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Qin Y, Li T, An P, Ren Z, Xi J, Tang B. Important role of DNA methylation hints at significant potential in tuberculosis. Arch Microbiol 2024; 206:177. [PMID: 38494532 DOI: 10.1007/s00203-024-03888-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 03/19/2024]
Abstract
Tuberculosis (TB), an infectious disease caused by Mycobacterium tuberculosis (Mtb) infection, has persisted as a major global public health threat for millennia. Until now, TB continues to challenge efforts aimed at controlling it, with drug resistance and latent infections being the two main factors hindering treatment efficacy. The scientific community is still striving to understand the underlying mechanisms behind Mtb's drug resistance and latent infection. DNA methylation, a critical epigenetic modification occurring throughout an individual's growth and development, has gained attention following advances in high-throughput sequencing technologies. Researchers have observed abnormal DNA methylation patterns in the host genome during Mtb infection. Given the escalating issue of drug-resistant Mtb, delving into the role of DNA methylation in TB's development is crucial. This review article explores DNA methylation's significance in human growth, development and disease, and its role in regulating Mtb's evolution and infection processes. Additionally, it discusses potential applications of DNA methylation research in tuberculosis.
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Affiliation(s)
- Yuexuan Qin
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Tianyue Li
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Peiyan An
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Zhi Ren
- First Affiliated Hospital of Bengbu Medical University, Bengbu, 233030, Anhui Province, China
| | - Jun Xi
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
| | - Bikui Tang
- School of Life Science, Anhui Province Key Laboratory of Immunology in Chronic Diseases, Anhui Key Laboratory of Infection and Immunity, Bengbu Medical University, Bengbu, 233030, Anhui Province, China.
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2
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Orgeur M, Sous C, Madacki J, Brosch R. Evolution and emergence of Mycobacterium tuberculosis. FEMS Microbiol Rev 2024; 48:fuae006. [PMID: 38365982 PMCID: PMC10906988 DOI: 10.1093/femsre/fuae006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 01/12/2024] [Accepted: 02/13/2024] [Indexed: 02/18/2024] Open
Abstract
Tuberculosis (TB) remains one of the deadliest infectious diseases in human history, prevailing even in the 21st century. The causative agents of TB are represented by a group of closely related bacteria belonging to the Mycobacterium tuberculosis complex (MTBC), which can be subdivided into several lineages of human- and animal-adapted strains, thought to have shared a last common ancestor emerged by clonal expansion from a pool of recombinogenic Mycobacterium canettii-like tubercle bacilli. A better understanding of how MTBC populations evolved from less virulent mycobacteria may allow for discovering improved TB control strategies and future epidemiologic trends. In this review, we highlight new insights into the evolution of mycobacteria at the genus level, describing different milestones in the evolution of mycobacteria, with a focus on the genomic events that have likely enabled the emergence and the dominance of the MTBC. We also review the recent literature describing the various MTBC lineages and highlight their particularities and differences with a focus on host preferences and geographic distribution. Finally, we discuss on putative mechanisms driving the evolution of tubercle bacilli and mycobacteria in general, by taking the mycobacteria-specific distributive conjugal transfer as an example.
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Affiliation(s)
- Mickael Orgeur
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Camille Sous
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
| | - Jan Madacki
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 2000, Unit for Human Evolutionary Genetics, 75015 Paris, France
| | - Roland Brosch
- Institut Pasteur, Université Paris Cité, CNRS UMR 6047, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France
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Brenner E, Sreevatsan S. Cold Cas: reevaluating the occurrence of CRISPR/Cas systems in Mycobacteriaceae. Front Microbiol 2023; 14:1204838. [PMID: 37440893 PMCID: PMC10333696 DOI: 10.3389/fmicb.2023.1204838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/22/2023] [Indexed: 07/15/2023] Open
Abstract
Bacterial CRISPR/Cas systems target foreign genetic elements such as phages and regulate gene expression by some pathogens, even in the host. The system is a marker for evolutionary history and has been used for inferences in Mycobacterium tuberculosis for 30 years. However, knowledge about mycobacterial CRISPR/Cas systems remains limited. It is believed that Type III-A Cas systems are exclusive to Mycobacterium canettii and the M. tuberculosis complex (MTBC) of organisms and that very few of the >200 diverse species of non-tuberculous mycobacteria (NTM) possess any CRISPR/Cas system. This study sought unreported CRISPR/Cas loci across NTM to better understand mycobacterial evolution, particularly in species phylogenetically near the MTBC. An analysis of available mycobacterial genomes revealed that Cas systems are widespread across Mycobacteriaceae and that some species contain multiple types. The phylogeny of Cas loci shows scattered presence in many NTM, with variation even within species, suggesting gains/losses of these loci occur frequently. Cas Type III-A systems were identified in pathogenic Mycobacterium heckeshornense and the geological environmental isolate Mycobacterium SM1. In summary, mycobacterial CRISPR/Cas systems are numerous, Type III-A systems are unreliable as markers for MTBC evolution, and mycobacterial horizontal gene transfer appears to be a frequent source of genetic variation.
