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Ghajavand H, Kargarpour Kamakoli M, Khanipour S, Pourazar Dizaji S, Masoumi M, Rahimi Jamnani F, Fateh A, Yaseri M, Siadat SD, Vaziri F. Scrutinizing the drug resistance mechanism of multi- and extensively-drug resistant Mycobacterium tuberculosis: mutations versus efflux pumps. Antimicrob Resist Infect Control 2019; 8:70. [PMID: 31073401 PMCID: PMC6498538 DOI: 10.1186/s13756-019-0516-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 03/29/2019] [Indexed: 02/03/2023] Open
Abstract
Background In order to shorten the course of treatment and its effectiveness, it is essential to gain an in-depth insight into the drug resistance mechanisms of Mycobacterium tuberculosis (M. tuberculosis). Methods In this study, we evaluated the contribution of 26 drug efflux pumps plus target gene mutations to the drug resistance levels in multi-drug resistant (MDR)/pre-extensively drug-resistant (pre-XDR)/extensively drug-resistant (XDR) and mono-drug resistant clinical isolates of M. tuberculosis. The panels of 25 M. tuberculosis clinical strains were characterized for drug resistance-associated mutations with whole-genome sequencing and antibiotic profiles in the presence and absence of efflux inhibitor verapamil (VP). Results Different MICs were observed for the same target gene mutations. Out of the 16 MDR/pre-XDR/XDR isolates, 6 (37.5%) and 3 (18.8%) isolates demonstrated a significant decrease in rifampicin (RIF) MIC and isoniazid (INH) MIC due to the VP exposure (64 μg/mL), respectively. Susceptibility to RIF was fully restored in two isolates after VP exposure. Moreover, the efflux pump genes of Rv2938, Rv2936, Rv1145, Rv1146, Rv933, Rv1250, Rv876, Rv2333, Rv2459, Rv849, and Rv1819 were overexpressed in the presence of anti-TB drugs, showing the contribution of these efflux pumps to the overall resistance phenotype. Conclusions Our results clearly showed that efflux systems, besides spontaneous mutations, play a role in the development of INH/RIF resistance. In addition, although VP was effective in reducing the expression of some efflux pumps, it was not very successful at the phenotypic level.
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Affiliation(s)
- Hasan Ghajavand
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Mansour Kargarpour Kamakoli
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Sharareh Khanipour
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Shahin Pourazar Dizaji
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Morteza Masoumi
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Fatemeh Rahimi Jamnani
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Abolfazl Fateh
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Mehdi Yaseri
- 3Department of Epidemiology and Biostatistics, Tehran University of Medical Sciences, Tehran, Iran
| | - Seyed Davar Siadat
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
| | - Farzam Vaziri
- 1Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran.,2Microbiology Research Center (MRC), Pasteur Institute of Iran, No. 358, 12th Farvardin Ave, Jomhoori St, Tehran, 1316943551 Iran
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202
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Pi R, Liu Q, Jiang Q, Gao Q. Characterization of linezolid-resistance-associated mutations in Mycobacterium tuberculosis through WGS. J Antimicrob Chemother 2019; 74:1795-1798. [DOI: 10.1093/jac/dkz150] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 03/10/2019] [Accepted: 03/18/2019] [Indexed: 12/17/2022] Open
Abstract
Abstract
Objectives
Linezolid is becoming an important antibiotic for treating MDR/XDR TB, but the mutations conferring resistance to linezolid remain inadequately characterized. Herein, we investigated the linezolid-resistance-associated mutations on a whole-genome scale through parallel selections of resistant isolates in vitro.
Methods
Ten parallel Mycobacterium tuberculosis H37Rv cultures were subjected to spontaneous mutant selection on 7H11 agar plates containing 2.5 mg/L linezolid. The linezolid resistance of resulting colonies was confirmed by growth on a second linezolid plate. WGS was then performed to identify mutations associated with linezolid resistance.
Results
Of 181 colonies appearing on the initial linezolid plates, 154 were confirmed to be linezolid resistant. WGS showed that 88.3% (136/154) of these isolates had a T460C mutation in rplC, resulting in a C154R substitution. The other 18 isolates harboured a single mutation in the rrl gene, with G2814T and G2270T mutations accounting for 7.8% (12/154) and 3.9% (6/154), respectively.
Conclusions
No mutations in novel genes were associated with linezolid resistance in a whole-genome investigation of 154 linezolid-resistant isolates selected in vitro. These results emphasize that rrl and rplC genes should be the major targets for molecular detection of linezolid resistance.
