanid and linezolid. None known gene mutation associated with delamanid resistance was detected. All four isolates with cross-resistance to bedaquiline and clofazimine had a detected gene mutation in Rv0678. Three of five strains with linezolid resistance had a detected gene mutation in rplC. CONCLUSION Detection of resistance to new anti-TB drugs emphasises the pressing need for intensive surveillance for such resistance before their wide usage.
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Affiliation(s)
- Wencong He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Chunfa Liu
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Dongxin Liu
- Shenzhen Third People's Hospital, Longgang District, Shenzhen City, China
| | - Aijing Ma
- Shenzhen Third People's Hospital, Longgang District, Shenzhen City, China
| | - Yimeng Song
- Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Ping He
- National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jingjing Bao
- Fourth Hospital of Inner Mongolia Autonomous Region, Hohhot, Inner Mongolia Autonomous Region, China
| | - Yuanchun Li
- Beijing Hospital, National Center of Gerontology, Beijing 100730, China
| | - Bing Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jiale Fan
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qian Cheng
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Yanlin Zhao
- National Tuberculosis Reference Laboratory, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
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Khosravi AD, Tabandeh MR, Shahi F, Salmanzadeh S. Linezolid resistance among multidrug-resistant Mycobacterium tuberculosis clinical isolates in Iran. Acta Microbiol Immunol Hung 2021. [PMID: 34174037 DOI: 10.1556/030.2021.01490] [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: 05/04/2021] [Accepted: 06/09/2021] [Indexed: 11/19/2022]
Abstract
The management of multidrug-resistant (MDR) and extensively drug-resistant tuberculosis (XDR-TB) presents a main challenge and the drug options for treating these infections are very limited. Linezolid (LNZ) has recently been approved for the treatment of MDR and XDR-TB. But, there are narrow data on genotypic and phenotypic LNZ resistance in clinical isolates. So, we aimed to determine the prevalence of LNZ resistance and to identify the mutations associated with LNZ resistance among clinical MDR-TB isolates. The minimum inhibitory concentration (MIC) values of LNZ for 22 MDR-TB isolates were determined by broth microdilution method. All MDR-TB isolates were sequenced in the rrl and rplC genes conferring LNZ resistance. LNZ resistance was found in 3 (13.6%) of 22 MDR-TB isolates. The MICs of LNZ were 8 μg/mL for two isolates and 16 μg/mL for one isolate. The 421 (A/G) and 449 (T/A) mutations in rplC gene were detected in one of the LNZ-resistant isolates. There was no mutation in rrl gene. The results reveal that the prevalence of LNZ-resistant isolates is 13.6% among MDR-TB isolates and drug susceptibility testing (DST) against LNZ is useful in the management of complicated and drug-resistant cases. However, further studies could identify other possible genetic mechanism of resistance in TB.
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Affiliation(s)
- Azar Dokht Khosravi
- 1Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 3Iranian Study Group on Microbial Drug Resistance,Iran
| | - Mohammad Reza Tabandeh
- 4Department of Basic Sciences, Division of Biochemistry and Molecular Biology, Faculty of Veterinary Medicine, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Fatemeh Shahi
- 1Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 2Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Shokrollah Salmanzadeh
- 1Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- 5Tropical Medicine Ward, Razi Teaching Hospital, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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29
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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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Chauhan A, Kumar M, Kumar A, Kanchan K. Comprehensive review on mechanism of action, resistance and evolution of antimycobacterial drugs. Life Sci 2021; 274:119301. [PMID: 33675895 DOI: 10.1016/j.lfs.2021.119301] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/14/2021] [Accepted: 02/24/2021] [Indexed: 01/04/2023]
Abstract
Tuberculosis is one of the deadliest infectious diseases existing in the world since ancient times and still possesses serious threat across the globe. Each year the number of cases increases due to high drug resistance shown by Mycobacterium tuberculosis (Mtb). Available antimycobacterial drugs have been classified as First line, Second line and Third line antibiotics depending on the time of their discoveries and their effectiveness in the treatment. These antibiotics have a broad range of targets ranging from cell wall to metabolic processes and their non-judicious and uncontrolled usage in the treatment for years has created a significant problem called multi-drug resistant (MDR) tuberculosis. In this review, we have summarized the mechanism of action of all the classified antibiotics currently in use along with the resistance mechanisms acquired by Mtb. We have focused on the new drug candidates/repurposed drugs, and drug in combinations, which are in clinical trials for either treating the MDR tuberculosis more effectively or involved in reducing the time required for the chemotherapy of drug sensitive TB. This information is not discussed very adequately on a single platform. Additionally, we have discussed the recent technologies that are being used to discover novel resistance mechanisms acquired by Mtb and for exploring novel drugs. The story of intrinsic resistance mechanisms and evolution in Mtb is far from complete. Therefore, we have also discussed intrinsic resistance mechanisms of Mtb and their evolution with time, emphasizing the hope for the development of novel antimycobacterial drugs for effective therapy of tuberculosis.
