1
|
Xia F, Zhang H, Yang H, Zheng M, Min W, Sun C, Yuan K, Yang P. Targeting polyketide synthase 13 for the treatment of tuberculosis. Eur J Med Chem 2023; 259:115702. [PMID: 37544185 DOI: 10.1016/j.ejmech.2023.115702] [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: 06/17/2023] [Revised: 07/15/2023] [Accepted: 07/29/2023] [Indexed: 08/08/2023]
Abstract
Tuberculosis (TB) is one of the most threatening diseases for humans, however, the drug treatment strategy for TB has been stagnant and inadequate, which could not meet current treatment needs. TB is caused by Mycobacterial tuberculosis, which has a unique cell wall that plays a crucial role in its growth, virulence, and drug resistance. Polyketide synthase 13 (Pks13) is an essential enzyme that catalyzes the biosynthesis of the cell wall and its critical role is only found in Mycobacteria. Therefore, Pks13 is a promising target for developing novel anti-TB drugs. In this review, we first introduced the mechanism of targeting Pks13 for TB treatment. Subsequently, we focused on summarizing the recent advance of Pks13 inhibitors, including the challenges encountered during their discovery and the rational design strategies employed to overcome these obstacles, which could be helpful for the development of novel Pks13 inhibitors in the future.
Collapse
Affiliation(s)
- Fei Xia
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Haoling Zhang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Huanaoyu Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Mingming Zheng
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Wenjian Min
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China
| | - Chengliang Sun
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Kai Yuan
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China.
| | - Peng Yang
- State Key Laboratory of Natural Medicines and Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing, 210009, China; Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing, 211198, China; Institute of Innovative Drug Discovery and Development, China Pharmaceutical University, Nanjing, 211198, China.
| |
Collapse
|
2
|
Leowattana W, Leowattana P, Leowattana T. Tuberculosis of the spine. World J Orthop 2023; 14:275-293. [PMID: 37304201 PMCID: PMC10251269 DOI: 10.5312/wjo.v14.i5.275] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/24/2023] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Pott's spine, commonly known as spinal tuberculosis (TB), is an extrapulmonary form of TB caused by Mycobacterium TB. Pott's paraplegia occurs when the spine is involved. Spinal TB is usually caused by the hematogenous spread of infection from a central focus, which can be in the lungs or another location. Spinal TB is distinguished by intervertebral disc involvement caused by the same segmental arterial supply, which can result in severe morbidity even after years of approved therapy. Neurological impairments and spine deformities are caused by progressive damage to the anterior vertebral body. The clinical, radiographic, microbiological, and histological data are used to make the diagnosis of spinal TB. In Pott's spine, combination multidrug antitubercular therapy is the basis of treatment. The recent appearance of multidrug-resistant/extremely drug-resistant TB and the growth of human immunodeficiency virus infection have presented significant challenges in the battle against TB infection. Patients who come with significant kyphosis or neurological impairments are the only ones who require surgical care. Debridement, fusion stabilization, and correction of spinal deformity are the cornerstones of surgical treatment. Clinical results for the treatment of spinal TB are generally quite good with adequate and prompt care.
Collapse
Affiliation(s)
- Wattana Leowattana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Rachatawee 10400, Bangkok, Thailand
| | - Pathomthep Leowattana
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Rachatawee 10400, Bangkok, Thailand
| | - Tawithep Leowattana
- Department of Medicine, Faculty of Medicine, Srinakarinwirot University, Wattana 10110, Bangkok, Thailand
| |
Collapse
|
3
|
Fekadu G, Tolossa T, Turi E, Bekele F, Fetensa G. Pretomanid development and its clinical roles in treating tuberculosis. J Glob Antimicrob Resist 2022; 31:175-184. [PMID: 36087906 DOI: 10.1016/j.jgar.2022.09.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Revised: 08/19/2022] [Accepted: 09/01/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB) is the leading infectious cause of mortality worldwide. Despite the development of different antituberculosis drugs, managing resistant mycobacteria is still challenging. The discovery of novel drugs and new methods of targeted drug delivery have the potential to improve treatment outcomes, lower the duration of treatment, and reduce adverse events. Following bedaquiline and delamanid, pretomanid is the third medicine approved as part of a novel drug regimen for treating drug-resistant TB. It is a promising drug that has the capacity to shape TB treatment and achieve the End TB strategy set by the World Health Organization. The effectiveness of pretomanid has been reported in different observational and clinical studies. However, long-term safety data in humans are not yet available and the pretomanid-based regimen is recommended under an operational research framework that prohibits its wider and programmatic use. Further research is needed before pretomanid can be celebrated as a promising candidate for the treatment of different categories of TB and specific patients. This review covers the update on pretomanid development and its clinical roles in treating Mycobacterium tuberculosis.
Collapse
Affiliation(s)
- Ginenus Fekadu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong; Department of Pharmacy, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia.
| | - Tadesse Tolossa
- Department of Public Health, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Deakin Health Economics, Institute for Health Transformation, Deakin University, Geelong, Victoria
| | - Ebisa Turi
- Department of Public Health, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Deakin Health Economics, Institute for Health Transformation, Deakin University, Geelong, Victoria
| | - Firomsa Bekele
- Department of Pharmacy, College of Health Science, Mattu University, Mattu, Ethiopia
| | - Getahun Fetensa
- Department of Nursing, School of Nursing and Midwifery, Institute of Health Sciences, Wollega University, Nekemte, Ethiopia; Department of Health behaviour and Society, Faculty of Public Health, Jimma Medical Center, Jimma University, Ethiopia
| |
Collapse
|
4
|
Prabhu P, Fernandes T, Damani M, Chaubey P, Narayanan S, Sawarkar S. 2Receptor Specific Ligand conjugated Nanocarriers: an Effective Strategy for Targeted Therapy of Tuberculosis. Curr Drug Deliv 2021; 19:830-845. [PMID: 34915835 DOI: 10.2174/1567201819666211216141942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 08/09/2021] [Accepted: 10/27/2021] [Indexed: 11/22/2022]
Abstract
Tuberculosis (TB) is an ancient chronic disease caused by the bacillus Mycobacterium tuberculosis, which has affected mankind for more than 4,000 years. Compliance with the standard conventional treatment can assure recovery from tuberculosis, but emergence of drug resistant strains pose a great challenge for effective management of tuberculosis. The process of discovery and development of new therapeutic entities with better specificity and efficacy is unpredictable and time consuming. Hence, delivery of pre-existing drugs with improved targetability is the need of the hour. Enhanced delivery and targetability can ascertain improved bioavailability, reduced toxicity, decreased frequency of dosing and therefore better patient compliance. Nanoformulations are being explored for effective delivery of therapeutic agents, however optimum specificity is not guaranteed. In order to achieve specificity, ligands specific to receptors or cellular components of macrophage and Mycobacteria can be conjugatedto nanocarriers. This approach can improve localization of existing drug molecules at the intramacrophageal site where the parasites reside, improve targeting to the unique cell wall structure of Mycobacterium or improve adhesion to epithelial surface of intestine or alveolar tissue (lectins). Present review focuses on the investigation of various ligands like Mannose, Mycolic acid, Lectin, Aptamers etc. installed nanocarriers that are being envisaged for targeting antitubercular drugs.
Collapse
Affiliation(s)
- Pratiksha Prabhu
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, University of Mumbai. Saudi Arabia
| | - Trinette Fernandes
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, University of Mumbai. Saudi Arabia
| | - Mansi Damani
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, University of Mumbai. Saudi Arabia
| | - Pramila Chaubey
- Department of Pharmaceutics, College of Pharmacy, Shaqra University, Al-Dawadmi. Saudi Arabia
| | - Shridhar Narayanan
- Foundation for Neglected Disease Research, 20A, KIADB Industrial Area Veerapura, Doddaballapur, Bengaluru, Karnataka 561203. India
| | - Sujata Sawarkar
- Department of Pharmaceutics, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, University of Mumbai. Saudi Arabia
| |
Collapse
|
5
|
Davies-Bolorunduro OF, Ajayi A, Adeleye IA, Kristanti AN, Aminah NS. Bioprospecting for antituberculosis natural products – A review. OPEN CHEM 2021. [DOI: 10.1515/chem-2021-0095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Abstract
There has been an increase in the reported cases of tuberculosis, a disease caused by Mycobacterium tuberculosis, which is still currently affecting most of the world’s population, especially in resource-limited countries. The search for novel antitubercular chemotherapeutics from underexplored natural sources is therefore of paramount importance. The renewed interest in studies related to natural products, driven partly by the growing incidence of MDR-TB, has increased the prospects of discovering new antitubercular drug leads. This is because most of the currently available chemotherapeutics such as rifampicin and capreomycin used in the treatment of TB were derived from natural products, which are proven to be an abundant source of novel drugs used to treat many diseases. To meet the global need for novel antibiotics from natural sources, various strategies for high-throughput screening have been designed and implemented. This review highlights the current antitubercular drug discovery strategies from natural sources.
