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Avanzi C, Lécorché E, Rakotomalala FA, Benjak A, Rapelanoro Rabenja F, Ramarozatovo LS, Cauchoix B, Rakoto-Andrianarivelo M, Tió-Coma M, Leal-Calvo T, Busso P, Boy-Röttger S, Chauffour A, Rasamoelina T, Andrianarison A, Sendrasoa F, Spencer JS, Singh P, Dashatwar DR, Narang R, Berland JL, Jarlier V, Salgado CG, Moraes MO, Geluk A, Randrianantoandro A, Cambau E, Cole ST. Population Genomics of Mycobacterium leprae Reveals a New Genotype in Madagascar and the Comoros. Front Microbiol 2020; 11:711. [PMID: 32477280 PMCID: PMC7233131 DOI: 10.3389/fmicb.2020.00711] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 03/26/2020] [Indexed: 01/06/2023] Open
Abstract
Human settlement of Madagascar traces back to the beginning of the first millennium with the arrival of Austronesians from Southeast Asia, followed by migrations from Africa and the Middle East. Remains of these different cultural, genetic, and linguistic legacies are still present in Madagascar and other islands of the Indian Ocean. The close relationship between human migration and the introduction and spread of infectious diseases, a well-documented phenomenon, is particularly evident for the causative agent of leprosy, Mycobacterium leprae. In this study, we used whole-genome sequencing (WGS) and molecular dating to characterize the genetic background and retrace the origin of the M. leprae strains circulating in Madagascar (n = 30) and the Comoros (n = 3), two islands where leprosy is still considered a public health problem and monitored as part of a drug resistance surveillance program. Most M. leprae strains (97%) from Madagascar and Comoros belonged to a new genotype as part of branch 1, closely related to single nucleotide polymorphism (SNP) type 1D, named 1D-Malagasy. Other strains belonged to the genotype 1A (3%). We sequenced 39 strains from nine other countries, which, together with previously published genomes, amounted to 242 genomes that were used for molecular dating. Specific SNP markers for the new 1D-Malagasy genotype were used to screen samples from 11 countries and revealed this genotype to be restricted to Madagascar, with the sole exception being a strain from Malawi. The overall analysis thus ruled out a possible introduction of leprosy by the Austronesian settlers and suggests a later origin from East Africa, the Middle East, or South Asia.
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Affiliation(s)
- Charlotte Avanzi
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, United States
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Emmanuel Lécorché
- AP-HP, Hôpital Lariboisière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France
- Université de Paris, INSERM, IAME UMR1137, Paris, France
| | | | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Fahafahantsoa Rapelanoro Rabenja
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
| | - Lala S. Ramarozatovo
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
- Department of Medecine-Interne, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
| | | | | | - Maria Tió-Coma
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | - Thyago Leal-Calvo
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Philippe Busso
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Stefanie Boy-Röttger
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Aurélie Chauffour
- Sorbonne Université, INSERM U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
| | | | - Aina Andrianarison
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
| | - Fandresena Sendrasoa
- Unité de Soin, de Formations et de Recherche de Dermatologie, University Hospital Joseph Raseta Befelatanana, Antananarivo, Madagascar
| | - John S. Spencer
- Department of Microbiology, Immunology and Pathology, Mycobacteria Research Laboratories, Colorado State University, Fort Collins, CO, United States
| | - Pushpendra Singh
- National Institute of Research in Tribal Health (Indian Council of Medical Research), Jabalpur, India
| | | | - Rahul Narang
- Mahatma Gandhi Institute of Medical Sciences, Wardha, India
| | - Jean-Luc Berland
- Fondation Merieux, Lyon, France
- CIRI, Centre International de Recherche en Infectiologie, Inserm U1111, Lyon, France
| | - Vincent Jarlier
- Sorbonne Université, INSERM U1135, Centre d’Immunologie et des Maladies Infectieuses, CIMI-Paris, Paris, France
- AP-HP, Hôpital Pitié-Salpêtrière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la résistance des Mycobactéries aux Antituberculeux, Paris, France
| | - Claudio G. Salgado
- Laboratório de Dermato-Imunologia Universidade Federal do Pará (UFPA), Marituba, Brazil
| | - Milton O. Moraes
- Laboratório de Hanseníase, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
| | - Annemieke Geluk
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Emmanuelle Cambau