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Affiliation(s)
| | - Srinand Sreevatsan
- Department of Pathobiology and Diagnostic Investigation, College of Veterinary Medicine, Michigan State University, East Lansing, MI, United States
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Anes E, Pires D, Mandal M, Azevedo-Pereira JM. ESAT-6 a Major Virulence Factor of Mycobacterium tuberculosis. Biomolecules 2023; 13:968. [PMID: 37371548 DOI: 10.3390/biom13060968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/31/2023] [Accepted: 06/07/2023] [Indexed: 06/29/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb), the causative agent of human tuberculosis (TB), is one of the most successfully adapted human pathogens. Human-to-human transmission occurs at high rates through aerosols containing bacteria, but the pathogen evolved prior to the establishment of crowded populations. Mtb has developed a particular strategy to ensure persistence in the host until an opportunity for transmission arises. It has refined its lifestyle to obviate the need for virulence factors such as capsules, flagella, pili, or toxins to circumvent mucosal barriers. Instead, the pathogen uses host macrophages, where it establishes intracellular niches for its migration into the lung parenchyma and other tissues and for the induction of long-lived latency in granulomas. Finally, at the end of the infection cycle, Mtb induces necrotic cell death in macrophages to escape to the extracellular milieu and instructs a strong inflammatory response that is required for the progression from latency to disease and transmission. Common to all these events is ESAT-6, one of the major virulence factors secreted by the pathogen. This narrative review highlights the recent advances in understanding the role of ESAT-6 in hijacking macrophage function to establish successful infection and transmission and its use as a target for the development of diagnostic tools and vaccines.
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Affiliation(s)
- Elsa Anes
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - David Pires
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
- Center for Interdisciplinary Research in Health, Católica Medical School, Universidade Católica Portuguesa, Estrada Octávio Pato, 2635-631 Rio de Mouro, Portugal
| | - Manoj Mandal
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
| | - José Miguel Azevedo-Pereira
- Host-Pathogen Interactions Unit, Research Institute for Medicines, iMed.ULisboa, Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003 Lisboa, Portugal
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Rehan M, Alhusays A, Serag AM, Boubakri H, Pujic P, Normand P. The cadCA and cadB/DX operons are possibly induced in cadmium resistance mechanism by Frankia alni ACN14a. ELECTRON J BIOTECHN 2022. [DOI: 10.1016/j.ejbt.2022.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
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6
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Wang X, Liu Y. Offense and Defense in Granulomatous Inflammation Disease. Front Cell Infect Microbiol 2022; 12:797749. [PMID: 35846773 PMCID: PMC9277142 DOI: 10.3389/fcimb.2022.797749] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 05/30/2022] [Indexed: 11/13/2022] Open
Abstract
Granulomatous inflammation (GI) diseases are a group of chronic inflammation disorders characterized by focal collections of multinucleated giant cells, epithelioid cells and macrophages, with or without necrosis. GI diseases are closely related to microbes, especially virulent intracellular bacterial infections are important factors in the progression of these diseases. They employ a range of strategies to survive the stresses imposed upon them and persist in host cells, becoming the initiator of the fighting. Microbe-host communication is essential to maintain functions of a healthy host, so defense capacity of hosts is another influence factor, which is thought to combine to determine the result of the fighting. With the development of gene research technology, many human genetic loci were identified to be involved in GI diseases susceptibility, providing more insights into and knowledge about GI diseases. The current review aims to provide an update on the most recent progress in the identification and characterization of bacteria in GI diseases in a variety of organ systems and clinical conditions, and examine the invasion and escape mechanisms of pathogens that have been demonstrated in previous studies, we also review the existing data on the predictive factors of the host, mainly on genetic findings. These strategies may improve our understanding of the mechanisms underlying GI diseases, and open new avenues for the study of the associated conditions in the future.