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Affiliation(s)
- Rui Pi
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qingyun Liu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, School of Basic Medical Sciences and Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
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203
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Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2019; 63:AAC.02175-18. [PMID: 30718257 PMCID: PMC6496161 DOI: 10.1128/aac.02175-18] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 01/25/2019] [Indexed: 01/10/2023] Open
Abstract
Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from the Democratic Republic of the Congo, Ivory Coast, Peru, Thailand, and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD Bactec MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.
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204
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Farha MA, Brown ED. Drug repurposing for antimicrobial discovery. Nat Microbiol 2019; 4:565-577. [PMID: 30833727 DOI: 10.1038/s41564-019-0357-1] [Citation(s) in RCA: 189] [Impact Index Per Article: 37.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/03/2019] [Indexed: 12/17/2022]
Abstract
Antimicrobial resistance continues to be a public threat on a global scale. The ongoing need to develop new antimicrobial drugs that are effective against multi-drug-resistant pathogens has spurred the research community to invest in various drug discovery strategies, one of which is drug repurposing-the process of finding new uses for existing drugs. While still nascent in the antimicrobial field, the approach is gaining traction in both the public and private sector. While the approach has particular promise in fast-tracking compounds into clinical studies, it nevertheless has substantial obstacles to success. This Review covers the art of repurposing existing drugs for antimicrobial purposes. We discuss enabling screening platforms for antimicrobial discovery and present encouraging findings of novel antimicrobial therapeutic strategies. Also covered are general advantages of repurposing over de novo drug development and challenges of the strategy, including scientific, intellectual property and regulatory issues.
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Affiliation(s)
- Maya A Farha
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada
| | - Eric D Brown
- Michael G. DeGroote Institute for Infectious Disease Research, Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Ontario, Canada.
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205
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Blanquart F. Evolutionary epidemiology models to predict the dynamics of antibiotic resistance. Evol Appl 2019; 12:365-383. [PMID: 30828361 PMCID: PMC6383707 DOI: 10.1111/eva.12753] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 11/22/2018] [Accepted: 11/29/2018] [Indexed: 12/12/2022] Open
Abstract
The evolution of resistance to antibiotics is a major public health problem and an example of rapid adaptation under natural selection by antibiotics. The dynamics of antibiotic resistance within and between hosts can be understood in the light of mathematical models that describe the epidemiology and evolution of the bacterial population. "Between-host" models describe the spread of resistance in the host community, and in more specific settings such as hospitalized hosts (treated by antibiotics at a high rate), or farm animals. These models make predictions on the best strategies to limit the spread of resistance, such as reducing transmission or adapting the prescription of several antibiotics. Models can be fitted to epidemiological data in the context of intensive care units or hospitals to predict the impact of interventions on resistance. It has proven harder to explain the dynamics of resistance in the community at large, in particular because models often do not reproduce the observed coexistence of drug-sensitive and drug-resistant strains. "Within-host" models describe the evolution of resistance within the treated host. They show that the risk of resistance emergence is maximal at an intermediate antibiotic dose, and some models successfully explain experimental data. New models that include the complex host population structure, the interaction between resistance-determining loci and other loci, or integrating the within- and between-host levels will allow better interpretation of epidemiological and genomic data from common pathogens and better prediction of the evolution of resistance.
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Affiliation(s)
- François Blanquart
- Centre for Interdisciplinary Research in Biology (CIRB), Collège de France, CNRS, INSERMPSL Research UniversityParisFrance
- IAME, UMR 1137, INSERMUniversité Paris DiderotParisFrance
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206
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Chaidir L, Ruesen C, Dutilh BE, Ganiem AR, Andryani A, Apriani L, Huynen MA, Ruslami R, Hill PC, van Crevel R, Alisjahbana B. Use of whole-genome sequencing to predict Mycobacterium tuberculosis drug resistance in Indonesia. J Glob Antimicrob Resist 2019; 16:170-177. [DOI: 10.1016/j.jgar.2018.08.018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 06/06/2018] [Accepted: 08/23/2018] [Indexed: 10/28/2022] Open
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Moreno-Molina M, Comas I, Furió V. The Future of TB Resistance Diagnosis: The Essentials on Whole Genome Sequencing and Rapid Testing Methods. Arch Bronconeumol 2019; 55:421-426. [PMID: 30795867 DOI: 10.1016/j.arbres.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/11/2019] [Accepted: 01/14/2019] [Indexed: 12/25/2022]
Abstract
Tuberculosis resistance diagnostics have vastly improved in recent years thanks to the development of standardised phenotypic and molecular testing methods. However, these methods are either slow or limited in the number of resistant genotypes they can detect. With the advent of next-generation sequencing (NGS) we can sidestep all those problems, as we can sequence whole tuberculosis genomes at increasingly smaller costs and requiring less and less DNA. In this review, we explain how accumulated knowledge in the field has allowed us to go from phenotypic testing to molecular methods to Whole Genome Sequencing (WGS) for resistance diagnostics. We compare current diagnostic methods with WGS as to their efficacy in detecting resistant cases, and show how forthcoming advances in NGS technologies will be crucial in widespread implementation of WGS as a diagnostic tool.