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Affiliation(s)
- Aditi Chauhan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India
| | - Manoj Kumar
- Amity Food and Agriculture Foundation, Amity University Uttar Pradesh, Noida 201313, India
| | - Awanish Kumar
- Department of Bio Technology, National Institute of Technology, Raipur, India
| | - Kajal Kanchan
- Amity Institute of Molecular Medicine and Stem Cell Research, Amity University Uttar Pradesh, Noida 201313, India.
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31
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Wang G, Jiang G, Jing W, Zong Z, Yu X, Chen S, Li W, Huang H. Prevalence and molecular characterizations of seven additional drug resistance among multidrug-resistant tuberculosis in China: A subsequent study of a national survey. J Infect 2021; 82:371-377. [PMID: 33556430 DOI: 10.1016/j.jinf.2021.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 11/08/2020] [Accepted: 02/02/2021] [Indexed: 11/26/2022]
Abstract
The drug resistance prevalence data facilitates selection of the initial drug for treating multidrug-resistant tuberculosis (MDR-TB). The aim of this study was to investigate the prevalence and molecular characterization of seven additional types of drug resistances among MDR-TB isolates collected from the first/only nationwide drug resistance surveillance in China. A total of 391 out of the 401 MDR-TB strains were successfully recovered by Löwenstein-Jensen medium. Drug susceptibility testing was performed against moxifloxacin (Mfx), bedaquiline (Bdq), linezolid (Lzd), clofazimine (Cfz), cycloserine (Cs), delamanid (Dlm) and pyrazinamide (PZA). The strains were subjected to whole-genome sequencing for the analysis corresponding drug resistant genes and their profiles. 269 (68.80%) were simple MDR-TB, 28 (7.16%) were extensively drug-resistant tuberculosis (XDR-TB) and 94 (24.04%) were pre-XDR-TB. Dlm, Lzd, Cfz and Bdq presented the lowest drug resistant rates i.e. 3.32% (13/391), 3.84% (15/391),6.65% (26/391) and 7.16% (28/391), respectively. Mfx (17.39%, 68/391) and CS (13.55%, 53/391) also demonstrated strong potencies against the MDR strains, whereas PZA (38.36%, 150/391) presented much higher resistant rate. 54.41% (37/68) Mfx-resistant strains carried mutations located within gyrA or gyrB. 70.15% (94/134) PZA-resistant strains had pncA mutations. Two of the 26 Cfz-resistant isolates had mutation in Rv0678 were also resistant to Bdq. Dlm, Lzd, Cfz and Bdq exhibited excellent activity against MDR-TB, including XDR-TB. These data highlighted the necessity of a timely, feasible and reliable DST, while genotypic DST for Mfx and PZA is promising at this moment.
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Affiliation(s)
- Guirong Wang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Guanglu Jiang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Wei Jing
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Zaojing Zong
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Xia Yu
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Suting Chen
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Weimin Li
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China
| | - Hairong Huang
- National Tuberculosis Clinical Laboratory, Beijing Key laboratory for Drug-resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beiguan St #9, Beijing 101149, China.
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32
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Mishra A, Behura A, Kumar A, Ghosh A, Naik L, Mawatwal S, Mohanty SS, Mishra A, Saha S, Bhutia SK, Singh R, Dhiman R. Soybean lectin induces autophagy through P2RX7 dependent activation of NF-κB-ROS pathway to kill intracellular mycobacteria. Biochim Biophys Acta Gen Subj 2021; 1865:129806. [PMID: 33253803 DOI: 10.1016/j.bbagen.2020.129806] [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: 05/29/2020] [Revised: 11/02/2020] [Accepted: 11/25/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Host-directed therapy is considered a novel anti-tuberculosis strategy in tackling the tuberculosis burden through autophagy induction by various inducers to curtail the growth of intracellular Mycobacterium tuberculosis. METHODS In this study, we investigated the anti-tubercular role of soybean lectin, a lectin isolated from Glycine max (Soybean). Effect of SBL on intracellular mycobacterial viability through autophagy and the mechanism involved in differentiated THP-1 cells was studied using different experimental approaches. RESULTS We initially performed a time kinetic experiment with the non-cytotoxic dose of SBL (20 μg/ml) and observed autophagy induction after 24 h of treatment. Abrogation of autophagy in the presence of 3-MA and an increase in LC3 puncta formation upon Baf-A1 addition elucidated the specific effect on autophagy and autophagic flux. SBL treatment also led to autophagy induction in mycobacteria infected macrophages that restricted the intracellular mycobacterial growth, thus emphasizing the host defensive role of SBL induced autophagy. Mechanistic studies revealed an increase in P2RX7 expression, NF-κB activation and reactive oxygen species generation upon SBL treatment. Inhibition of P2RX7 expression suppressed NF-κB dependent ROS level in SBL treated cells. Moreover, SBL induced autophagy was abrogated in the presence of either different inhibitors or P2RX7 siRNA, leading to the reduced killing of intracellular mycobacteria. CONCLUSION Taken together, these results conclude that SBL induced autophagy exerts an anti-mycobacterial effect in P2RX7-NF-κB dependent manner through the generation of ROS. GENERAL SIGNIFICANCE This study has provided a novel anti-mycobacterial role of SBL, which may play an important role in devising new therapeutic interventions.