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Affiliation(s)
- Xinwen Wang
- Shaanxi Clinical Research Center for Oral Diseases, National Clinical Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Oral Medicine, School of Stomatology, The Fourth Military Medical University, Xi'an, China
| | - Yuan Liu
- Shaanxi International Joint Research Center for Oral Diseases, State Key Laboratory of Military Stomatology, Department of Histology and Pathology, School of Stomatology, The Fourth Military Medical University, Xi'an, China
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Pepperell CS. Evolution of Tuberculosis Pathogenesis. Annu Rev Microbiol 2022; 76:661-680. [PMID: 35709500 DOI: 10.1146/annurev-micro-121321-093031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Mycobacterium tuberculosis is a globally distributed, lethal pathogen of humans. The virulence armamentarium of M. tuberculosis appears to have been developed on a scaffold of antiphagocytic defenses found among diverse, mostly free-living species of Mycobacterium. Pathoadaptation was further aided by the modularity, flexibility, and interactivity characterizing mycobacterial effectors and their regulators. During emergence of M. tuberculosis, novel genetic material was acquired, created, and integrated with existing tools. The major mutational mechanisms underlying these adaptations are discussed in this review, with examples. During its evolution, M. tuberculosis lost the ability and/or opportunity to engage in lateral gene transfer, but despite this it has retained the adaptability that characterizes mycobacteria. M. tuberculosis exemplifies the evolutionary genomic mechanisms underlying adoption of the pathogenic niche, and studies of its evolution have uncovered a rich array of discoveries about how new pathogens are made. Expected final online publication date for the Annual Review of Microbiology, Volume 76 is September 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Caitlin S Pepperell
- Division of Infectious Diseases, Department of Medicine, and Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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Patti G, Pellegrino C, Ricciardi A, Novara R, Cotugno S, Papagni R, Guido G, Totaro V, De Iaco G, Romanelli F, Stolfa S, Minardi ML, Ronga L, Fato I, Lattanzio R, Bavaro DF, Gualano G, Sarmati L, Saracino A, Palmieri F, Di Gennaro F. Potential Role of Vitamins A, B, C, D and E in TB Treatment and Prevention: A Narrative Review. Antibiotics (Basel) 2021; 10:1354. [PMID: 34827292 PMCID: PMC8614960 DOI: 10.3390/antibiotics10111354] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 10/31/2021] [Accepted: 11/04/2021] [Indexed: 12/26/2022] Open
Abstract
(1) Background: Tuberculosis (TB) is one of the world's top infectious killers, in fact every year 10 million people fall ill with TB and 1.5 million people die from TB. Vitamins have an important role in vital functions, due to their anti-oxidant, pro-oxidant, anti-inflammatory effects and to metabolic functions. The aim of this review is to discuss and summarize the evidence and still open questions regarding vitamin supplementation as a prophylactic measure in those who are at high risk of Mycobacterium tuberculosis (MTB) infection and active TB; (2) Methods: We conducted a search on PubMed, Scopus, Google Scholar, EMBASE, Cochrane Library and WHO websites starting from March 1950 to September 2021, in order to identify articles discussing the role of Vitamins A, B, C, D and E and Tuberculosis; (3) Results: Supplementation with multiple micronutrients (including zinc) rather than vitamin A alone may be more beneficial in TB. The WHO recommend Pyridoxine (vitamin B6) when high-dose isoniazid is administered. High concentrations of vitamin C sterilize drug-susceptible, MDR and extensively drug-resistant MTB cultures and prevent the emergence of drug persisters; Vitamin D suppresses the replication of mycobacterium in vitro while VE showed a promising role in TB management as a result of its connection with oxidative balance; (4) Conclusions: Our review suggests and encourages the use of vitamins in TB patients. In fact, their use may improve outcomes by helping both nutritionally and by interacting directly and/or indirectly with MTB. Several and more comprehensive trials are needed to reinforce these suggestions.