Collapse
Affiliation(s)
- Olabisi Flora Davies-Bolorunduro
- Centre for Tuberculosis Research, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
| | - Abraham Ajayi
- Molecular Biology and Biotechnology Department, Nigerian Institute of Medical Research , Yaba , Lagos , Nigeria
- Department of Microbiology, University of Lagos , Akoka , Lagos , Nigeria
| | | | - Alfinda Novi Kristanti
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
| | - Nanik Siti Aminah
- Department of Chemistry, Faculty of Science and Technology, Universitas Airlangga , Surabaya , Indonesia
- Biotechnology of Tropical Medicinal Plants Research Group, Universitas Airlangga , Surabaya , Indonesia
| |
Collapse
|
6
|
Fekadu G, To KKW, You JHS. WITHDRAWN: Pretomanid for the treatment of Mycobacterium tuberculosis: Evidence on the development and clinical roles. J Infect Public Health 2021:S1876-0341(21)00324-5. [PMID: 34742640 DOI: 10.1016/j.jiph.2021.09.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/04/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022] Open
Abstract
This article has been withdrawn at the request of the author(s) and/or editor. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Ginenus Fekadu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
| | - Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
| | - Joyce H S You
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T, Hong Kong.
| |
Collapse
|
7
|
Fekadu G, Chow DYW, You JHS. The pharmacotherapeutic management of pulmonary tuberculosis: an update of the state-of-the-art. Expert Opin Pharmacother 2021; 23:139-148. [PMID: 34402698 DOI: 10.1080/14656566.2021.1967930] [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] [Indexed: 10/20/2022]
Abstract
INTRODUCTION Pulmonary tuberculosis (TB) remains an important global health challenge of the 21st century, and the emerging resistance against anti-TB drugs is still a growing concern. And while there was a significant cumulative reduction in the incidence of TB between 2015 and 2019, 2.8% of all TB cases in 2019 were reported to be drug resistant. AREA COVERED This review provides the reader with an update on pharmacotherapy for patients with TB susceptible or resistant to drug therapy. The authors also include promising investigational drugs herein. Finally, the authors share with the reader their expert opinions on the current state of the art and their future perspectives. EXPERT OPINION The current pharmacotherapeutic management aims to enhance favorable treatment outcomes and reduce treatment-related adverse events. One approach is to use shorter and all-oral regimens for eligible patients. Traditional longer regimens for most patients are also optimized to lower incidence of treatment failure and serious adverse events.
Collapse
Affiliation(s)
- Ginenus Fekadu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Dilys Yan-Wing Chow
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| | - Joyce H S You
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, NT, Hong Kong
| |
Collapse
|
8
|
Maruri F, Guo Y, Blackman A, van der Heijden YF, Rebeiro PF, Sterling TR. Resistance-Conferring Mutations on Whole-Genome Sequencing of Fluoroquinolone-resistant and -Susceptible Mycobacterium tuberculosis Isolates: A Proposed Threshold for Identifying Resistance. Clin Infect Dis 2021; 72:1910-1918. [PMID: 32348473 PMCID: PMC8315129 DOI: 10.1093/cid/ciaa496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Fluoroquinolone resistance in Mycobacterium tuberculosis (Mtb) is conferred by DNA gyrase mutations, but not all fluoroquinolone-resistant Mtb isolates have mutations detected. The optimal allele frequency threshold to identify resistance-conferring mutations by whole-genome sequencing is unknown. METHODS Phenotypically ofloxacin-resistant and lineage-matched ofloxacin-susceptible Mtb isolates underwent whole-genome sequencing at an average coverage depth of 868 reads. Polymorphisms within the quinolone-resistance-determining region (QRDR) of gyrA and gyrB were identified. The allele frequency threshold using the Genome Analysis Toolkit pipeline was ~8%; allele-level data identified the predominant variant allele frequency and mutational burden (ie, sum of all variant allele frequencies in the QRDR) in gyrA, gyrB, and gyrA + gyrB for each isolate. Receiver operating characteristic (ROC) curves assessed the optimal measure of allele frequency and potential thresholds for identifying phenotypically resistant isolates. RESULTS Of 42 ofloxacin-resistant Mtb isolates, area under the ROC curve (AUC) was highest for predominant variant allele frequency, so that measure was used to evaluate optimal mutation detection thresholds. AUCs for 8%, 2.5%, and 0.8% thresholds were 0.8452, 0.9286, and 0.9069, respectively. Sensitivity and specificity were 69% and 100% for 8%, 86% and 100% for 2.5%, 91% and 91% for 0.8%. The sensitivity of the 2.5% and 0.8% thresholds were significantly higher than the 8% threshold (P = .016 and .004, respectively) but not significantly different between one another (P = .5). CONCLUSIONS A predominant mutation allele frequency threshold of 2.5% had the highest AUC for detecting DNA gyrase mutations that confer ofloxacin resistance, and was therefore the optimal threshold.
Collapse
Affiliation(s)
- Fernanda Maruri
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yan Guo
- Department of Internal Medicine, University of New Mexico, Albuquerque, New Mexico, USA
| | - Amondrea Blackman
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Yuri F van der Heijden
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- The Aurum Institute, Johannesburg, South Africa
| | - Peter F Rebeiro
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Timothy R Sterling
- Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
- Vanderbilt Tuberculosis Center, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| |
Collapse
|
9
|
Narain A, Dubey RK, Verma AK, Srivastava A, Kant S. Potential Role of Proteasome Accessory Factor-C in Resistance against Second Line Drugs in Mycobacteria. J Lab Physicians 2021; 12:250-262. [PMID: 33390674 PMCID: PMC7773444 DOI: 10.1055/s-0040-1722552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Objectives Mycobacterium tuberculosis (MTB), the causative agent of tuberculosis (TB), can survive inside the host granuloma courtesy the various extrinsic and intrinsic factors involved. Continuous use or misuse of the anti TB drugs over the years has led to the development of resistance in MTB against antibiotics. Drug-resistant TB in particular has been a menace since treating it requires exposing the patient to drugs for a prolonged period of time. Multidrug-resistant (MDR) and extensively drug resistant TB cases have increased over the years mostly due to the exposure of MTB to suboptimal levels of drug. Proteasomes provide MTB its pathogenicity and hence helps it to survive inside the host even in the presence of drugs. Materials and Methods The recombinantly expressed proteasome accessory factor-C (PafC) protein was purified via Ni-NTA affinity chromatography and overexpressed in the nonpathogenic strain of mycobacteria (Mycobacterium smegmatis) for the comparative analysis of minimum inhibitory concentrations of antimycobacterial drugs. The bacteria were subjected to various stress conditions. Secretory nature of PafC was analyzed by probing the purified protein against patient sera. Quantitative mRNA analysis of paf C, lex A, and rec A was performed to check for their level under fluoroquinolone (FQ) presence. The data were validated in clinical samples of pulmonary TB patients. Results pafC , that forms one part of paf operon, is involved in providing MTB its resistance against FQs. Through a series of experiments, we established the fact that PafC is upregulated in mycobacteria upon exposure to FQs and it leads to the increased intracellular survival of mycobacteria under the stresses generated by FQs. The study also refers to the correlation of pafC to deoxyribonucleic acid (DNA) damage repair enzymes lexA and recA at transcriptional level. The results obtained in vitro corroborated when the pulmonary TB patients' samples were subjected to the same molecular analysis. Statistical Analysis All experiments were conducted at least in triplicate. p -Value of <0.05 was considered to be statistically significant Conclusion PafC plays a significant role in providing resistance to mycobacteria against FQ class of drugs by increasing its intracellular survival through increased drug efflux and getting involved with DNA damage repair machinery.
Collapse
Affiliation(s)
- Apoorva Narain
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Rikesh K Dubey
- Department of Microbiology, Central Drug Research Institute (CSIR), Lucknow, Uttar Pradesh, India
| | - Ajay Kumar Verma
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Anand Srivastava
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| | - Surya Kant
- Department of Respiratory Medicine, King George's Medical University, Lucknow, Uttar Pradesh, India
| |
Collapse
|
10
|
Khawbung JL, Nath D, Chakraborty S. Drug resistant Tuberculosis: A review. Comp Immunol Microbiol Infect Dis 2020; 74:101574. [PMID: 33249329 DOI: 10.1016/j.cimid.2020.101574] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Accepted: 11/05/2020] [Indexed: 12/14/2022]
Abstract
Tuberculosis (TB) was announced as a global emergency in 1993. There was an alarming counter attack of TB worldwide. However, when it was known that TB can be cured completely, the general public became ignorant towards the infection. The pathogenic organism Mycobacterium tuberculosis continuously evolved to resist the antagonist drugs. This has led to the outbreak of resistant strain that gave rise to "Multi Drug Resistant-Tuberculosis" and "Extensively Drug Resistant Tuberculosis" that can still be cured with a lower success rate. While the mechanism of resistance proceeds further, it ultimately causes unmanageable totally drug resistant TB (TDR-TB). Studying the molecular mechanisms underlying the resistance to drugs would help us grasp the genetics and pathophysiology of the disease. In this review, we present the molecular mechanisms behind Mycobacterium tolerance to drugs and their approach towards the development of multi-drug resistant, extremely drug resistant and totally drug resistant TB.