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Affiliation(s)
- Abtar Mishra
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Assirbad Behura
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ashish Kumar
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Abhirupa Ghosh
- Divison of Bioinformatics, Bose Institute, Kolkata 700054, West Bengal, India
| | - Lincoln Naik
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Shradha Mawatwal
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Subhashree Subhasmita Mohanty
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Rajasthan 342011, India
| | - Sudipto Saha
- Divison of Bioinformatics, Bose Institute, Kolkata 700054, West Bengal, India
| | - Sujit K Bhutia
- Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Ramandeep Singh
- Tuberculosis Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, PO Box # 4, Faridabad 121001, Haryana, India
| | - Rohan Dhiman
- Laboratory of Mycobacterial Immunology, Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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Borham M, Oreiby A, El-Gedawy A, Hegazy Y, Hemedan A, Al-Gaabary M. Abattoir survey of bovine tuberculosis in tanta, centre of the Nile delta, with in silico analysis of gene mutations and protein-protein interactions of the involved mycobacteria. Transbound Emerg Dis 2021; 69:434-450. [PMID: 33484233 DOI: 10.1111/tbed.14001] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 12/18/2020] [Accepted: 01/19/2021] [Indexed: 12/31/2022]
Abstract
Bovine tuberculosis is a transboundary disease of high economic and public health burden worldwide. In this study, post-mortem examination of 750 cattle and buffalo in Tanta abattoir, Centre of the Nile Delta, revealed visible TB in 4% of animals and a true prevalence of 6.85% (95% CI: 5.3%-8.9%). Mycobacterial culture, histopathology and RT-PCR targeting all members of M. tuberculosis complex were performed, upon which 85%, 80% and 100% of each tested lesions were confirmed as TB, respectively. Mpb70-targeting PCR was conducted on ten RT-PCR positive samples for sequencing and identified nine Mycobacterium (M.) bovis strains and, interestingly, one M. tuberculosis (Mtb) strain from a buffalo. Bioinformatics tools were used for prediction of mutations, nucleotide polymorphisms, lineages, drug resistance and protein-protein interactions (PPI) of the sequenced strains. The Mtb strain was resistant to rifampicin, isoniazid and streptomycin, and to the best of our knowledge, this is the first report of multidrug resistant (MDR)-Mtb originating from buffaloes. Seven M. bovis strains were resistant to ethambutol and ethionamide. Such resistances were associated with KatG, rpoB, rpsL, embB and ethA genes mutations. Other mutations and nucleotide polymorphisms were also predicted, some are reported for the first time and require experimental work for validation. PPI revealed more interactions than what would be expected for a random set of proteins of similar size and had dense interactions between nodes that are biologically connected, as a group. Two M. bovis strains belonged to BOV AFRI lineage (Spoligotypes BOV 1; BOV 2) and eight strains belonged to East-Asian (Beijing) lineage. In conclusion, visible TB was prevalent in the study area, RT-PCR is the best to confirm the disease, MDR-Mtb is associated with buffalo TB, and mycobacteria of different lineages carry many resistance genes to chemotherapeutic agents used in treatment of human TB constituting a major public health risk.