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Affiliation(s)
| | - Iñaki Comas
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain; CIBER in Epidemiology and Public Health, Spain
| | - Victoria Furió
- Biomedicine Institute of Valencia (CSIC), Valencia, Spain.
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208
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Catalão MJ, Filipe SR, Pimentel M. Revisiting Anti-tuberculosis Therapeutic Strategies That Target the Peptidoglycan Structure and Synthesis. Front Microbiol 2019; 10:190. [PMID: 30804921 PMCID: PMC6378297 DOI: 10.3389/fmicb.2019.00190] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2018] [Accepted: 01/23/2019] [Indexed: 12/27/2022] Open
Abstract
Tuberculosis (TB), which is caused by Mycobacterium tuberculosis (Mtb), is one of the leading cause of death by an infectious diseases. The biosynthesis of the mycobacterial cell wall (CW) is an area of increasing research significance, as numerous antibiotics used to treat TB target biosynthesis pathways of essential CW components. The main feature of the mycobacterial cell envelope is an intricate structure, the mycolyl-arabinogalactan-peptidoglycan (mAGP) complex responsible for its innate resistance to many commonly used antibiotics and involved in virulence. A hallmark of mAGP is its unusual peptidoglycan (PG) layer, which has subtleties that play a key role in virulence by enabling pathogenic species to survive inside the host and resist antibiotic pressure. This dynamic and essential structure is not a target of currently used therapeutics as Mtb is considered naturally resistant to most β-lactam antibiotics due to a highly active β-lactamase (BlaC) that efficiently hydrolyses many β-lactam drugs to render them ineffective. The emergence of multidrug- and extensive drug-resistant strains to the available antibiotics has become a serious health threat, places an immense burden on health care systems, and poses particular therapeutic challenges. Therefore, it is crucial to explore additional Mtb vulnerabilities that can be used to combat TB. Remodeling PG enzymes that catalyze biosynthesis and recycling of the PG are essential to the viability of Mtb and are therefore attractive targets for novel antibiotics research. This article reviews PG as an alternative antibiotic target for TB treatment, how Mtb has developed resistance to currently available antibiotics directed to PG biosynthesis, and the potential of targeting this essential structure to tackle TB by attacking alternative enzymatic activities involved in Mtb PG modifications and metabolism.
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Affiliation(s)
- Maria João Catalão
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
| | - Sérgio R. Filipe
- UCIBIO-REQUIMTE, Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Caparica, Portugal
- Laboratory of Bacterial Cell Surfaces and Pathogenesis, Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa, Oeiras, Portugal
| | - Madalena Pimentel
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
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209
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Genetic Diversity of Multi- and Extensively Drug-Resistant Mycobacterium tuberculosis Isolates in the Capital of Iran, Revealed by Whole-Genome Sequencing. J Clin Microbiol 2019; 57:JCM.01477-18. [PMID: 30404943 DOI: 10.1128/jcm.01477-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Accepted: 11/01/2018] [Indexed: 01/23/2023] Open
Abstract
The emergence and spread of multidrug resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains is a critical global health problem. Between 2014 and 2018, 606 MTBC strains were isolated from 13,892 suspected pulmonary tuberculosis (TB) patients in Tehran, Iran, including 16 (2.6%) MDR-TB cases. A combination of phenotypic and genotypic methods (whole-genome sequencing) was employed for the identification of additional drug resistances and strain-to-strain genetic distances as a marker for recent transmission events. MDR and extensively drug-resistant (XDR) TB cases were almost exclusively infected by lineage 2/Beijing strains (14/16, P < 0.001). We further showed that recent transmission and/or recent introduction of lineage 2/Beijing strains contribute to high XDR-TB rates among all MDR-TB cases and should be considered an emerging threat for TB control in Tehran. In addition, the extensive pre-existing drug resistance profiles of MDR/XDR strains will further challenge TB diagnostics in the region.