Collapse
Affiliation(s)
| | - Durbba Nath
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India
| | - Supriyo Chakraborty
- Department of Biotechnology, Assam University, Silchar, 788011, Assam, India.
| |
Collapse
|
11
|
Cui ZJ, Zhang WT, Zhu Q, Zhang QY, Zhang HY. Using a Heat Diffusion Model to Detect Potential Drug Resistance Genes of Mycobacterium tuberculosis. Protein Pept Lett 2020; 27:711-717. [PMID: 32167422 DOI: 10.2174/0929866527666200313113157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 12/01/2019] [Accepted: 12/21/2019] [Indexed: 01/01/2023]
Abstract
BACKGROUND Tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), is one of the oldest known and most dangerous diseases. Although the spread of TB was controlled in the early 20th century using antibiotics and vaccines, TB has again become a threat because of increased drug resistance. There is still a lack of effective treatment regimens for a person who is already infected with multidrug-resistant Mtb (MDR-Mtb) or extensively drug-resistant Mtb (XDRMtb). In the past decades, many research groups have explored the drug resistance profiles of Mtb based on sequence data by GWAS, which identified some mutations that were significantly linked with drug resistance, and attempted to explain the resistance mechanisms. However, they mainly focused on several significant mutations in drug targets (e.g. rpoB, katG). Some genes which are potentially associated with drug resistance may be overlooked by the GWAS analysis. OBJECTIVE In this article, our motivation is to detect potential drug resistance genes of Mtb using a heat diffusion model. METHODS All sequencing data, which contained 127 samples of Mtb, i.e. 34 ethambutol-, 65 isoniazid-, 53 rifampicin- and 45 streptomycin-resistant strains. The raw sequence data were preprocessed using Trimmomatic software and aligned to the Mtb H37Rv reference genome using Bowtie2. From the resulting alignments, SAMtools and VarScan were used to filter sequences and call SNPs. The GWAS was performed by the PLINK package to obtain the significant SNPs, which were mapped to genes. The P-values of genes calculated by GWAS were transferred into a heat vector. The heat vector and the Mtb protein-protein interactions (PPI) derived from the STRING database were inputted into the heat diffusion model to obtain significant subnetworks by HotNet2. Finally, the most significant (P < 0.05) subnetworks associated with different phenotypes were obtained. To verify the change of binding energy between the drug and target before and after mutation, the method of molecular dynamics simulation was performed using the AMBER software. RESULTS We identified significant subnetworks in rifampicin-resistant samples. Excitingly, we found rpoB and rpoC, which are drug targets of rifampicin. From the protein structure of rpoB, the mutation location was extremely close to the drug binding site, with a distance of only 3.97 Å. Molecular dynamics simulation revealed that the binding energy of rpoB and rifampicin decreased after D435V mutation. To a large extent, this mutation can influence the affinity of drug-target binding. In addition, topA and pyrG were reported to be linked with drug resistance, and might be new TB drug targets. Other genes that have not yet been reported are worth further study. CONCLUSION Using a heat diffusion model in combination with GWAS results and protein-protein interactions, the significantly mutated subnetworks in rifampicin-resistant samples were found. The subnetwork not only contained the known targets of rifampicin (rpoB, rpoC), but also included topA and pyrG, which are potentially associated with drug resistance. Together, these results offer deeper insights into drug resistance of Mtb, and provides potential drug targets for finding new antituberculosis drugs.
Collapse
Affiliation(s)
- Ze-Jia Cui
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wei-Tong Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qiang Zhu
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qing-Ye Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong-Yu Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
12
|
Genetically Encoded Photosensitizers as Light-Triggered Antimicrobial Agents. Int J Mol Sci 2019; 20:ijms20184608. [PMID: 31533368 PMCID: PMC6769541 DOI: 10.3390/ijms20184608] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 09/12/2019] [Accepted: 09/13/2019] [Indexed: 02/08/2023] Open
Abstract
Diseases caused by multi-drug resistant pathogens have become a global concern. Therefore, new approaches suitable for treating these bacteria are urgently needed. In this study, we analyzed genetically encoded photosensitizers (PS) related to the green fluorescent protein (GFP) or light-oxygen-voltage (LOV) photoreceptors for their exogenous applicability as light-triggered antimicrobial agents. Depending on their specific photophysical properties and photochemistry, these PSs can produce different toxic ROS (reactive oxygen species) such as O2•− and H2O2 via type-I, as well as 1O2 via type-II reaction in response to light. By using cell viability assays and microfluidics, we could demonstrate differences in the intracellular and extracellular phototoxicity of the applied PS. While intracellular expression and exogenous supply of GFP-related PSs resulted in a slow inactivation of E. coli and pathogenic Gram-negative and Gram-positive bacteria, illumination of LOV-based PSs such as the singlet oxygen photosensitizing protein SOPP3 resulted in a fast and homogeneous killing of these microbes. Furthermore, our data indicate that the ROS type and yield as well as the localization of the applied PS protein can strongly influence the antibacterial spectrum and efficacy. These findings open up new opportunities for photodynamic inactivation of pathogenic bacteria.
Collapse
|
13
|
Kim S, Kim Y, Chang Y, Hirgo WK, Chang CL, Shim TS, Uh Y, Lee H. Comparison of Quantamatrix Multiplexed Assay Platform and GenoType MTBDR Assay Using Smear-Positive Sputum Specimens From Patients With Multidrug- Resistant/Extensively Drug-Resistant Tuberculosis in South Korea. Front Microbiol 2019; 10:1075. [PMID: 31139175 PMCID: PMC6527879 DOI: 10.3389/fmicb.2019.01075] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Accepted: 04/29/2019] [Indexed: 11/17/2022] Open
Abstract
Rapid detection of drug-resistant tuberculosis (DR-TB) is crucial for timely treatment and management. The GenoType MTBDRplus and MTBDRsl (MTBDR) assays have been endorsed by the World Health Organization (WHO) for the detection of DR-TB. However, MTBDR assays cannot simultaneously detect multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Furthermore, interpretation of the MTBDR assay requires trained people, and the assay has low sample throughput, processing only up to 12 samples in parallel. We have developed the Quantamatrix Multiplexed Assay Platform (QMAP) to detect MDR-/XDR-TB simultaneously. The interpretation of QMAP results is automated, and the platform can process up to 96 samples in parallel. To compare the performance of QMAP with MTBDR assays, we performed QMAP and the MTBDR assay on 76 smear-positive, Mycobacterium tuberculosis culture-positive sputum specimens. Compared with phenotypic drug susceptibility testing (DST) results, the sensitivity and specificity of QMAP were 100 and 98% for rifampin resistance, 80 and 100% for isoniazid resistance, 44.4 and 100% for ethambutol resistance, 100 and 100% for fluoroquinolone resistance, and 100 and 100% for second-line injectable drug resistance, respectively. The sensitivity and specificity of MTBDR assays were 100 and 98% for rifampin resistance, 80 and 100% for isoniazid resistance, 44.4 and 98.1% for ethambutol resistance, 100 and 100% for fluoroquinolone resistance, and 100 and 100% for second-line injectable drug resistance, respectively. The sensitivity and specificity of QMAP were 85.0 and 100%, respectively, for the detection of MDR-TB and 100 and 100%, respectively, for XDR-TB. The sensitivity and specificity of MTBDR assays was consistent with those of QMAP. Our study showed that the QMAP assay has sensitivity and specificity equivalent to that of MTBDR assays in smear-positive sputum specimens. In combination with phenotypic DST, QMAP might be useful as a supplementary DST assay for rapid detection of MDR-/XDR-TB.
Collapse
Affiliation(s)
- Seoyong Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, South Korea
| | - Yeun Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, South Korea
| | - Yunhee Chang
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, South Korea
| | - Workneh Korma Hirgo
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, South Korea
| | - Chulhun L Chang
- Department of Laboratory Medicine, Pusan National University Yangsan Hospital, Yangsan, South Korea
| | - Tae-Sun Shim
- Division of Pulmonary and Critical Care Medicine, Department of Internal Medicine, Asan Medical Center, University of Ulsan College of Medicine, Seoul, South Korea
| | - Young Uh
- Department of Laboratory Medicine, Yonsei University Wonju College of Medicine, Wonju, South Korea
| | - Hyeyoung Lee
- Department of Biomedical Laboratory Science, College of Health Sciences, Yonsei University, Wonju, South Korea
| |
Collapse
|
14
|
Dixit A, Freschi L, Vargas R, Calderon R, Sacchettini J, Drobniewski F, Galea JT, Contreras C, Yataco R, Zhang Z, Lecca L, Kolokotronis SO, Mathema B, Farhat MR. Whole genome sequencing identifies bacterial factors affecting transmission of multidrug-resistant tuberculosis in a high-prevalence setting. Sci Rep 2019; 9:5602. [PMID: 30944370 PMCID: PMC6447560 DOI: 10.1038/s41598-019-41967-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 03/20/2019] [Indexed: 11/09/2022] Open
Abstract
Whole genome sequencing (WGS) can elucidate Mycobacterium tuberculosis (Mtb) transmission patterns but more data is needed to guide its use in high-burden settings. In a household-based TB transmissibility study in Peru, we identified a large MIRU-VNTR Mtb cluster (148 isolates) with a range of resistance phenotypes, and studied host and bacterial factors contributing to its spread. WGS was performed on 61 of the 148 isolates. We compared transmission link inference using epidemiological or genomic data and estimated the dates of emergence of the cluster and antimicrobial drug resistance (DR) acquisition events by generating a time-calibrated phylogeny. Using a set of 12,032 public Mtb genomes, we determined bacterial factors characterizing this cluster and under positive selection in other Mtb lineages. Four of the 61 isolates were distantly related and the remaining 57 isolates diverged ca. 1968 (95%HPD: 1945-1985). Isoniazid resistance arose once and rifampin resistance emerged subsequently at least three times. Emergence of other DR types occurred as recently as within the last year of sampling. We identified five cluster-defining SNPs potentially contributing to transmissibility. In conclusion, clusters (as defined by MIRU-VNTR typing) may be circulating for decades in a high-burden setting. WGS allows for an enhanced understanding of transmission, drug resistance, and bacterial fitness factors.
Collapse
Affiliation(s)
- Avika Dixit
- Boston Children's Hospital, Boston, MA, USA.