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Affiliation(s)
- Mohamed Borham
- Bacteriology Department, Animal Health Research Institute Matrouh Lab, Matrouh, Egypt
| | - Atef Oreiby
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Attia El-Gedawy
- Bacteriology Department, Animal Health Research Institute, Cairo, Egypt
| | - Yamen Hegazy
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
| | - Ahmed Hemedan
- Bioinformatics Core, Luxembourg Centre For Systems Biomedicine, Luxembourg University, Luxembourg, Luxembourg
| | - Magdy Al-Gaabary
- Department of Animal Medicine (Infectious Diseases), Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El-Sheikh, Egypt
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Shyam M, Shilkar D, Verma H, Dev A, Sinha BN, Brucoli F, Bhakta S, Jayaprakash V. The Mycobactin Biosynthesis Pathway: A Prospective Therapeutic Target in the Battle against Tuberculosis. J Med Chem 2020; 64:71-100. [PMID: 33372516 DOI: 10.1021/acs.jmedchem.0c01176] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The alarming rise in drug-resistant clinical cases of tuberculosis (TB) has necessitated the rapid development of newer chemotherapeutic agents with novel mechanisms of action. The mycobactin biosynthesis pathway, conserved only among the mycolata family of actinobacteria, a group of intracellularly surviving bacterial pathogens that includes Mycobacterium tuberculosis, generates a salicyl-capped peptide mycobactin under iron-stress conditions in host macrophages to support the iron demands of the pathogen. This in vivo essentiality makes this less explored mycobactin biosynthesis pathway a promising endogenous target for novel lead-compounds discovery. In this Perspective, we have provided an up-to-date account of drug discovery efforts targeting selected enzymes (MbtI, MbtA, MbtM, and PPTase) from the mbt gene cluster (mbtA-mbtN). Furthermore, a succinct discussion on non-specific mycobactin biosynthesis inhibitors and the Trojan horse approach adopted to impair iron metabolism in mycobacteria has also been included in this Perspective.
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Affiliation(s)
- Mousumi Shyam
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Deepak Shilkar
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Harshita Verma
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Abhimanyu Dev
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Barij Nayan Sinha
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
| | - Federico Brucoli
- Leicester School of Pharmacy, De Montfort University, The Gateway, Leicester LE1 9BH, U.K
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, U.K
| | - Venkatesan Jayaprakash
- Department of Pharmaceutical Sciences & Technology, Birla Institute of Technology, Mesra, Ranchi 835215 Jharkhand, India
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Characterization of Genomic Variants Associated with Resistance to Bedaquiline and Delamanid in Naive Mycobacterium tuberculosis Clinical Strains. J Clin Microbiol 2020; 58:JCM.01304-20. [PMID: 32907992 DOI: 10.1128/jcm.01304-20] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 09/02/2020] [Indexed: 02/06/2023] Open
Abstract
The role of mutations in genes associated with phenotypic resistance to bedaquiline (BDQ) and delamanid (DLM) in Mycobacterium tuberculosis complex (MTBc) strains is poorly characterized. A clear understanding of the genetic variants' role is crucial to guide the development of molecular-based drug susceptibility testing (DST). In this work, we analyzed all mutations in candidate genomic regions associated with BDQ- and DLM-resistant phenotypes using a whole-genome sequencing (WGS) data set from a collection of 4,795 MTBc clinical isolates from six countries with a high burden of tuberculosis (TB). From WGS analysis, we identified 61 and 163 unique mutations in genomic regions potentially involved in BDQ- and DLM-resistant phenotypes, respectively. Importantly, all strains were isolated from patients who likely have never been exposed to these medicines. To characterize the role of mutations, we calculated the free energy variation upon mutations in the available protein structures of Ddn (DLM), Fgd1 (DLM), and Rv0678 (BDQ) and performed MIC assays on a subset of MTBc strains carrying mutations to assess their phenotypic effect. The combination of structural and phenotypic data allowed for cataloguing the mutations clearly associated with resistance to BDQ (n = 4) and DLM (n = 35), only two of which were previously described, as well as about a hundred genetic variants without any correlation with resistance. Significantly, these results show that both BDQ and DLM resistance-related mutations are diverse and distributed across the entire region of each gene target, which is of critical importance for the development of comprehensive molecular diagnostic tools.
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Reichmuth ML, Hömke R, Zürcher K, Sander P, Avihingsanon A, Collantes J, Loiseau C, Borrell S, Reinhard M, Wilkinson RJ, Yotebieng M, Fenner L, Böttger EC, Gagneux S, Egger M, Keller PM. Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients. Antimicrob Agents Chemother 2020; 64:e00513-20. [PMID: 32868333 PMCID: PMC7577131 DOI: 10.1128/aac.00513-20] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 08/19/2020] [Indexed: 02/06/2023] Open
Abstract
Mutations in the genes of the F420 signaling pathway of Mycobacterium tuberculosis complex, including dnn, fgd1, fbiA, fbiB, fbiC, and fbiD, can lead to delamanid resistance. We searched for such mutations among 129 M. tuberculosis strains from Asia, South America, and Africa using whole-genome sequencing; 70 (54%) strains had at least one mutation in one of the genes. For 10 strains with mutations, we determined the MIC of delamanid. We found one strain from a delamanid-naive patient carrying the natural polymorphism Tyr29del (ddn) that was associated with a critical delamanid MIC.