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210
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Waman VP, Vedithi SC, Thomas SE, Bannerman BP, Munir A, Skwark MJ, Malhotra S, Blundell TL. Mycobacterial genomics and structural bioinformatics: opportunities and challenges in drug discovery. Emerg Microbes Infect 2019; 8:109-118. [PMID: 30866765 PMCID: PMC6334779 DOI: 10.1080/22221751.2018.1561158] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Revised: 12/03/2018] [Accepted: 12/09/2018] [Indexed: 01/08/2023]
Abstract
Of the more than 190 distinct species of Mycobacterium genus, many are economically and clinically important pathogens of humans or animals. Among those mycobacteria that infect humans, three species namely Mycobacterium tuberculosis (causative agent of tuberculosis), Mycobacterium leprae (causative agent of leprosy) and Mycobacterium abscessus (causative agent of chronic pulmonary infections) pose concern to global public health. Although antibiotics have been successfully developed to combat each of these, the emergence of drug-resistant strains is an increasing challenge for treatment and drug discovery. Here we describe the impact of the rapid expansion of genome sequencing and genome/pathway annotations that have greatly improved the progress of structure-guided drug discovery. We focus on the applications of comparative genomics, metabolomics, evolutionary bioinformatics and structural proteomics to identify potential drug targets. The opportunities and challenges for the design of drugs for M. tuberculosis, M. leprae and M. abscessus to combat resistance are discussed.
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Affiliation(s)
| | | | | | | | - Asma Munir
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Marcin J. Skwark
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Sony Malhotra
- Institute of Structural and Molecular Biology, Department of Biological Sciences, Birkbeck College, University of London, London, UK
| | - Tom L. Blundell
- Department of Biochemistry, University of Cambridge, Cambridge, UK
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211
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Ravan P, Nejad Sattari T, Siadat SD, Vaziri F. Evaluation of the expression of cytokines and chemokines in macrophages in response to rifampin-monoresistant Mycobacterium tuberculosis and H37Rv strain. Cytokine 2018; 115:127-134. [PMID: 30594437 DOI: 10.1016/j.cyto.2018.12.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Revised: 11/17/2018] [Accepted: 12/02/2018] [Indexed: 01/02/2023]
Abstract
Macrophages are the primary phagocytes in the lungs and a part of the host defense system against Mycobacterium tuberculosis (Mtb), involved in the primary immune response. While several studies have assessed the effects of resistance to rifampin on Mtb physiology, the consequences of mutations in genes encoding the beta subunit of RNA polymerase (rpoB) for host-pathogen interactions remain poorly understood. In this study, rifampin-monoresistant (RMR) Mtb and H37Rv strains were used to infect the THP-1-derived macrophages. Real-time quantitative reverse transcription PCR assay was carried out to determine mRNA expression in 84 cytokine and chemokine genes. Production of specific cytokines and chemokines was measured by ELISA assay. In conclusion, the current study shed more light on the fitness cost of RMR strain and the potential effects of rpoB gene mutations on Mtb-host interactions. These results initially demonstrate that the Mtb carrying the rpoB-S450L can modulate macrophage responses to mediate bacterial survival.
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Affiliation(s)
- Parvaneh Ravan
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Taher Nejad Sattari
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Seyed Davar Siadat
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Farzam Vaziri
- Department of Mycobacteriology and Pulmonary Research, Pasteur Institute of Iran, Tehran, Iran; Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran.
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212
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Genetic diversity of Mycobacterium tuberculosis isolates causing pulmonary and extrapulmonary tuberculosis in the capital of Iran. Mol Phylogenet Evol 2018; 132:46-52. [PMID: 30513341 DOI: 10.1016/j.ympev.2018.11.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 11/24/2018] [Accepted: 11/26/2018] [Indexed: 01/12/2023]
Abstract
OBJECTIVES Evaluation of the genetic diversity of Mycobacterium tuberculosis (M.tb) and determining if the association between a specific genotype and the site of infection is crucial. Accordingly, the current study aimed at comparing predominant M.tb genotypes in pulmonary (PTB) and extrapulmonary tuberculosis (EPTB) isolates circulating in the capital of Iran. METHODS The genetic diversity of culture-confirmed PTB and EPTB isolates were evaluated by Spoligotyping and MIRU-VNTR (mycobacterial interspersed repetitive-unit-variable-number tandem-repeat) typing methods. Genotyping data were analyzed with SITVIT, MIRU-VNTRplus, and TBminer databases. To assess adjusted associations, chi-square/the Fisher exact test and multiple logistic regression model were applied. RESULTS URAL2 (NEW-1) (28/88; 31.8%) and CAS1-DELHI (25/84; 29.8%) genotypes were predominant in EPTB and PTB strains, respectively. Based on MIRU-VNTR typing, 158 different MIRU-VNTR patterns were identified. Clustering rate and minimum estimate of the proportion of TB caused by recent transmission was 4.1% and 8.1%, respectively. CONCLUSIONS The current study provided new insight into circulating genotypes of M.tb in PTB and EPTB patients in Tehran, Iran. This low percentage of TB transmission rate, demonstrated that mode of TB transmission was mainly associated with reactivation of latent TB rather than recently transmitted infection in this region. There was no significant difference in the association between the genotypes of M.tb strains and the site of the disease.