- Harvard Medical School, Boston, MA, USA.
| | | | | | | | | | | | | | | | | | - Zibiao Zhang
- Harvard Medical School, Boston, MA, USA
- Brigham and Women's Hospital, Boston, MA, USA
| | - Leonid Lecca
- Harvard Medical School, Boston, MA, USA
- Socios En Salud, Lima, Peru
| | | | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Maha R Farhat
- Harvard Medical School, Boston, MA, USA
- Massachussetts General Hospital, Boston, MA, USA
| |
Collapse
|
15
|
Miotto P, Zhang Y, Cirillo DM, Yam WC. Drug resistance mechanisms and drug susceptibility testing for tuberculosis. Respirology 2018; 23:1098-1113. [PMID: 30189463 DOI: 10.1111/resp.13393] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 08/03/2018] [Accepted: 08/12/2018] [Indexed: 12/12/2022]
Abstract
Tuberculosis (TB) caused by Mycobacterium tuberculosis (MTB) is the deadliest infectious disease and the associated global threat has worsened with the emergence of drug resistance, in particular multidrug-resistant TB (MDR-TB) and extensively drug-resistant TB (XDR-TB). Although the World Health Organization (WHO) End-TB Strategy advocates for universal access to antimicrobial susceptibility testing, this is not widely available and/or it is still underused. The majority of drug resistance in clinical MTB strains is attributed to chromosomal mutations. Resistance-related mutations could also exert certain fitness cost to the drug-resistant MTB strains and growth fitness could be restored by the presence of compensatory mutations. Understanding these underlying mechanisms could provide an important insight into TB pathogenesis and predict the future trend of MDR-TB global pandemic. This review covers the mechanisms of resistance in MTB and provides a comprehensive overview of current phenotypic and molecular approaches for drug susceptibility testing, with particular attention to the methods endorsed and recommended by the WHO.
Collapse
Affiliation(s)
- Paolo Miotto
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Ying Zhang
- Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Daniela Maria Cirillo
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS Ospedale San Raffaele, Milano, Italy
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital Compound, The University of Hong Kong, Hong Kong, China
| |
Collapse
|
16
|
Hage-Hülsmann J, Grünberger A, Thies S, Santiago-Schübel B, Klein AS, Pietruszka J, Binder D, Hilgers F, Domröse A, Drepper T, Kohlheyer D, Jaeger KE, Loeschcke A. Natural biocide cocktails: Combinatorial antibiotic effects of prodigiosin and biosurfactants. PLoS One 2018; 13:e0200940. [PMID: 30024935 PMCID: PMC6053208 DOI: 10.1371/journal.pone.0200940] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2018] [Accepted: 07/05/2018] [Indexed: 11/18/2022] Open
Abstract
Bacterial secondary metabolites are naturally produced to prevail amongst competitors in a shared habitat and thus represent a valuable source for antibiotic discovery. The transformation of newly discovered antibiotic compounds into effective drugs often requires additional surfactant components for drug formulation. Nature may also provide blueprints in this respect: A cocktail of two compounds consisting of the antibacterial red pigment prodigiosin and the biosurfactant serrawettin W1 is naturally produced by the bacterium Serratia marcescens, which occurs in highly competitive habitats including soil. We show here a combinatorial antibacterial effect of these compounds, but also of prodigiosin mixed with other (bio)surfactants, against the soil-dwelling bacterium Corynebacterium glutamicum taken as a model target bacterium. Prodigiosin exerted a combinatorial inhibitory effect with all tested surfactants in a disk diffusion assay which was especially pronounced in combination with N-myristoyltyrosine. Minimal inhibitory and bactericidal concentrations (MIC and MBC) of the individual compounds were 2.56 μg/mL prodigiosin and 32 μg/mL N-myristoyltyrosine, and the MIC of prodigiosin was decreased by 3 orders of magnitude to 0.005 μg/mL in the presence of 16 μg/mL N-myristoyltyrosine, indicative of synergistic interaction. Investigation of bacterial survival revealed similar combinatorial effects; moreover, antagonistic effects were observed at higher compound concentrations. Finally, the investigation of microcolony formation under combined application of concentrations just below the MBC revealed heterogeneity of responses with cell death or delayed growth. In summary, this study describes the combinatorial antibacterial effects of microbial biomolecules, which may have ecological relevance by inhibiting cohabiting species, but shall furthermore inspire drug development in the combat of infectious disease.
Collapse
Affiliation(s)
- Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Alexander Grünberger
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Multiscale Bioengineering, Bielefeld University, Bielefeld, Germany
| | - Stephan Thies
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
| | - Beatrix Santiago-Schübel
- Central Division of Analytical Chemistry ZEA-3: Analytik/Biospec, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Andreas Sebastian Klein
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Jörg Pietruszka
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Institute of Bioorganic Chemistry, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Dennis Binder
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Andreas Domröse
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
| | - Dietrich Kohlheyer
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
- Aachener Verfahrenstechnik (AVT.MSB), RWTH Aachen University, Aachen, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- IBG-1: Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Forschungszentrum Jülich, Jülich, Germany
- Bioeconomy Science Center (BioSC), Forschungszentrum Jülich, Jülich, Germany
- * E-mail:
| |
Collapse
|
17
|
Guitor AK, Wright GD. Antimicrobial Resistance and Respiratory Infections. Chest 2018; 154:1202-1212. [PMID: 29959904 DOI: 10.1016/j.chest.2018.06.019] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/06/2018] [Accepted: 06/18/2018] [Indexed: 11/17/2022] Open
Abstract
Since their introduction into health care and clinical practice in the early 20th century, antibiotics have revolutionized medicine. Alarmingly, these drugs are increasingly threatened by bacteria that have developed a broad diversity of resistance mechanisms. Antibiotic resistance can be transferred between bacteria, often on mobile genetic elements; be acquired from the environment; or arise through mutation because of selective pressures of the drugs themselves. There are various strategies to resistance, including active efflux of the drug from the bacterial cell, reduced permeability of the cell envelope, alteration of the drug's target within the bacterial cell, and modification or destruction of the antibiotic. Streptococcus pneumoniae, Haemophilus influenzae, Pseudomonas aeruginosa, and Mycobacterium tuberculosis frequently are implicated in respiratory infections, often manifesting with reduced susceptibility to multiple classes of antibiotics. Some mechanisms of resistance, such as the β-lactamases that confer resistance to penicillins and related drugs, have been well characterized and are widespread in clinical isolates. Other newly identified determinants, including the colistin resistance gene mcr-1, are spreading rapidly worldwide and threaten last-resort treatments of multidrug-resistant organisms. Various approaches to detecting antibiotic resistance provide surveys of the determinants that are available for transfer into pathogenic bacteria. Together with molecular characterization of newly identified mechanisms, this surveillance can target drug discovery efforts and increase antibiotic stewardship. A greater understanding of the mechanisms of antibiotic resistance in respiratory pathogens combined with rapid diagnostics ultimately will reduce treatment failure due to inappropriate antibiotic use and prevent further spread of resistance.
Collapse
Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
| |
Collapse
|
18
|
Farhat MR, Jacobson KR, Franke MF, Kaur D, Murray M, Mitnick CD. Fluoroquinolone Resistance Mutation Detection Is Equivalent to Culture-Based Drug Sensitivity Testing for Predicting Multidrug-Resistant Tuberculosis Treatment Outcome: A Retrospective Cohort Study. Clin Infect Dis 2018; 65:1364-1370. [PMID: 29017248 DOI: 10.1093/cid/cix556] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 07/10/2017] [Indexed: 11/12/2022] Open
Abstract
Background Molecular diagnostics that rapidly and accurately predict fluoroquinolone (FQ) resistance promise to improve treatment outcomes for individuals with multidrug-resistant (MDR) tuberculosis (TB). Mutations in the gyr genes, though, can cause variable levels of in vitro FQ resistance, and some in vitro resistance remains unexplained by gyr mutations alone, but the implications of these discrepancies for treatment outcome are unknown. Methods We performed a retrospective cohort study of 172 subjects with MDR/extensively drug-resistant TB subjects and sequenced the full gyrA and gyrB open reading frames in their respective sputum TB isolates. The gyr mutations were classified into 2 categories: a set of mutations that encode high-level FQ resistance and a second set that encodes intermediate resistance levels. We constructed a Cox proportional model to assess the effect of the gyr mutation type on the time to death or treatment failure and compared this with in vitro FQ resistance, controlling for host and treatment factors. Results Controlling for other host and treatment factors and compared with patients with isolates without gyr resistance mutations, "high-level" gyr mutations significantly predict poor treatment outcomes with a hazard ratio of 2.6 (1.2-5.6). We observed a hazard of death and treatment failure with "intermediate-level" gyr mutations of 1.3 (0.6-3.1), which did not reach statistical significance. The gyr mutations were not different than culture-based FQ drug susceptibility testing in predicting the hazard of death or treatment failure and may be superior. Conclusions FQ molecular-based diagnostic tests may better predict treatment response than traditional drug susceptibility testing and open avenues for personalizing TB therapy.