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Affiliation(s)
- Martina L Reichmuth
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Rico Hömke
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Kathrin Zürcher
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Peter Sander
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Anchalee Avihingsanon
- The HIV Netherlands Australia Thailand (HIV-NAT) Research Collaboration, Thai Red Cross AIDS Research Centre and Tuberculosis Research Unit, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Jimena Collantes
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Chloé Loiseau
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Miriam Reinhard
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Robert J Wilkinson
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, Republic of South Africa
- Department of Infectious Diseases, Imperial College, London, United Kingdom
- The Francis Crick Institute, London, United Kingdom
| | - Marcel Yotebieng
- National TB Lab, Kinshasa, Democratic Republic of the Congo
- Albert Einstein College of Medicine, New York, New York, USA
| | - Lukas Fenner
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Erik C Böttger
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Matthias Egger
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
- Centre for Infectious Disease Epidemiology and Research, Faculty of Health Sciences, University of Cape Town, Cape Town, Republic of South Africa
| | - Peter M Keller
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Swiss National Center for Mycobacteria, Zurich, Switzerland
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
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Yang J, Pang Y, Zhang T, Xian X, Li Y, Wang R, Wang P, Zhang M, Wang J. Molecular characteristics and in vitro susceptibility to bedaquiline of Mycobacterium tuberculosis isolates circulating in Shaanxi, China. Int J Infect Dis 2020; 99:163-170. [PMID: 32738481 DOI: 10.1016/j.ijid.2020.07.044] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/10/2020] [Accepted: 07/24/2020] [Indexed: 10/23/2022] Open
Abstract
OBJECTIVE The aim of this study was to investigate the molecular characteristics and in vitro susceptibility to bedaquiline of Mycobacterium tuberculosis (MTB) isolates from Shaanxi, China. METHODS The minimum inhibitory concentration (MIC) of bedaquiline was determined using the microplate alamarBlue assay for 518 MTB isolates from Shaanxi. Isolates with MIC values of bedaquiline ≥0.12 μg/mL were sequenced for the atpE, Rv0678, and pepQ genes. Drug susceptibility testing and spoligotyping were also conducted for all strains. RESULTS Ten (1.93%) bedaquiline-resistant strains were isolated from 518 tuberculosis patients. The resistance rate of bedaquiline was not correlated to sex, age, treatment history, region, or genotype. Five bedaquiline-resistant isolates and one bedaquiline-susceptible isolate were found to carry Rv0678 mutations; six mutation types were identified, including G5T, A263G, C185T, G19deletion, C265T, and T323C. No mutations within the atpE and pepQ genes were observed. CONCLUSIONS Bedaquiline showed strong in vitro antibacterial activity against MTB isolates, and the Rv0678 gene serves as the major mechanism contributing to bedaquiline resistance among MTB isolates from Shaanxi, China. Three novel mutation types (G19deletion, C265T, and T323C) of the Rv0678 gene were associated with resistance to bedaquiline. Furthermore, in addition to the current three resistance-associated genes (atpE, Rv0678, and pepQ), other mechanisms of resistance to bedaquiline may exist that need further study.
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Affiliation(s)
- Jian Yang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China; Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China.
| | - Yu Pang
- National Clinical Laboratory on Tuberculosis, BeijingKey Laboratory for Drug Resistant Tuberculosis Research, BeijingChest Hospital, Capital Medical University, BeijingTuberculosis and Thoracic Tumor Institute, Beijing, 102206, China
| | - Tianhua Zhang
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Xiaoping Xian
- Administration Office, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Yan Li
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Rui Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Panting Wang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Meng Zhang
- Clinical Laboratory, Shaanxi Provincial Institute for Tuberculosis Control and Prevention, Xi'an, Shaanxi 710048, China
| | - Junyang Wang
- Department of Pathogenic Biology and Immunology, School of Basic Medical Sciences, Xi'an Jiaotong University Health Science Center, Xi'an, Shaanxi 710061, China.