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213
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Jaillard M, Lima L, Tournoud M, Mahé P, van Belkum A, Lacroix V, Jacob L. A fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events. PLoS Genet 2018; 14:e1007758. [PMID: 30419019 PMCID: PMC6258240 DOI: 10.1371/journal.pgen.1007758] [Citation(s) in RCA: 101] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/26/2018] [Accepted: 10/12/2018] [Indexed: 11/21/2022] Open
Abstract
Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular, it does not require prior annotation or reference genomes. It produces subgraphs representing phenotype-associated genetic variants such as local polymorphisms and mobile genetic elements (MGE). It offers a graphical framework which helps interpret GWAS results. Importantly it is also computationally efficient-experiments took one hour and a half on average. We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis, and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa-along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature. An open-source tool implementing DBGWAS is available at https://gitlab.com/leoisl/dbgwas.
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Affiliation(s)
- Magali Jaillard
- bioMérieux, Marcy l’Étoile, France
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
| | - Leandro Lima
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | | | | | | | - Vincent Lacroix
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
- EPI ERABLE - Inria Grenoble, Rhône-Alpes, France
| | - Laurent Jacob
- Univ Lyon, Université Lyon 1, CNRS, Laboratoire de Biométrie et Biologie Evolutive UMR5558 F-69622 Villeurbanne, France
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214
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Nguyen QH, Contamin L, Nguyen TVA, Bañuls A. Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis. Evol Appl 2018; 11:1498-1511. [PMID: 30344622 PMCID: PMC6183457 DOI: 10.1111/eva.12654] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/25/2018] [Accepted: 05/27/2018] [Indexed: 01/01/2023] Open
Abstract
At present, the successful transmission of drug-resistant Mycobacterium tuberculosis, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains, in human populations, threatens tuberculosis control worldwide. Differently from many other bacteria, M. tuberculosis drug resistance is acquired mainly through mutations in specific drug resistance-associated genes. The panel of mutations is highly diverse, but depends on the affected gene and M. tuberculosis genetic background. The variety of genetic profiles observed in drug-resistant clinical isolates underlines different evolutionary trajectories towards multiple drug resistance, although some mutation patterns are prominent. This review discusses the intrinsic processes that may influence drug resistance evolution in M. tuberculosis, such as mutation rate, drug resistance-associated mutations, fitness cost, compensatory mutations and epistasis. This knowledge should help to better predict the risk of emergence of highly resistant M. tuberculosis strains and to develop new tools and strategies to limit the development and spread of MDR and XDR strains.
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Affiliation(s)
- Quang Huy Nguyen
- Department of Pharmacological, Medical and Agronomical BiotechnologyUniversity of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
| | - Lucie Contamin
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Thi Van Anh Nguyen
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
| | - Anne‐Laure Bañuls
- Institute of Research for DevelopmentUMR MIVEGEC (CNRS‐IRD‐University of Montpellier)MontpellierFrance
- LMI Drug Resistance in South East Asia (LMI DRISA)University of Science and Technology of HanoiVietnam Academy of Science and Technology (VAST)HanoiVietnam
- Department of BacteriologyNational Institute of Hygiene and Epidemiology (NIHE)HanoiVietnam
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215
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Genetics and roadblocks of drug resistant tuberculosis. INFECTION GENETICS AND EVOLUTION 2018; 72:113-130. [PMID: 30261266 DOI: 10.1016/j.meegid.2018.09.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/20/2018] [Accepted: 09/22/2018] [Indexed: 11/22/2022]
Abstract
Considering the extensive evolutionary history of Mycobacterium tuberculosis, anti-Tuberculosis (TB) drug therapy exerts a recent selective pressure. However, in a microorganism devoid of horizontal gene transfer and with a strictly clonal populational structure such as M. tuberculosis the usual, but not sole, path to overcome drug susceptibility is through de novo mutations on a relatively strict set of genes. The possible allelic diversity that can be associated with drug resistance through several mechanisms such as target alteration or target overexpression, will dictate how these genes can become associated with drug resistance. The success demonstrated by this pathogenic microbe in this latter process and its ability to spread is currently one of the major obstacles to an effective TB elimination. This article reviews the action mechanism of the more important anti-TB drugs, including bedaquiline and delamanid, along with new findings on specific resistance mechanisms. With the development, validation and endorsement of new in vitro molecular tests for drug resistance, knowledge on these resistance mechanisms and microevolutionary dynamics leading to the emergence and fixation of drug resistance mutations within the host is highly important. Additionally, the fitness toll imposed by resistance development is also herein discussed together with known compensatory mechanisms. By elucidating the possible mechanisms that enable one strain to reacquire the original fitness levels, it will be theoretically possible to make more informed decisions and develop novel strategies that can force M. tuberculosis microevolutionary trajectory down through a path of decreasing fitness levels.