Collapse
Affiliation(s)
- Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School.,Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine
| | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School
| | - Devinder Kaur
- University of Massachusetts Medical School, Massachusetts Supranational Tuberculosis Reference Laboratory
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School.,Department of Epidemiology, Harvard School of Public Health
| | - Carole D Mitnick
- Department of Global Health and Social Medicine, Harvard Medical School.,Department of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts
| |
Collapse
|
19
|
Baddam R, Kumar N, Wieler LH, Lankapalli AK, Ahmed N, Peacock SJ, Semmler T. Analysis of mutations in pncA reveals non-overlapping patterns among various lineages of Mycobacterium tuberculosis. Sci Rep 2018; 8:4628. [PMID: 29545614 PMCID: PMC5854631 DOI: 10.1038/s41598-018-22883-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 03/01/2018] [Indexed: 02/06/2023] Open
Abstract
Pyrazinamide (PZA) is an important first-line anti-tuberculosis drug, resistance to which occurs primarily due to mutations in pncA (Rv2043c) that encodes the pyrazinamidase enzyme responsible for conversion of pro-drug PZA into its active form. Previous studies have reported numerous resistance-conferring mutations distributed across the entire length of pncA without any hotspot regions. As different lineages of Mycobacterium tuberculosis display a strong geographic association, we sought to understand whether the genetic background influenced the distribution of mutations in pncA. We analyzed the whole genome sequence data of 1,480 clinical isolates representing four major M. tuberculosis lineages to identify the distribution of mutations in the complete operon (Rv2044c-pncA-Rv2042c) and its upstream promoter region. We observed a non-overlapping pattern of mutations among various lineages and identified a lineage 3-specific frame-shift deletion in gene Rv2044c upstream of pncA that disrupted the stop codon and led to its fusion with pncA. This resulted in the addition of a novel domain of unknown function (DUF2784) to the pyrazinamidase enzyme. The variant molecule was computationally modelled and physico-chemical parameters determined to ascertain stability. Although the functional impact of this mutation remains unknown, its lineage specific nature highlights the importance of genetic background and warrants further study.
Collapse
Affiliation(s)
- Ramani Baddam
- Robert Koch Institute, Berlin, 13353, Germany
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, Bangladesh
| | - Narender Kumar
- Department of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
| | | | - Aditya Kumar Lankapalli
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, School of Life Sciences, University of Hyderabad, Hyderabad, 500084, India
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Niyaz Ahmed
- Department of Biotechnology and Bioinformatics, Pathogen Biology Laboratory, School of Life Sciences, University of Hyderabad, Hyderabad, 500084, India
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research Bangladesh, Dhaka, 1212, Bangladesh
| | - Sharon J Peacock
- Department of Clinical Medicine, University of Cambridge, Cambridge, CB2 0QQ, United Kingdom
- London School of Hygiene and Tropical Medicine, London, WC1E 7HT, United Kingdom
| | | |
Collapse
|
20
|
Ngabonziza JCS, Diallo AB, Tagliani E, Diarra B, Kadanga AE, Togo ACG, Thiam A, de Rijk WB, Alagna R, Houeto S, Ba F, Dagnra AY, Ivan E, Affolabi D, Schwoebel V, Trebucq A, de Jong BC, Rigouts L, Daneau G. Half of rifampicin-resistant Mycobacterium tuberculosis complex isolated from tuberculosis patients in Sub-Saharan Africa have concomitant resistance to pyrazinamide. PLoS One 2017; 12:e0187211. [PMID: 29088294 PMCID: PMC5663438 DOI: 10.1371/journal.pone.0187211] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/16/2017] [Indexed: 11/18/2022] Open
Abstract
Background Besides inclusion in 1st line regimens against tuberculosis (TB), pyrazinamide (PZA) is used in 2nd line anti-TB regimens, including in the short regimen for multidrug-resistant TB (MDR-TB) patients. Guidelines and expert opinions are contradictory about inclusion of PZA in case of resistance. Moreover, drug susceptibility testing (DST) for PZA is not often applied in routine testing, and the prevalence of resistance is unknown in several regions, including in most African countries. Methods Six hundred and twenty-three culture isolates from rifampicin-resistant (RR) patients were collected in twelve Sub-Saharan African countries. Among those isolates, 71% were from patients included in the study on the Union short-course regimen for MDR-TB in Benin, Burkina Faso, Burundi, Cameroon, Central Africa Republic, the Democratic Republic of the Congo, Ivory Coast, Niger, and Rwanda PZA resistance, and the rest (29%) were consecutive isolates systematically stored from 2014–2015 in Mali, Rwanda, Senegal, and Togo. Besides national guidelines, the isolates were tested for PZA resistance through pncA gene sequencing. Results Over half of these RR-TB isolates (54%) showed a mutation in the pncA gene, with a significant heterogeneity between countries. Isolates with fluoroquinolone resistance (but not with injectable resistance or XDR) were more likely to have concurrent PZA resistance. The pattern of mutations in the pncA gene was quite diverse, although some isolates with an identical pattern of mutations in pncA and other drug-related genes were isolated from the same reference center, suggesting possible transmission of these strains. Conclusion Similar to findings in other regions, more than half of the patients having RR-TB in West and Central Africa present concomitant resistance to PZA. Further investigations are needed to understand the relation between resistance to PZA and resistance to fluoroquinolones, and whether continued use of PZA in the face of PZA resistance provides clinical benefit to the patients.
Collapse
Affiliation(s)
- Jean Claude Semuto Ngabonziza
- National Reference Laboratory Division, Biomedical Services Department, Rwanda Biomedical Centre, Kigali, Rwanda
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | - Awa Ba Diallo
- Mycobacteriology Unit, Bacteriology- Virology Laboratory, CHNU Aristide le Dantec, Dakar, Senegal
| | - Elisa Tagliani
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Bassirou Diarra
- SEREFO/UCRC Program, University of Sciences, Techniques and Technologies of Bamako, Bamako, Mali
| | | | | | - Aliou Thiam
- Mycobacteriology Unit, Bacteriology- Virology Laboratory, CHNU Aristide le Dantec, Dakar, Senegal
| | - Willem Bram de Rijk
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Riccardo Alagna
- Emerging Bacterial Pathogens Unit, Division of Immunology, Transplantation and Infectious Diseases, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Sabine Houeto
- Laboratoire de Référence des Mycobactéries, Cotonou, Benin
| | - Fatoumata Ba
- Laboratoire de Reference des Mycobactéries, Dakar, Senegal
| | | | - Emil Ivan
- National Reference Laboratory Division, Biomedical Services Department, Rwanda Biomedical Centre, Kigali, Rwanda
| | | | - Valérie Schwoebel
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Arnaud Trebucq
- International Union Against Tuberculosis and Lung Disease, Paris, France
| | - Bouke Catherine de Jong
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Géraldine Daneau
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical section, Haute Ecole Francisco Ferrer, Brussels, Belgium
| | | |
Collapse
|
21
|
Sheen P, Requena D, Gushiken E, Gilman RH, Antiparra R, Lucero B, Lizárraga P, Cieza B, Roncal E, Grandjean L, Pain A, McNerney R, Clark TG, Moore D, Zimic M. A multiple genome analysis of Mycobacterium tuberculosis reveals specific novel genes and mutations associated with pyrazinamide resistance. BMC Genomics 2017; 18:769. [PMID: 29020922 PMCID: PMC5637355 DOI: 10.1186/s12864-017-4146-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 10/02/2017] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Tuberculosis (TB) is a major global health problem and drug resistance compromises the efforts to control this disease. Pyrazinamide (PZA) is an important drug used in both first and second line treatment regimes. However, its complete mechanism of action and resistance remains unclear. RESULTS We genotyped and sequenced the complete genomes of 68 M. tuberculosis strains isolated from unrelated TB patients in Peru. No clustering pattern of the strains was verified based on spoligotyping. We analyzed the association between PZA resistance with non-synonymous mutations and specific genes. We found mutations in pncA and novel genes significantly associated with PZA resistance in strains without pncA mutations. These included genes related to transportation of metal ions, pH regulation and immune system evasion. CONCLUSIONS These results suggest potential alternate mechanisms of PZA resistance that have not been found in other populations, supporting that the antibacterial activity of PZA may hit multiple targets.
Collapse
Affiliation(s)
- Patricia Sheen
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Eduardo Gushiken
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Robert H. Gilman
- Department of International Health, Johns Hopkins Bloomberg School of Public Health, 615 North Wolfe St., Room 5515, Baltimore, MD 21205 USA
| | - Ricardo Antiparra
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Bryan Lucero
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Pilar Lizárraga
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Basilio Cieza
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Elisa Roncal
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| | - Louis Grandjean
- Department of Infection, Immunology and Rheumatology, Institute of Child Health, University College London, 30 Guilford St, London, WC1N 1EH UK
| | - Arnab Pain
- Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science & Technology, Thuwal, Kingdom of Saudi Arabia
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - David Moore
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, WC1E 7HT UK
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular. Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Av. Honorio Delgado 430, San Martín de Porras, 31 Lima, Peru
| |
Collapse
|
22
|
Todd I, Negm OH, Reps J, Radford P, Figueredo G, McDermott EM, Drewe E, Powell RJ, Bainbridge S, Hamed M, Crouch S, Garibaldi J, St-Gallay S, Fairclough LC, Tighe PJ. A signalome screening approach in the autoinflammatory disease TNF receptor associated periodic syndrome (TRAPS) highlights the anti-inflammatory properties of drugs for repurposing. Pharmacol Res 2017; 125:188-200. [PMID: 28860008 DOI: 10.1016/j.phrs.2017.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/10/2017] [Accepted: 08/22/2017] [Indexed: 12/26/2022]
Abstract
TNF receptor associated periodic syndrome (TRAPS) is an autoinflammatory disease caused by mutations in TNF Receptor 1 (TNFR1). Current therapies for TRAPS are limited and do not target the pro-inflammatory signalling pathways that are central to the disease mechanism. Our aim was to identify drugs for repurposing as anti-inflammatories based on their ability to down-regulate molecules associated with inflammatory signalling pathways that are activated in TRAPS. This was achieved using rigorously optimized, high through-put cell culture and reverse phase protein microarray systems to screen compounds for their effects on the TRAPS-associated inflammatory signalome. 1360 approved, publically available, pharmacologically active substances were investigated for their effects on 40 signalling molecules associated with pro-inflammatory signalling pathways that are constitutively upregulated in TRAPS. The drugs were screened at four 10-fold concentrations on cell lines expressing both wild-type (WT) TNFR1 and TRAPS-associated C33Y mutant TNFR1, or WT TNFR1 alone; signalling molecule levels were then determined in cell lysates by the reverse-phase protein microarray. A novel mathematical methodology was developed to rank the compounds for their ability to reduce the expression of signalling molecules in the C33Y-TNFR1 transfectants towards the level seen in the WT-TNFR1 transfectants. Seven high-ranking drugs were selected and tested by RPPA for effects on the same 40 signalling molecules in lysates of peripheral blood mononuclear cells (PBMCs) from C33Y-TRAPS patients compared to PBMCs from normal controls. The fluoroquinolone antibiotic lomefloxacin, as well as others from this class of compounds, showed the most significant effects on multiple pro-inflammatory signalling pathways that are constitutively activated in TRAPS; lomefloxacin dose-dependently significantly reduced expression of 7/40 signalling molecules across the Jak/Stat, MAPK, NF-κB and PI3K/AKT pathways. This study demonstrates the power of signalome screening for identifying candidates for drug repurposing.