- AP-HP, Hôpital Lariboisière, Service de Bactériologie, Centre National de Référence des Mycobactéries et de la Résistance des Mycobactéries aux Antituberculeux - Laboratoire Associé, Paris, France
- Université de Paris, INSERM, IAME UMR1137, Paris, France
| | - Stewart T. Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- Institut Pasteur, Paris, France
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Rybniker J, Chen JM, Sala C, Hartkoorn RC, Vocat A, Benjak A, Boy-Röttger S, Zhang M, Székely R, Greff Z, Orfi L, Szabadkai I, Pató J, Kéri G, Cole ST. Anticytolytic screen identifies inhibitors of mycobacterial virulence protein secretion. Cell Host Microbe 2015; 16:538-48. [PMID: 25299337 DOI: 10.1016/j.chom.2014.09.008] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 08/20/2014] [Accepted: 09/17/2014] [Indexed: 11/18/2022]
Abstract
Mycobacterium tuberculosis (Mtb) requires protein secretion systems like ESX-1 for intracellular survival and virulence. The major virulence determinant and ESX-1 substrate, EsxA, arrests phagosome maturation and lyses cell membranes, resulting in tissue damage and necrosis that promotes pathogen spread. To identify inhibitors of Mtb protein secretion, we developed a fibroblast survival assay exploiting this phenotype and selected molecules that protect host cells from Mtb-induced lysis without being bactericidal in vitro. Hit compounds blocked EsxA secretion and promoted phagosome maturation in macrophages, thus reducing bacterial loads. Target identification studies led to the discovery of BTP15, a benzothiophene inhibitor of the histidine kinase MprB that indirectly regulates ESX-1, and BBH7, a benzyloxybenzylidene-hydrazine compound. BBH7 affects Mtb metal-ion homeostasis and revealed zinc stress as an activating signal for EsxA secretion. This screening approach extends the target spectrum of small molecule libraries and will help tackle the mounting problem of antibiotic-resistant mycobacteria.
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Affiliation(s)
- Jan Rybniker
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland; 1(st) Department of Internal Medicine, University of Cologne, 50937 Cologne, Germany
| | - Jeffrey M Chen
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Claudia Sala
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ruben C Hartkoorn
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anthony Vocat
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Andrej Benjak
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Stefanie Boy-Röttger
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Ming Zhang
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Rita Székely
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Zoltán Greff
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - László Orfi
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; Department of Pharmaceutical Chemistry, Semmelweis University, Hőgyes Endre u. 9, 1092 Budapest, Hungary
| | - István Szabadkai
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - János Pató
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary
| | - György Kéri
- Vichem Chemie Research Ltd., Herman Otto u. 15, 1022 Budapest, Hungary; MTA-SE Pathobiochemistry Research Group, Department of Medical Chemistry, Semmelweis University, 1094 Budapest, Hungary
| | - Stewart T Cole
- Global Health Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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Chen JM, Zhang M, Rybniker J, Boy-Röttger S, Dhar N, Pojer F, Cole ST. Mycobacterium tuberculosis EspB binds phospholipids and mediates EsxA-independent virulence. Mol Microbiol 2013; 89:1154-66. [PMID: 23869560 DOI: 10.1111/mmi.12336] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/17/2013] [Indexed: 02/06/2023]
Abstract
The type-VII ESX-1 secretion apparatus, encoded by the esx-1 genetic locus, is essential for the export of EsxA and EsxB, two major virulence factors of Mycobacterium tuberculosis. ESX-1 also requires the products of the unlinked espACD operon for optimal function and these proteins are considered integral parts of the secretion apparatus. Here we show that the espACD operon is not necessary for the secretion of EspB, another ESX-1 substrate, and this unimpeded secretion of EspB is associated with significant residual virulence. Upon further investigation, we found that purified EspB can facilitate M. tb virulence even in the absence of EsxA and EsxB, and may do so by binding the bioactive phospholipids phosphatidic acid and phosphatidylserine, both of which are potent bioactive molecules with prominent roles in eukaryotic cell signalling. Our findings provide new insights into the impact of the espACD operon on the ESX-1 apparatus and reveal a distinct virulence function for EspB with novel implications in M. tb-host interactions.