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216
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Ismail N, Omar SV, Ismail NA, Peters RPH. In vitro approaches for generation of Mycobacterium tuberculosis mutants resistant to bedaquiline, clofazimine or linezolid and identification of associated genetic variants. J Microbiol Methods 2018; 153:1-9. [PMID: 30165087 DOI: 10.1016/j.mimet.2018.08.011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 08/21/2018] [Accepted: 08/21/2018] [Indexed: 11/19/2022]
Abstract
Bedaquiline, clofazimine and linezolid are pertinent drugs for drug-resistant tuberculosis. Drug-resistant mutants provide insight into important resistance acquisition mechanisms. Methods for in vitro Mycobacterium tuberculosis mutant generation are poorly described. Induction (serial passaging) and spontaneous (adapted Luria-Delbrück assay) approaches using M. tuberculosis ATCC reference strains (one fully-susceptible, four unique mono-resistant) were performed. Mutant MIC values were confirmed (MGIT960) and resultant RAVs compared between approaches and to a catalog of previously published RAVs. Mutant MIC values showed a 3-4-fold (induced) and a 1-4-fold (spontaneous) increase compared to baseline. The pyrazinamide-resistant strain had higher baseline MIC values and acquired resistance (≥4-fold) in fewer passages than other strains (induction approach) for bedaquiline. Previously described and novel RAVs in atpE (8 vs. 1) and rv0678 (4 vs. 12) genes were identified in bedaquiline- and clofazimine-resistant mutants. No rv1979c and rv2535c RAVs were identified. Previously described RAVs were identified in rplC and rrl genes for linezolid-resistant mutants. Both approaches successfully led to in vitro mutants with novel RAVs being described in atpE and rv0678 genes. It was observed that pre-existing resistance may influence mutant phenotypic and genotypic characteristics and warrants further attention.
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Affiliation(s)
- N Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa
| | - S V Omar
- Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - N A Ismail
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Centre for Tuberculosis, National Institute for Communicable Diseases, National Health Laboratory Service, Sandringham, Gauteng, South Africa
| | - R P H Peters
- Department of Medical Microbiology, Faculty of Health Sciences, University of Pretoria, 0002 Prinshof, Gauteng, South Africa; Department of Medical Microbiology, Maastricht University Medical Centre, School CAPHRI, Care and Public Health Research Institute, Maastricht University, Maastricht, the Netherlands.
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217
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Godfroid M, Dagan T, Kupczok A. Recombination Signal in Mycobacterium tuberculosis Stems from Reference-guided Assemblies and Alignment Artefacts. Genome Biol Evol 2018; 10:1920-1926. [PMID: 30010866 PMCID: PMC6086087 DOI: 10.1093/gbe/evy143] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 12/31/2022] Open
Abstract
DNA acquisition via genetic recombination is considered advantageous as it has the potential to bring together beneficial mutations that emerge independently within a population. Furthermore, recombination is considered to contribute to the maintenance of genome stability by purging slightly deleterious mutations. The prevalence of recombination differs among prokaryotic species and depends on the accessibility of DNA transfer mechanisms. An exceptional example is the human pathogen Mycobacterium tuberculosis (MTB) where no clear transfer mechanisms have been so far characterized and the presence of recombination is questioned. Here, we analyze completely assembled MTB genomes in search for evidence of recombination. We find that putative recombination events are enriched in strains reconstructed by reference-guided assembly and in regions with unreliable alignments. In addition, assembly and alignment artefacts introduce phylogenetic signals that are conflicting the established MTB phylogeny. Our results reveal that the so far reported recombination events in MTB are likely to stem from methodological artefacts. We conclude that no reliable signal of recombination is observed in the currently available MTB genomes. Moreover, our study demonstrates the limitations of reference-guided genome assembly for phylogenetic reconstructions. Rigorously de novo assembled genomes of high quality are mandatory in order to distinguish true evolutionary signal from noise, in particular for low diversity species such as MTB.