Collapse
Affiliation(s)
- Ian Todd
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| | - Ola H Negm
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK; Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, Egypt
| | - Jenna Reps
- Advanced Data Analysis Centre, School of Computer Science, The University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, UK
| | - Paul Radford
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| | - Grazziela Figueredo
- Advanced Data Analysis Centre, School of Computer Science, The University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, UK
| | - Elizabeth M McDermott
- Nottingham University Hospitals National Health Service Trust, Queen's Medical Centre Campus, Nottingham NG7 2UH, UK
| | - Elizabeth Drewe
- Nottingham University Hospitals National Health Service Trust, Queen's Medical Centre Campus, Nottingham NG7 2UH, UK
| | - Richard J Powell
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| | - Susan Bainbridge
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| | - Mohamed Hamed
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| | - Sharon Crouch
- Business Engagement and Innovation Services, The University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, UK
| | - Jon Garibaldi
- Advanced Data Analysis Centre, School of Computer Science, The University of Nottingham, Jubilee Campus, Nottingham NG8 1BB, UK
| | - Steve St-Gallay
- Sygnature Discovery Limited, BioCity, Pennyfoot Street, Nottingham NG1 1GF, UK
| | - Lucy C Fairclough
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK.
| | - Patrick J Tighe
- School of Life Sciences, The University of Nottingham, Life Sciences Building, University Park, Nottingham NG7 2RD, UK
| |
Collapse
|
23
|
Takawira FT, Mandishora RSD, Dhlamini Z, Munemo E, Stray-Pedersen B. Mutations in rpoB and katG genes of multidrug resistant mycobacterium tuberculosis undetectable using genotyping diagnostic methods. Pan Afr Med J 2017; 27:145. [PMID: 28904673 PMCID: PMC5567934 DOI: 10.11604/pamj.2017.27.145.10883] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 06/12/2017] [Indexed: 02/01/2023] Open
Abstract
INTRODUCTION Tuberculosis remains the leading causes of death worldwide with frequencies of mutations in rifampicin and isoniazid resistant Mycobacterium tuberculosis isolates varying according to geographical location. There is limited information in Zimbabwe on specific antibiotic resistance gene mutation patterns in MTB and hence, increased rate of discordant results and mortality due to inappropriate antibiotic prescriptions. The rpoB and katG genes molecular markers are used for detecting rifampicin and isoniazid resistance respectively. Some mutations within these gene sequences are associated with drug resistance as they directly alter gene function. The objectives of this research was to determine the drug resistance profiles in M. tuberculosis isolates that are phenotypically resistant but not detected by the GeneXpert and MTBDRplus kit and also to detect mutations in the rpoB and katG genes which are not detected by the Hain Genotype MTBDRplus kit and GeneXpert diagnosis. METHODS PCR was used for the amplification of the rpoB and katG genes from MTB isolates collected from human clinical samples between 2008 and 2015. The genes were sequenced and compared to the wild type MTB H37Rv rpoB (accession number L27989) and kat G genes (KP46920), respectively. Sequence analysis results were compared to genotyping results obtained from molecular assays and culture results of all isolates. RESULTS The most frequent mutation responsible for rifampicin resistance was (25/92) S531L that was detected by using all molecular assays. Some inconsistencies were observed between phenotypic and genotypic assay results for both katG and rpoB genes in 30 strains. For these, eight codons; G507S, T508A, L511V, del513-526, P520P, L524L, R528H, R529Q and S531F were novel mutations. In addition, the I572P/F, E562Q, P564S, and Q490Y mutations were identified as novel mutations outside the rifampicin resistance determining region. In katG gene, amino acid changes to threonine, asparagine and isoleucine exhibited high degrees of polymorphism such as V473N, D311N, and L427I. The R463L (20/92) amino acid substitution was most common but was not associated with isoniazid resistance. CONCLUSION These finding indicate that molecular assay kit diagnosis that is based on the rpoB and katG genes should be improved to cater for the genetic variations associated with the geographic specificity of the target genes and be able to detect most prevalent mutations in different areas.
Collapse
Affiliation(s)
- Faustinos Tatenda Takawira
- Department of Applied Biology and Biochemistry, National University of Science and Technology (NUST), Bulawayo, Zimbabwe
| | - Racheal Shamiso Dube Mandishora
- Department of Microbiology, College of Health Sciences, University of Zimbabwe, Mazowe Street, Parirenyatwa Complex, Avondale, Harare, Zimbabwe
| | - Zephaniah Dhlamini
- Department of Applied Biology and Biochemistry, National University of Science and Technology (NUST), Bulawayo, Zimbabwe
| | - Ellen Munemo
- National Microbiology Reference Laboratory, Harare Central Hospital, Southerton, Harare, Zimbabwe
| | - Babill Stray-Pedersen
- Division of Woman, Oslo University Hospital, Rikshospitalet and Institute of Clinical Medicine, University in Oslo, Norway
| |
Collapse
|
24
|
Shea J, Halse TA, Lapierre P, Shudt M, Kohlerschmidt D, Van Roey P, Limberger R, Taylor J, Escuyer V, Musser KA. Comprehensive Whole-Genome Sequencing and Reporting of Drug Resistance Profiles on Clinical Cases of Mycobacterium tuberculosis in New York State. J Clin Microbiol 2017; 55:1871-1882. [PMID: 28381603 PMCID: PMC5442544 DOI: 10.1128/jcm.00298-17] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Accepted: 03/28/2017] [Indexed: 12/19/2022] Open
Abstract
Whole-genome sequencing (WGS) is a newer alternative for tuberculosis (TB) diagnostics and is capable of providing rapid drug resistance profiles while performing species identification and capturing the data necessary for genotyping. Our laboratory developed and validated a comprehensive and sensitive WGS assay to characterize Mycobacterium tuberculosis and other M. tuberculosis complex (MTBC) strains, composed of a novel DNA extraction, optimized library preparation, paired-end WGS, and an in-house-developed bioinformatics pipeline. This new assay was assessed using 608 MTBC isolates, with 146 isolates during the validation portion of this study and 462 samples received prospectively. In February 2016, this assay was implemented to test all clinical cases of MTBC in New York State, including isolates and early positive Bactec mycobacterial growth indicator tube (MGIT) 960 cultures from primary specimens. Since the inception of the assay, we have assessed the accuracy of identification of MTBC strains to the species level, concordance with culture-based drug susceptibility testing (DST), and turnaround time. Species identification by WGS was determined to be 99% accurate. Concordance between drug resistance profiles generated by WGS and culture-based DST methods was 96% for eight drugs, with an average resistance-predictive value of 93% and susceptible-predictive value of 96%. This single comprehensive WGS assay has replaced seven molecular assays and has resulted in resistance profiles being reported to physicians an average of 9 days sooner than with culture-based DST for first-line drugs and 32 days sooner for second-line drugs.
Collapse
Affiliation(s)
- Joseph Shea
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Tanya A Halse
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Pascal Lapierre
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Matthew Shudt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Donna Kohlerschmidt
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Patrick Van Roey
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Ronald Limberger
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Jill Taylor
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| | - Kimberlee A Musser
- Wadsworth Center, New York State Department of Health, Albany, New York, USA
| |
Collapse
|
25
|
Evolution of Phenotypic and Molecular Drug Susceptibility Testing. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:221-246. [PMID: 29116638 DOI: 10.1007/978-3-319-64371-7_12] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Drug Resistant Tuberculosis (DRTB) is an emerging problem world-wide. In order to control the disease and decrease the number of cases overtime a prompt diagnosis followed by an appropriate treatment should be provided to patients. Phenotypic DST based on liquid automated culture has greatly reduced the time needed to generate reliable data but has the drawback to be expensive and prone to contamination in the absence of appropriate infrastructures. In the past 10 years molecular biology tools have been developed. Those tools target the main mutations responsible for DRTB and are now globally accessible in term of cost and infrastructures needed for the implementation. The dissemination of the Xpert MTB/rif has radically increased the capacity to perform the detection of rifampicin resistant TB cases. One of the main challenges for the large scale implementation of molecular based tests is the emergence of conflicting results between phenotypic and genotypic tests. This mines the confidence of clinicians in the molecular tests and delays the initiation of an appropriate treatment. A new technique is revolutionizing the genotypic approach to DST: the WGS by Next-Generation Sequencing technologies. This methodology promises to become the solution for a rapid access to universal DST, able indeed to overcome the limitations of the current phenotypic and genotypic assays. Today the use of the generated information is still challenging in decentralized facilities due to the lack of automation for sample processing and standardization in the analysis.The growing knowledge of the molecular mechanisms at the basis of drug resistance and the introduction of high-performing user-friendly tools at peripheral level should allow the very much needed accurate diagnosis of DRTB in the near future.