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Affiliation(s)
- Jeffrey M Chen
- École Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
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Neres J, Pojer F, Molteni E, Chiarelli LR, Dhar N, Boy-Röttger S, Buroni S, Fullam E, Degiacomi G, Lucarelli AP, Read RJ, Zanoni G, Edmondson DE, De Rossi E, Pasca MR, McKinney JD, Dyson PJ, Riccardi G, Mattevi A, Cole ST, Binda C. Structural basis for benzothiazinone-mediated killing of Mycobacterium tuberculosis. Sci Transl Med 2013; 4:150ra121. [PMID: 22956199 DOI: 10.1126/scitranslmed.3004395] [Citation(s) in RCA: 138] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The benzothiazinone BTZ043 is a tuberculosis drug candidate with nanomolar whole-cell activity. BTZ043 targets the DprE1 catalytic component of the essential enzyme decaprenylphosphoryl-β-D-ribofuranose-2'-epimerase, thus blocking biosynthesis of arabinans, vital components of mycobacterial cell walls. Crystal structures of DprE1, in its native form and in a complex with BTZ043, reveal formation of a semimercaptal adduct between the drug and an active-site cysteine, as well as contacts to a neighboring catalytic lysine residue. Kinetic studies confirm that BTZ043 is a mechanism-based, covalent inhibitor. This explains the exquisite potency of BTZ043, which, when fluorescently labeled, localizes DprE1 at the poles of growing bacteria. Menaquinone can reoxidize the flavin adenine dinucleotide cofactor in DprE1 and may be the natural electron acceptor for this reaction in the mycobacterium. Our structural and kinetic analysis provides both insight into a critical epimerization reaction and a platform for structure-based design of improved inhibitors.
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Affiliation(s)
- João Neres
- Global Health Institute, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
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Hartkoorn RC, Sala C, Neres J, Pojer F, Magnet S, Mukherjee R, Uplekar S, Boy-Röttger S, Altmann KH, Cole ST. Towards a new tuberculosis drug: pyridomycin - nature's isoniazid. EMBO Mol Med 2012; 4:1032-42. [PMID: 22987724 PMCID: PMC3491834 DOI: 10.1002/emmm.201201689] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 07/26/2012] [Accepted: 07/30/2012] [Indexed: 01/27/2023] Open
Abstract
Tuberculosis, a global threat to public health, is becoming untreatable due to widespread drug resistance to frontline drugs such as the InhA-inhibitor isoniazid. Historically, by inhibiting highly vulnerable targets, natural products have been an important source of antibiotics including potent anti-tuberculosis agents. Here, we describe pyridomycin, a compound produced by Dactylosporangium fulvum with specific cidal activity against mycobacteria. By selecting pyridomycin-resistant mutants of Mycobacterium tuberculosis, whole-genome sequencing and genetic validation, we identified the NADH-dependent enoyl- (Acyl-Carrier-Protein) reductase InhA as the principal target and demonstrate that pyridomycin inhibits mycolic acid synthesis in M. tuberculosis. Furthermore, biochemical and structural studies show that pyridomycin inhibits InhA directly as a competitive inhibitor of the NADH-binding site, thereby identifying a new, druggable pocket in InhA. Importantly, the most frequently encountered isoniazid-resistant clinical isolates remain fully susceptible to pyridomycin, thus opening new avenues for drug development.
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Affiliation(s)
- Ruben C Hartkoorn
- Ecole Polytechnique Fédérale de Lausanne, Global Health Institute, Lausanne, Switzerland
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