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Affiliation(s)
- Maxime Godfroid
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Tal Dagan
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Anne Kupczok
- Genomic Microbiology Group, Institute of General Microbiology, Kiel University, Kiel, Germany
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218
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Source of the Fitness Defect in Rifamycin-Resistant Mycobacterium tuberculosis RNA Polymerase and the Mechanism of Compensation by Mutations in the β' Subunit. Antimicrob Agents Chemother 2018; 62:AAC.00164-18. [PMID: 29661864 DOI: 10.1128/aac.00164-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 04/09/2018] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium tuberculosis is a critical threat to human health due to the increased prevalence of rifampin resistance (RMPr). Fitness defects have been observed in RMPr mutants with amino acid substitutions in the β subunit of RNA polymerase (RNAP). In clinical isolates, this fitness defect can be ameliorated by the presence of secondary mutations in the double-psi β-barrel (DPBB) domain of the β' subunit of RNAP. To identify factors contributing to the fitness defects observed in vivo, several in vitro RNA transcription assays were utilized to probe initiation, elongation, termination, and 3'-RNA hydrolysis with the wild-type and RMPrM. tuberculosis RNAPs. We found that the less prevalent RMPr mutants exhibit significantly poorer termination efficiencies relative to the wild type, an important factor for proper gene expression. We also found that several mechanistic aspects of transcription of the RMPr mutant RNAPs are impacted relative to the wild type. For the clinically most prevalent mutant, the βS450L mutant, these defects are mitigated by the presence of secondary/compensatory mutations in the DPBB domain of the β' subunit.
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219
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Craggs PD, Mouilleron S, Rejzek M, de Chiara C, Young RJ, Field RA, Argyrou A, de Carvalho LPS. The Mechanism of Acetyl Transfer Catalyzed by Mycobacterium tuberculosis GlmU. Biochemistry 2018; 57:3387-3401. [PMID: 29684272 PMCID: PMC6011181 DOI: 10.1021/acs.biochem.8b00121] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The biosynthetic pathway of peptidoglycan is essential for Mycobacterium tuberculosis. We report here the acetyltransferase substrate specificity and catalytic mechanism of the bifunctional N-acetyltransferase/uridylyltransferase from M. tuberculosis (GlmU). This enzyme is responsible for the final two steps of the synthesis of UDP- N-acetylglucosamine, which is an essential precursor of peptidoglycan, from glucosamine 1-phosphate, acetyl-coenzyme A, and uridine 5'-triphosphate. GlmU utilizes ternary complex formation to transfer an acetyl from acetyl-coenzyme A to glucosamine 1-phosphate to form N-acetylglucosamine 1-phosphate. Steady-state kinetic studies and equilibrium binding experiments indicate that GlmU follows a steady-state ordered kinetic mechanism, with acetyl-coenzyme A binding first, which triggers a conformational change in GlmU, followed by glucosamine 1-phosphate binding. Coenzyme A is the last product to dissociate. Chemistry is partially rate-limiting as indicated by pH-rate studies and solvent kinetic isotope effects. A novel crystal structure of a mimic of the Michaelis complex, with glucose 1-phosphate and acetyl-coenzyme A, helps us to propose the residues involved in deprotonation of glucosamine 1-phosphate and the loop movement that likely generates the active site required for glucosamine 1-phosphate to bind. Together, these results pave the way for the rational discovery of improved inhibitors against M. tuberculosis GlmU, some of which might become candidates for antibiotic discovery programs.