Collapse
|
26
|
Farhat MR, Sultana R, Iartchouk O, Bozeman S, Galagan J, Sisk P, Stolte C, Nebenzahl-Guimaraes H, Jacobson K, Sloutsky A, Kaur D, Posey J, Kreiswirth BN, Kurepina N, Rigouts L, Streicher EM, Victor TC, Warren RM, van Soolingen D, Murray M. Genetic Determinants of Drug Resistance in Mycobacterium tuberculosis and Their Diagnostic Value. Am J Respir Crit Care Med 2016; 194:621-30. [PMID: 26910495 PMCID: PMC5027209 DOI: 10.1164/rccm.201510-2091oc] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 02/22/2016] [Indexed: 11/16/2022] Open
Abstract
RATIONALE The development of molecular diagnostics that detect both the presence of Mycobacterium tuberculosis in clinical samples and drug resistance-conferring mutations promises to revolutionize patient care and interrupt transmission by ensuring early diagnosis. However, these tools require the identification of genetic determinants of resistance to the full range of antituberculosis drugs. OBJECTIVES To determine the optimal molecular approach needed, we sought to create a comprehensive catalog of resistance mutations and assess their sensitivity and specificity in diagnosing drug resistance. METHODS We developed and validated molecular inversion probes for DNA capture and deep sequencing of 28 drug-resistance loci in M. tuberculosis. We used the probes for targeted sequencing of a geographically diverse set of 1,397 clinical M. tuberculosis isolates with known drug resistance phenotypes. We identified a minimal set of mutations to predict resistance to first- and second-line antituberculosis drugs and validated our predictions in an independent dataset. We constructed and piloted a web-based database that provides public access to the sequence data and prediction tool. MEASUREMENTS AND MAIN RESULTS The predicted resistance to rifampicin and isoniazid exceeded 90% sensitivity and specificity but was lower for other drugs. The number of mutations needed to diagnose resistance is large, and for the 13 drugs studied it was 238 across 18 genetic loci. CONCLUSIONS These data suggest that a comprehensive M. tuberculosis drug resistance diagnostic will need to allow for a high dimension of mutation detection. They also support the hypothesis that currently unknown genetic determinants, potentially discoverable by whole-genome sequencing, encode resistance to second-line tuberculosis drugs.
Collapse
MESH Headings
- Antitubercular Agents/pharmacology
- Drug Resistance, Multiple, Bacterial/drug effects
- Drug Resistance, Multiple, Bacterial/genetics
- Genes, Bacterial/drug effects
- Genes, Bacterial/genetics
- Humans
- Molecular Diagnostic Techniques
- Mutation/drug effects
- Mutation/genetics
- Mycobacterium tuberculosis/drug effects
- Mycobacterium tuberculosis/genetics
- Mycobacterium tuberculosis/isolation & purification
- Sequence Analysis, DNA
- Tuberculosis, Multidrug-Resistant/drug therapy
- Tuberculosis, Multidrug-Resistant/genetics
- Tuberculosis, Multidrug-Resistant/microbiology
Collapse
Affiliation(s)
- Maha R. Farhat
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
| | - Razvan Sultana
- Genomics England, Queen Mary University, London, United Kingdom
| | - Oleg Iartchouk
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | | | - James Galagan
- Department of Biomedical Engineering
- Department of Microbiology, and
- Bioinformatics Program, Boston University, Boston, Massachusetts
| | | | | | - Hanna Nebenzahl-Guimaraes
- National Institute for Public Health and the Environment, Bilthoven, the Netherlands
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
- Life and Health Sciences Research Institute/3Bs, PT Government Associate Laboratory, Braga/Guimaraes, Portugal
| | - Karen Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Alexander Sloutsky
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - Devinder Kaur
- University of Massachusetts Medical School, Worcester, Massachusetts
| | - James Posey
- Division of Tuberculosis Elimination, National Center for HIV/AIDS, Viral Hepatitis, STD, and TB Prevention, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Barry N. Kreiswirth
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Natalia Kurepina
- Public Health Research Institute Tuberculosis Center, Rutgers University, Newark, New Jersey
| | - Leen Rigouts
- Mycobacteriology, Institute of Tropical Medicine, Antwerp, Belgium
- Biomedical Sciences, Antwerp University, Antwerp, Belgium; and
| | - Elizabeth M. Streicher
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Tommie C. Victor
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Robin M. Warren
- DST/NRF Center of Excellence for Biomedical TB Research/SAMRC Center for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Dick van Soolingen
- Department of Pulmonary Diseases and
- Department of Medical Microbiology, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
- Life and Health Sciences Research Institute, School of Health Sciences, University of Minho, Braga, Portugal
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts
| |
Collapse
|
27
|
Abstract
Antimicrobial resistance is a natural evolutionary process, which in the case of Mycobacterium tuberculosis is based on spontaneous chromosomal mutations, meaning that well-designed combination drug regimens provided under supervised therapy will prevent the emergence of drug-resistant strains. Unfortunately, limited resources, poverty, and neglect have led to the emergence of drug-resistant tuberculosis throughout the world. The international community has responded with financial and scientific support, leading to new rapid diagnostics, new drugs and regimens in advanced clinical development, and an increasingly sophisticated understanding of resistance mechanisms and their application to all aspects of TB control and treatment.
Collapse
Affiliation(s)
- Sebastian G Kurz
- Division of Pulmonary, Critical Care and Sleep Medicine, Department of Medicine, Tufts University School of Medicine, 800 Washington Street, #257, Boston, MA 02111, USA.
| | - Jennifer J Furin
- Department of Global Health and Social Medicine, Harvard Medical School, 641 Huntington Avenue, Boston, MA 02115, USA
| | - Charles M Bark
- Division of Infectious Diseases, Department of Medicine, MetroHealth Medical Center, Case Western Reserve University, 2500 MetroHealth Drive, Cleveland, OH 44109, USA
| |
Collapse
|
28
|
Farhat MR, Jacobson KR, Franke MF, Kaur D, Sloutsky A, Mitnick CD, Murray M. Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis. J Clin Microbiol 2016; 54:727-33. [PMID: 26763957 PMCID: PMC4767988 DOI: 10.1128/jcm.02775-15] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 01/04/2016] [Indexed: 11/20/2022] Open
Abstract
Molecular diagnostics that rapidly and accurately predict resistance to fluoroquinolone drugs and especially later-generation agents promise to improve treatment outcomes for patients with multidrug-resistant tuberculosis and prevent the spread of disease. Mutations in the gyr genes are known to confer most fluoroquinolone resistance, but knowledge about the effects of gyr mutations on susceptibility to early- versus later-generation fluoroquinolones and about the role of mutation-mutation interactions is limited. Here, we sequenced the full gyrA and gyrB open reading frames in 240 multidrug-resistant and extensively drug-resistant tuberculosis strains and quantified their ofloxacin and moxifloxacin MIC by testing growth at six concentrations for each drug. We constructed a multivariate regression model to assess both the individual mutation effects and interactions on the drug MICs. We found that gyrB mutations contribute to fluoroquinolone resistance both individually and through interactions with gyrA mutations. These effects were statistically significant. In these clinical isolates, several gyrA and gyrB mutations conferred different levels of resistance to ofloxacin and moxifloxacin. Consideration of gyr mutation combinations during the interpretation of molecular test results may improve the accuracy of predicting the fluoroquinolone resistance phenotype. Further, the differential effects of gyr mutations on the activity of early- and later-generation fluoroquinolones requires further investigation and could inform the selection of a fluoroquinolone for treatment.
Collapse
Affiliation(s)
- Maha R Farhat
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, Massachusetts, USA Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Karen R Jacobson
- Section of Infectious Diseases, Boston University School of Medicine, Boston, Massachusetts, USA DST/NRF Centre of Excellence for Biomedical TB Research/MRC Centre for Molecular and Cellular Biology, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa
| | - Molly F Franke
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA
| | - Devinder Kaur
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, Boston, Massachusetts, USA
| | - Alex Sloutsky
- University of Massachusetts Medical School, Massachusetts Supranational TB Reference Laboratory, Boston, Massachusetts, USA
| | - Carole D Mitnick
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA Department of Global Health Equity, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | - Megan Murray
- Department of Global Health and Social Medicine, Harvard Medical School, Boston, Massachusetts, USA Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
| |
Collapse
|
29
|
Zimenkov DV, Kulagina EV, Antonova OV, Zhuravlev VY, Gryadunov DA. Simultaneous drug resistance detection and genotyping of Mycobacterium tuberculosis using a low-density hydrogel microarray. J Antimicrob Chemother 2016; 71:1520-31. [PMID: 26929267 DOI: 10.1093/jac/dkw015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Accepted: 01/11/2016] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Nucleic acid amplification tests are widely used in TB diagnostics. Priority tasks in their development consist of increasing the specificity and sensitivity of the detection of resistance to a wide spectrum of anti-TB drugs. METHODS We developed a multiplexed assay allowing the detection of 116 drug resistance-determining mutations in the rpoB, katG, inhA, ahpC, gyrA, gyrB, rrs, eis and embB genes in the Mycobacterium tuberculosis complex genome and six SNPs to identify the main lineages circulating in Russia. The assay is based on the amplification of 17 fragments of the genome using the universal primer adapter technique and heat pulses at the elongation step, followed by hybridization on a microarray. RESULTS The method was evaluated using 264 pairs of clinical samples and corresponding isolates. A significant proportion (25%) of smear-negative samples were correctly analysed by microarray analysis in addition to 96% of smear-positive samples. The sensitivity and specificity of the assay exceeded 90% for rifampicin, isoniazid, ofloxacin and second-line injection drugs. In agreement with previous studies, the specificity of ethambutol resistance was as low as 57%, while the sensitivity was 89.9%. Strong association of the Beijing lineage with a resistant phenotype was observed. Euro-American lineage strains, excluding Ural and LAM, were predominantly associated with the susceptible phenotype. CONCLUSIONS The developed test has a high sensitivity and specificity and can be directly applied to clinical samples. The combination of mutation-based drug resistance profiling and basic genotyping could be useful for clinical microbiology studies and epidemiological surveillance of the M. tuberculosis complex.