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Affiliation(s)
- Giulia Patti
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Carmen Pellegrino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Aurelia Ricciardi
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Roberta Novara
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Sergio Cotugno
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Roberta Papagni
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Giacomo Guido
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Valentina Totaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Giuseppina De Iaco
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Federica Romanelli
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Stefania Stolfa
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Maria Letizia Minardi
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Luigi Ronga
- Microbiology and Virology Unit, University of Bari, University Hospital Policlinico, 70124 Bari, Italy; (F.R.); (S.S.); (L.R.)
| | - Ilenia Fato
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Rossana Lattanzio
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Davide Fiore Bavaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Gina Gualano
- National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00161 Rome, Italy;
| | - Loredana Sarmati
- Infectious Diseases Clinic, University Hospital “Tor Vergata”, Department of Systems Medicine, University of Rome Tor Vergata, 00173 Rome, Italy; (M.L.M.); (I.F.); (L.S.)
| | - Annalisa Saracino
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
| | - Fabrizio Palmieri
- National Institute for Infectious Diseases “L. Spallanzani” IRCCS, 00161 Rome, Italy;
| | - Francesco Di Gennaro
- Clinic of Infectious Diseases, Department of Biomedical Sciences and Human Oncology, University of Bari “Aldo Moro”, 70123 Bari, Italy; (G.P.); (C.P.); (A.R.); (R.N.); (S.C.); (R.P.); (G.G.); (V.T.); (G.D.I.); (R.L.); (D.F.B.); (A.S.); (F.D.G.)
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9
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Guan Q, Garbati M, Mfarrej S, AlMutairi T, Laval T, Singh A, Fagbo S, Smyth A, Browne J, urRahman M, Alruwaili A, Hoosen A, Meehan C, Nakajima C, Suzuki Y, Demangel C, Bhatt A, Gordon S, AlAsmari F, Pain A. Insights into the ancestry evolution of the Mycobacterium tuberculosis complex from analysis of Mycobacterium riyadhense. NAR Genom Bioinform 2021; 3:lqab070. [PMID: 34396095 PMCID: PMC8356964 DOI: 10.1093/nargab/lqab070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 06/10/2021] [Accepted: 07/19/2021] [Indexed: 01/08/2023] Open
Abstract
Current evolutionary scenarios posit the emergence of Mycobacterium tuberculosis from an environmental saprophyte through a cumulative process of genome adaptation. Mycobacterium riyadhense, a related bacillus, is being increasingly isolated from human clinical cases with tuberculosis-like symptoms in various parts of the world. To elucidate the evolutionary relationship between M. riyadhense and other mycobacterial species, including members of the M. tuberculosis complex (MTBC), eight clinical isolates of M. riyadhense were sequenced and analyzed. We show, among other features, that M. riyadhense shares a large number of conserved orthologs with M. tuberculosis and shows the expansion of toxin/antitoxin pairs, PE/PPE family proteins compared with other non-tuberculous mycobacteria. We observed M. riyadhense lacks wecE gene which may result in the absence of lipooligosaccharides (LOS) IV. Comparative transcriptomic analysis of infected macrophages reveals genes encoding inducers of Type I IFN responses, such as cytosolic DNA sensors, were relatively less expressed by macrophages infected with M. riyadhense or M. kansasii, compared to BCG or M. tuberculosis. Overall, our work sheds new light on the evolution of M. riyadhense, its relationship to the MTBC, and its potential as a system for the study of mycobacterial virulence and pathogenesis.