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38
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Nimmo C, Millard J, van Dorp L, Brien K, Moodley S, Wolf A, Grant AD, Padayatchi N, Pym AS, Balloux F, O'Donnell M. Population-level emergence of bedaquiline and clofazimine resistance-associated variants among patients with drug-resistant tuberculosis in southern Africa: a phenotypic and phylogenetic analysis. THE LANCET. MICROBE 2020; 1:e165-e174. [PMID: 32803174 PMCID: PMC7416634 DOI: 10.1016/s2666-5247(20)30031-8] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
BACKGROUND Bedaquiline and clofazimine are important drugs in the treatment of drug-resistant tuberculosis and are commonly used across southern Africa, although drug susceptibility testing is not routinely performed. In this study, we did a genotypic and phenotypic analysis of drug-resistant Mycobacterium tuberculosis isolates from cohort studies in hospitals in KwaZulu-Natal, South Africa, to identify resistance-associated variants (RAVs) and assess the extent of clofazimine and bedaquiline cross-resistance. We also used a comprehensive dataset of whole-genome sequences to investigate the phylogenetic and geographical distribution of bedaquiline and clofazimine RAVs in southern Africa. METHODS In this study, we included M tuberculosis isolates reported from the PRAXIS study of patients with drug-resistant tuberculosis treated with bedaquiline (King Dinuzulu Hospital, Durban) and three other cohort studies of drug-resistant tuberculosis in other KwaZulu-Natal hospitals, and sequential isolates from six persistently culture-positive patients with extensively drug-resistant tuberculosis at the KwaZulu-Natal provincial referral laboratory. Samples were collected between 2013 and 2019. Microbiological cultures were done as part of all parent studies. We sequenced whole genomes of included isolates and measured bedaquiline and clofazimine minimum inhibitory concentrations (MICs) for isolates identified as carrying any Rv0678 variant or previously published atpE, pepQ, and Rv1979c RAVs, which were the subject of the phenotypic study. We combined all whole-genome sequences of M tuberculosis obtained in this study with publicly available sequence data from other tuberculosis studies in southern Africa (defined as the countries of the Southern African Development Community), including isolates with Rv0678 variants identified by screening public genomic databases. We used this extended dataset to reconstruct phylogenetic relationships across lineage 2 and 4 M tuberculosis isolates. FINDINGS We sequenced the whole genome of 648 isolates from 385 patients with drug-resistant tuberculosis recruited into cohort studies in KwaZulu-Natal, and 28 isolates from six patients from the KwaZulu-Natal referral laboratory. We identified 30 isolates with Rv0678 RAVs from 16 (4%) of 391 patients. We did not identify any atpE, pepQ, or Rv1979c RAVs. MICs were measured for 21 isolates with Rv0678 RAVs. MICs were above the critical concentration for bedaquiline resistance in nine (43%) of 21 isolates, in the intermediate category in nine (43%) isolates, and within the wild-type range in three (14%) isolates. Clofazimine MICs in genetically wild-type isolates ranged from 0·12-0·5 μg/mL, and in isolates with RAVs from 0·25-4·0 μg/mL. Phylogenetic analysis of the extended dataset including M tuberculosis isolates from southern Africa resolved multiple emergences of Rv0678 variants in lineages 2 and 4, documented two likely nosocomial transmission events, and identified the spread of a possibly bedaquiline and clofazimine cross-resistant clone in eSwatini. We also identified four patients with pepQ frameshift mutations that may confer resistance. INTERPRETATION Bedaquiline and clofazimine cross-resistance in southern Africa is emerging repeatedly, with evidence of onward transmission largely due to Rv0678 mutations in M tuberculosis. Roll-out of bedaquiline and clofazimine treatment in the setting of limited drug susceptibility testing could allow further spread of resistance. Designing strong regimens would help reduce the emergence of resistance. Drug susceptibility testing is required to identify where resistance does emerge. FUNDING Wellcome Trust, National Institute of Allergy and Infectious Diseases and National Center for Advancing Translational Sciences of the National Institutes of Health.
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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
| | - 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
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Kayleen Brien
- Africa Health Research Institute, Durban, South Africa
| | | | - Allison Wolf
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Alison D Grant
- Africa Health Research Institute, Durban, South Africa
- TB Centre, London School of Hygiene & Tropical Medicine, London, UK
- School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nesri Padayatchi
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
| | | | | | - Max O'Donnell
- Department of Medicine, Columbia University Medical Center, New York, NY, USA
- Department of Epidemiology, Columbia University Medical Center, New York, NY, USA
- CAPRISA-MRC HIV-TB Pathogenesis and Treatment Research Unit, Centre for the Aids Programme of Research in South Africa (CAPRISA), Durban, KwaZulu-Natal, South Africa
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Lopez B, Siqueira de Oliveira R, Pinhata JMW, Chimara E, Pacheco Ascencio E, Puyén Guerra ZM, Wainmayer I, Simboli N, Del Granado M, Palomino JC, Ritacco V, Martin A. Bedaquiline and linezolid MIC distributions and epidemiological cut-off values for Mycobacterium tuberculosis in the Latin American region. J Antimicrob Chemother 2020; 74:373-379. [PMID: 30358851 DOI: 10.1093/jac/dky414] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 09/12/2018] [Indexed: 11/12/2022] Open
Abstract
Objectives To describe the distributions of bedaquiline and linezolid MIC values for the Mycobacterium tuberculosis WT population and to define the corresponding epidemiological cut-offs (ECOFFs) in three Latin American countries. Methods MICs of bedaquiline and linezolid were determined by the resazurin microtitre assay (REMA). In phase 1, interlaboratory reproducibility was assessed using a panel of 10 fully susceptible M. tuberculosis strains. Phase 2 involved MIC determination for 248 clinical isolates from Argentina (n = 58), Brazil (n = 100) and Peru (n = 90) from patients who were treatment-naive for bedaquiline and linezolid. We then determined the ECOFFs for bedaquiline and linezolid by the eyeball method and the ECOFFinder statistical calculator. Results Phase 1: REMA MIC values in the three sites were either identical to each other or differed by one 2-fold dilution from the consensus value with the exception of a single value. Phase 2: the bedaquiline MIC range was 0.0039-0.25 mg/L for pan-susceptible and drug-resistant isolates combined. The linezolid MIC range was 0.062-0.5 mg/L for pan-susceptible isolates and 0.031-4 mg/L for drug-resistant isolates. ECOFFs were 0.125 mg/L for bedaquiline and 0.50 mg/L for linezolid. Conclusions REMA is reproducible and robust for the determination of bedaquiline and linezolid MIC distributions and ECOFF values when applied in laboratories of medium/low-resource countries. We suggest that WT MIC distributions for both drugs should be used as a monitoring tool to control the possible rapid emergence of resistance.