Collapse
Affiliation(s)
- Danila V Zimenkov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Elena V Kulagina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Olga V Antonova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Dmitry A Gryadunov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russian Federation
| |
Collapse
|
30
|
Ssengooba W, Meehan CJ, Lukoye D, Kasule GW, Musisi K, Joloba ML, Cobelens FG, de Jong BC. Whole genome sequencing to complement tuberculosis drug resistance surveys in Uganda. INFECTION GENETICS AND EVOLUTION 2016; 40:8-16. [PMID: 26917365 PMCID: PMC4856735 DOI: 10.1016/j.meegid.2016.02.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2015] [Revised: 01/20/2016] [Accepted: 02/15/2016] [Indexed: 11/29/2022]
Abstract
Understanding the circulating Mycobacterium tuberculosis resistance mutations is vital for better TB control strategies, especially to inform a new MDR-TB treatment programme. We complemented the phenotypic drug susceptibility testing (DST) based drug resistance surveys (DRSs) conducted in Uganda between 2008 and 2011 with Whole Genome Sequencing (WGS) of 90 Mycobacterium tuberculosis isolates phenotypically resistant to rifampicin and/or isoniazid to better understand the extent of drug resistance. A total of 31 (34.4 %) patients had MDR-TB, 5 (5.6 %) mono-rifampicin resistance and 54 (60.0 %) mono-isoniazid resistance by phenotypic DST. Pyrazinamide resistance mutations were identified in 32.3% of the MDR-TB patients. Resistance to injectable agents was detected in 4/90 (4.4%), and none to fluoroquinolones or novel drugs. Compensatory mutations in rpoC were identified in two patients. The sensitivity and specificity of drug resistance mutations compared to phenotypic DST were for rpoB 88.6% and 98.1%, katG 60.0% and 100%, fabG1 16.5% and 100%, katG and/or fabG1 71.8% and 100%, embCAB 63.0% and 82.5%, rrs 11.4% and 100%, rpsL 20.5% and 95.7% and rrs and/or rpsL 31.8% and 95.7%. Phylogenetic analysis showed dispersed MDR-TB isolate, with only one cluster of three Beijing family from South West Uganda. Among tuberculosis patients in Uganda, resistance beyond first-line drugs as well as compensatory mutations remain low, and MDR-TB isolates did not arise from a dominant clone. Our findings show the potential use of sequencing for complementing DRSs or surveillance in this setting, with good specificity compared to phenotypic DST. The reported high confidence mutations can be included in molecular assays, and population-based studies can track transmission of MDR-TB including the Beijing family strains in the South West of the country.
Collapse
Affiliation(s)
- Willy Ssengooba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands.
| | - Conor J Meehan
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Deus Lukoye
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | | | - Kenneth Musisi
- National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Moses L Joloba
- Department of Medical Microbiology, College of Health Sciences Makerere University, Kampala, Uganda; National Tuberculosis Reference Laboratory, Ministry of Health, Kampala, Uganda
| | - Frank G Cobelens
- Department of Global Health and Amsterdam Institute of Global Health and Development, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands; KNCV Tuberculosis Foundation, The Hague, The Netherlands
| | - Bouke C de Jong
- Mycobacteriology Unit, Institute of Tropical Medicine, Antwerp, Belgium; Division of Infectious Diseases, New York University, New York, NY, USA
| |
Collapse
|
31
|
Zhao J, Liu Y, Jiang X, Guo P, Xu Y, Zhang P, Ji T, Lin Z, Wang W. Effect of C-5 position on the photochemical properties and phototoxicity of antofloxacin and levofloxacin: A stable and transient study. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 155:122-9. [DOI: 10.1016/j.jphotobiol.2015.12.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/24/2015] [Accepted: 12/07/2015] [Indexed: 01/06/2023]
|
32
|
Li F, Gao B, Xu W, Chen L, Xiong S. The Defect in Autophagy Induction by Clinical Isolates of Mycobacterium Tuberculosis Is Correlated with Poor Tuberculosis Outcomes. PLoS One 2016; 11:e0147810. [PMID: 26815035 PMCID: PMC4729487 DOI: 10.1371/journal.pone.0147810] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/08/2016] [Indexed: 01/29/2023] Open
Abstract
Background Tuberculosis (TB) represents a major global health problem. The prognosis of clinically active tuberculosis depends on the complex interactions between Mycobacterium tuberculosis (Mtb) and its host. In recent years, autophagy receives particular attention for its role in host defense against intracellular pathogens, including Mtb. In present study, we aim to investigate the relationship of autophagy induction by clinical isolates of Mtb with the clinical outcomes in patients with TB. Methodology/Principal Findings We collected 185 clinical isolates of Mtb, and determined the effect of these Mtb isolates on autophagy induction in macrophages. It was found that most of clinical isolates of Mtb were able to induce autophagosome formation in macrophages, however, the autophagy-inducing ability varied significantly among different isolates. Of importance, our results revealed that patients infected by Mtb with poor autophagy-inducing ability displayed more severe radiographic extent of disease (p<0.001), and were more likely to have unfavorable treatment outcomes (p<0.001). No significant association was observed between the extent of Mtb-induced autophagy with some socio-demographic characteristics (such as gender, age and tobacco consumption), and some laboratory tests (such as hemoglobin, leukocyte count and erythrocyte sedimentation rate). Furthermore, results from logistic regression analysis demonstrated that the defect in autophagy induction by clinical isolates of Mtb was an independent risk factor for far-advanced radiographic disease (aOR 4.710 [1.93–11.50]) and unfavorable treatment outcomes (aOR 8.309 [2.22–28.97]) in TB. Conclusion/Significance These data indicated that the defect in autophagy induction by Mtb isolates increased the risk of poor clinical outcomes in TB patients, and detection of clinical isolates-induced autophagosome formation might help evaluate the TB outcomes.
Collapse
Affiliation(s)
- Furong Li
- Institute for Immunobiology, Department of Immunology, Shanghai Medical College of Fudan University, Shanghai 200032, P.R. China
| | - Bo Gao
- Institute for Immunobiology, Department of Immunology, Shanghai Medical College of Fudan University, Shanghai 200032, P.R. China
- * E-mail: (SX); (BG)
| | - Wei Xu
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215006, P.R. China
| | - Ling Chen
- Department of Respiratory Medicine, Affiliated Hospital of Zunyi Medical College, Zunyi 563000, P.R. China
| | - Sidong Xiong
- Institute for Immunobiology, Department of Immunology, Shanghai Medical College of Fudan University, Shanghai 200032, P.R. China
- Jiangsu Key Laboratory of Infection and Immunity, Institutes of Biology and Medical Sciences, Soochow University, Suzhou 215006, P.R. China
- * E-mail: (SX); (BG)
| |
Collapse
|
33
|
Peterson ND, Rosen BC, Dillon NA, Baughn AD. Uncoupling Environmental pH and Intrabacterial Acidification from Pyrazinamide Susceptibility in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2015; 59:7320-6. [PMID: 26369957 PMCID: PMC4649215 DOI: 10.1128/aac.00967-15] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 09/07/2015] [Indexed: 01/17/2023] Open
Abstract
Pyrazinamide (PZA) is a first-line antitubercular drug for which the mode of action remains unresolved. Mycobacterium tuberculosis lacks measurable susceptibility to PZA under standard laboratory growth conditions. However, susceptibility to this drug can be induced by cultivation of the bacilli in an acidified growth medium. Previous reports suggested that the active form of PZA, pyrazinoic acid (POA), operates as a proton ionophore that confers cytoplasmic acidification when M. tuberculosis is exposed to an acidic environment. In this study, we demonstrate that overexpression of the PZA-activating enzyme PncA can confer PZA susceptibility to M. tuberculosis under neutral and even alkaline growth conditions. Furthermore, we find that wild-type M. tuberculosis displays increased susceptibility to POA relative to PZA in neutral and alkaline media. Utilizing a strain of M. tuberculosis that expresses a pH-sensitive green fluorescent protein (GFP), we find that unlike the bona fide ionophores monensin and carbonyl cyanide 3-chlorophenylhydrazone, PZA and POA do not induce rapid uncoupling or cytoplasmic acidification under conditions that promote susceptibility. Thus, based on these observations, we conclude that the antitubercular action of POA is independent of environmental pH and intrabacterial acidification.
Collapse
Affiliation(s)
- Nicholas D Peterson
- Department of Microbiology and Immunology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Brandon C Rosen
- Department of Microbiology and Immunology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Nicholas A Dillon
- Department of Microbiology and Immunology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Anthony D Baughn
- Department of Microbiology and Immunology, Center for Infectious Diseases and Microbiology Translational Research, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| |
Collapse
|
34
|
|