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Affiliation(s)
- Peter D Craggs
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
| | | | | | | | - Robert J Young
- Platform Technology and Science , GlaxoSmithKline , Stevenage , U.K
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220
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221
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Singh P, Kumar SK, Maurya VK, Mehta BK, Ahmad H, Dwivedi AK, Chaturvedi V, Thakur TS, Sinha S. S-Enantiomer of the Antitubercular Compound S006-830 Complements Activity of Frontline TB Drugs and Targets Biogenesis of Mycobacterium tuberculosis Cell Envelope. ACS OMEGA 2017; 2:8453-8465. [PMID: 30023583 PMCID: PMC6045410 DOI: 10.1021/acsomega.7b01281] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 10/31/2017] [Indexed: 05/15/2023]
Abstract
A synthetic molecule S006-830, belonging to the class of thiophene-containing trisubstituted methanes, had shown good in vitro and in vivo bactericidal activity against drug-sensitive and drug-resistant Mycobacterium tuberculosis (Mtb). The molecule had also shown good druglike pharmacokinetic properties. However, S006-830 is a racemic mixture of two enantiomers, one of which could possess a better pharmacological profile than the other. We purified both the enantiomers on a chiral column and observed that S-enantiomer has a significantly higher inhibitory and cidal activity against Mtb than the R-enantiomer. Action of S-S006-830 was "synergistic" for rifampicin and "additive" for isoniazid and ethambutol. The combination of S-S006-830 and rifampicin produced 100% kill of Mtb within 8 days. In a chemical proteomics approach using matrix-bound compound to pull down its target protein(s) from Mtb membrane, FabG4 (β-ketoacyl CoA reductase, EC 1.1.1.100) emerged as the most likely target for S-S006-830. In target validation assays, the compound exhibited 2-fold higher inhibitory concentration for an Mtb construct overexpressing FabG4. In addition, it inhibited mycolic acid biosynthesis and formation of biofilms by Mtb. Molecular docking of S-S006-830 with FabG4 was consistent with the experimental data. These results support the development of S-S006-830 as a novel lead against tuberculosis.
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Affiliation(s)
- Padam Singh
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Shashi Kant Kumar
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Vineet Kumar Maurya
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- Department
of Botany and Microbiology, HNB Garhwal
University, Srinagar, Uttarakhand 246174, India
| | - Basant Kumar Mehta
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Hafsa Ahmad
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Anil Kumar Dwivedi
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
| | - Vinita Chaturvedi
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- E-mail: (V.C.)
| | - Tejender S. Thakur
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- E-mail: (T.S.T.)
| | - Sudhir Sinha
- Division
of Biochemistry, Division of Molecular and Structural Biology, and Division of Pharmaceutics, CSIR-Central Drug Research Institute, Sector-10, Jankipuram Extension, Lucknow 226031, India
- Department
of Clinical Immunology, SGPG Institute of
Medical Sciences, Raebareli Road, Lucknow 226014, India
- E-mail: (S.S.)
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222
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Brites D, Gagneux S. The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:1-26. [DOI: 10.1007/978-3-319-64371-7_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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223
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Banaei-Esfahani A, Nicod C, Aebersold R, Collins BC. Systems proteomics approaches to study bacterial pathogens: application to Mycobacterium tuberculosis. Curr Opin Microbiol 2017; 39:64-72. [PMID: 29032348 DOI: 10.1016/j.mib.2017.09.013] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/15/2017] [Accepted: 09/26/2017] [Indexed: 12/13/2022]
Abstract
Significant developments and improvements in basic and clinical research notwithstanding, infectious diseases still claim at least 13 million lives annually. Classical research approaches have deciphered many molecular mechanisms underlying infection. Today it is increasingly recognized that multiple molecular mechanisms cooperate to constitute a complex system that is used by a given pathogen to interfere with the biochemical processes of the host. Therefore, systems-level approaches now complement the standard molecular biology techniques to investigate pathogens and their interactions with the human host. Here we review omic studies in Mycobacterium tuberculosis, the causative agent of tuberculosis, with a particular focus on proteomic methods and their application to the bacilli. Likewise, the discussed methods are directly portable to other bacterial pathogens.
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Affiliation(s)
- Amir Banaei-Esfahani
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Charlotte Nicod
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; PhD Program in Systems Biology, Life Science Zurich Graduate School, University of Zurich and ETH Zurich, Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland; Faculty of Science, University of Zurich, Zurich, Switzerland.
| | - Ben C Collins
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.
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224
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Borrell S, Trauner A. Strain Diversity and the Evolution of Antibiotic Resistance. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:263-279. [PMID: 29116640 DOI: 10.1007/978-3-319-64371-7_14] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Drug resistance is best thought of as an ongoing biological process. Resistant bacteria must emerge, become established and ultimately transmit in order to be relevant to human health. In this context, genetic diversity can influence the rate and likelihood of resistance emerging; it can also modulate the net physiological impact of resistance and the propensity of an organism to improve any defects that arise from it. Combined, these effects can have an impact on a larger scale, with highly transmissible drug-resistant bacterial strains posing a formidable threat to global health. These considerations are pertinent to the future of tuberculosis control as well. In this chapter, we review our current understanding of the impact of genetic diversity in the broadest sense on the evolution of drug-resistant members of the Mycobacterium tuberculosis complex.
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Affiliation(s)
- Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland. .,University of Basel, Basel, Switzerland.
| | - Andrej Trauner
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4002, Basel, Switzerland.,University of Basel, Basel, Switzerland
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