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Affiliation(s)
- Beatriz Lopez
- Instituto Nacional de Enfermedades Infecciosas, ANLIS "Dr. Carlos G Malbrán", Departamento de Bacteriología, Buenos Aires, Argentina
| | | | - Juliana M W Pinhata
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz São Paulo, São Paulo, Brazil
| | - Erica Chimara
- Núcleo de Tuberculose e Micobacterioses, Centro de Bacteriologia, Instituto Adolfo Lutz São Paulo, São Paulo, Brazil
| | - Edson Pacheco Ascencio
- Instituto Nacional de Salud, Laboratorio de Referencia Nacional de Micobacterias, Lima, Peru
| | - Zully M Puyén Guerra
- Instituto Nacional de Salud, Laboratorio de Referencia Nacional de Micobacterias, Lima, Peru
| | - Ingrid Wainmayer
- Instituto Nacional de Enfermedades Infecciosas ANLIS "Dr. Carlos G Malbrán", Servicio de Micobacterias, Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires, Argentina
| | - Norberto Simboli
- Instituto Nacional de Enfermedades Infecciosas ANLIS "Dr. Carlos G Malbrán", Servicio de Micobacterias, Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires, Argentina
| | | | - Juan Carlos Palomino
- Ghent University, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent, Belgium
| | - Viviana Ritacco
- Instituto Nacional de Enfermedades Infecciosas ANLIS "Dr. Carlos G Malbrán", Servicio de Micobacterias, Consejo Nacional de Investigaciones Científicas y Técnicas CONICET, Buenos Aires, Argentina
| | - Anandi Martin
- Université catholique de Louvain, Institute of Experimental and Clinical Research, Laboratory of Medical Microbiology, Brussels, Belgium
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40
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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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41
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Conradie F, Diacon AH, Ngubane N, Howell P, Everitt D, Crook AM, Mendel CM, Egizi E, Moreira J, Timm J, McHugh TD, Wills GH, Bateson A, Hunt R, Van Niekerk C, Li M, Olugbosi M, Spigelman M. Treatment of Highly Drug-Resistant Pulmonary Tuberculosis. N Engl J Med 2020; 382:893-902. [PMID: 32130813 PMCID: PMC6955640 DOI: 10.1056/nejmoa1901814] [Citation(s) in RCA: 470] [Impact Index Per Article: 117.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
BACKGROUND Patients with highly drug-resistant forms of tuberculosis have limited treatment options and historically have had poor outcomes. METHODS In an open-label, single-group study in which follow-up is ongoing at three South African sites, we investigated treatment with three oral drugs - bedaquiline, pretomanid, and linezolid - that have bactericidal activity against tuberculosis and to which there is little preexisting resistance. We evaluated the safety and efficacy of the drug combination for 26 weeks in patients with extensively drug-resistant tuberculosis and patients with multidrug-resistant tuberculosis that was not responsive to treatment or for which a second-line regimen had been discontinued because of side effects. The primary end point was the incidence of an unfavorable outcome, defined as treatment failure (bacteriologic or clinical) or relapse during follow-up, which continued until 6 months after the end of treatment. Patients were classified as having a favorable outcome at 6 months if they had resolution of clinical disease, a negative culture status, and had not already been classified as having had an unfavorable outcome. Other efficacy end points and safety were also evaluated. RESULTS A total of 109 patients were enrolled in the study and were included in the evaluation of efficacy and safety end points. At 6 months after the end of treatment in the intention-to-treat analysis, 11 patients (10%) had an unfavorable outcome and 98 patients (90%; 95% confidence interval, 83 to 95) had a favorable outcome. The 11 unfavorable outcomes were 7 deaths (6 during treatment and 1 from an unknown cause during follow-up), 1 withdrawal of consent during treatment, 2 relapses during follow-up, and 1 loss to follow-up. The expected linezolid toxic effects of peripheral neuropathy (occurring in 81% of patients) and myelosuppression (48%), although common, were manageable, often leading to dose reductions or interruptions in treatment with linezolid. CONCLUSIONS The combination of bedaquiline, pretomanid, and linezolid led to a favorable outcome at 6 months after the end of therapy in a high percentage of patients with highly drug-resistant forms of tuberculosis; some associated toxic effects were observed. (Funded by the TB Alliance and others; ClinicalTrials.gov number, NCT02333799.).
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Affiliation(s)
- Francesca Conradie
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Andreas H Diacon
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Nosipho Ngubane
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Pauline Howell
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Daniel Everitt
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Angela M Crook
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Carl M Mendel
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Erica Egizi
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Joanna Moreira
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Juliano Timm
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Timothy D McHugh
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Genevieve H Wills
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Anna Bateson
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Robert Hunt
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Christo Van Niekerk
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Mengchun Li
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Morounfolu Olugbosi
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
| | - Melvin Spigelman
- From the Clinical HIV Research Unit, Faculty of Health Sciences, University of Witwatersrand, Johannesburg (F.C., N.N., P.H.), Sizwe Tropical Disease Hospital, Sandringham (F.C., P.H.), Task Applied Science and Stellenbosch University, Cape Town (A.H.D.), King DiniZulu Hospital Complex, Durban (N.N.), and the TB Alliance, Pretoria (C.V.N., M.O.) - all in South Africa; the TB Alliance, New York (D.E., C.M.M., E.E., J.M., J.T., M.L., M.S.); and the MRC Clinical Trials Unit at UCL (A.M.C., G.H.W.) and the UCL Centre for Clinical Microbiology (T.D.M., A.B., R.H.), University College London, London
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42
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Kardan-Yamchi J, Kazemian H, Battaglia S, Abtahi H, Rahimi Foroushani A, Hamzelou G, Cirillo DM, Ghodousi A, Feizabadi MM. Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran. J Clin Med 2020; 9:jcm9020465. [PMID: 32046149 PMCID: PMC7073636 DOI: 10.3390/jcm9020465] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 12/15/2019] [Accepted: 12/18/2019] [Indexed: 01/30/2023] Open
Abstract
Accurate and timely detection of drug resistance can minimize the risk of further resistance development and lead to effective treatment. The aim of this study was to determine the resistance to first/second-line anti-tuberculosis drugs in rifampicin/multidrug-resistant Mycobacterium tuberculosis (RR/MDR-MTB) isolates. Molecular epidemiology of strains was determined using whole genome sequencing (WGS)-based genotyping. A total of 35 RR/MDR-MTB isolates were subjected to drug susceptibility testing against first/second-line drugs using 7H9 Middlebrook in broth microdilution method. Illumina technology was used for paired-end WGS applying a Maxwell 16 Cell DNA Purification kit and the NextSeq platform. Data analysis and single nucleotide polymorphism calling were performed using MTBseq pipeline. The genome-based resistance to each drug among the resistant phenotypes was as follows: rifampicin (97.1%), isoniazid (96.6%), ethambutol (100%), levofloxacin (83.3%), moxifloxacin (83.3%), amikacin (100%), kanamycin (100%), capreomycin (100%), prothionamide (100%), D-cycloserine (11.1%), clofazimine (20%), bedaquiline (0.0%), and delamanid (44.4%). There was no linezolid-resistant phenotype, and a bedaquiline-resistant strain was wild type for related genes. The Beijing, Euro-American, and Delhi-CAS were the most populated lineage/sublineages. Drug resistance-associated mutations were mostly linked to minimum inhibitory concentration results. However, the role of well-known drug-resistant genes for D-cycloserine, clofazimine, bedaquiline, and delamanid was found to be more controversial.
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Affiliation(s)
- Jalil Kardan-Yamchi
- Division of Microbiology, Department of Pathobiology, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Hossein Kazemian
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Simone Battaglia
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Hamidreza Abtahi
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Abbas Rahimi Foroushani
- Department of Epidemiology and Biostatistics, School of Public Health, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Gholamreza Hamzelou
- Tehran Regional Reference Laboratory for Tuberculosis, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
| | - Arash Ghodousi
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, 20132 Milan, Italy; (S.B.)
- Correspondence: (A.G.); (M.M.F.)
| | - Mohammad Mehdi Feizabadi
- Department of Microbiology, School of Medicine, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Thoracic Research Center, Imam Khomeini Hospital Complex, Tehran University of Medical Sciences, Tehran 1417653911, Iran;
- Correspondence: (A.G.); (M.M.F.)
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