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Affiliation(s)
- Qingtian Guan
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | - Musa Garbati
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Sara Mfarrej
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal-Jeddah, 23955, Saudi Arabia
| | | | - Thomas Laval
- Immunobiology of Infection Unit, Institut Pasteur, INSERM U1221, Paris, France
- Université Paris Diderot, Sorbonne Paris Cité, 75205 CEDEX 13, Paris, France
| | | | | | | | - John A Browne
- UCD School of Agriculture and Food Science, University College Dublin, Dublin, D04 W6F6, Ireland
| | | | - Alya Alruwaili
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Anwar Hoosen
- King Fahad Medical City (KFMC), Riyadh, 11525, Saudi Arabia
| | - Conor J Meehan
- School of Chemistry and Biosciences, University of Bradford, Bradford, BD7 1AZ, UK
| | - Chie Nakajima
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | - Yasuhiko Suzuki
- Global Institution for Collaborative Research and Education, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
- Research Center for Zoonosis Control, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo, Japan
| | | | | | | | | | - Arnab Pain
- To whom correspondence should be addressed. Tel: +966 54 470 0687;
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Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli. Nat Microbiol 2021; 6:1082-1093. [PMID: 34294904 DOI: 10.1038/s41564-021-00938-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 06/18/2021] [Indexed: 12/31/2022]
Abstract
Pathogenomic evidence suggests that Mycobacterium tuberculosis (MTB) evolved from an environmental ancestor similar to Mycobacterium canettii, a rare human pathogen. Although the adaptations responsible for this transition are poorly characterized, the ability to persist in humans seems to be important. We set out to identify the adaptations contributing to the evolution of persistence in MTB. We performed an experimental evolution of eight M. canettii populations in mice; four populations were derived from the isolate STB-K (phylogenomically furthest from MTB) and four from STB-D (closest to MTB), which were monitored for 15 and 6 cycles, respectively. We selected M. canettii mutants with enhanced persistence in vivo compared with the parental strains, which were phenotypically closer to MTB. Genome sequencing of 140 mutants and complementation analysis revealed that mutations in two loci were responsible for enhanced persistence. Most of the tested mutants were more resistant than their parental strains to nitric oxide, an important effector of immunity. Modern MTB were similarly more resistant to nitric oxide than M. canettii. Our findings demonstrate phenotypic convergence during experimental evolution of M. canettii, which mirrors natural evolution of MTB. Furthermore, they indicate that the ability to withstand host-induced stresses was key for the emergence of persistent MTB.
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Abstract
Current models of horizontal gene transfer (HGT) in mycobacteria are based on “distributive conjugal transfer” (DCT), an HGT type described in the fast-growing, saprophytic model organism Mycobacterium smegmatis, which creates genome mosaicism in resulting strains and depends on an ESX-1 type VII secretion system. In contrast, only few data on interstrain DNA transfer are available for tuberculosis-causing mycobacteria, for which chromosomal DNA transfer between two Mycobacterium canettii strains was reported, a process which, however, was not observed for Mycobacterium tuberculosis strains. Here, we have studied a wide range of human- and animal-adapted members of the Mycobacterium tuberculosis complex (MTBC) using an optimized filter-based mating assay together with three selected strains of M. canettii that acted as DNA recipients. Unlike in previous approaches, we obtained a high yield of thousands of recombinants containing transferred chromosomal DNA fragments from various MTBC donor strains, as confirmed by whole-genome sequence analysis of 38 randomly selected clones. While the genome organizations of the obtained recombinants showed mosaicisms of donor DNA fragments randomly integrated into a recipient genome backbone, reminiscent of those described as being the result of ESX-1-mediated DCT in M. smegmatis, we observed similar transfer efficiencies when ESX-1-deficient donor and/or recipient mutants were used, arguing that in tubercle bacilli, HGT is an ESX-1-independent process. These findings provide new insights into the genetic events driving the pathoevolution of M. tuberculosis and radically change our perception of HGT in mycobacteria, particularly for those species that show recombinogenic population structures despite the natural absence of ESX-1 secretion systems.
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12
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Rens C, Chao JD, Sexton DL, Tocheva EI, Av-Gay Y. Roles for phthiocerol dimycocerosate lipids in Mycobacterium tuberculosis pathogenesis. MICROBIOLOGY-SGM 2021; 167. [PMID: 33629944 DOI: 10.1099/mic.0.001042] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The success of Mycobacterium tuberculosis as a pathogen is well established: tuberculosis is the leading cause of death by a single infectious agent worldwide. The threat of multi- and extensively drug-resistant bacteria has renewed global concerns about this pathogen and understanding its virulence strategies will be essential in the fight against tuberculosis. The current review will focus on phthiocerol dimycocerosates (PDIMs), a long-known and well-studied group of complex lipids found in the M. tuberculosis cell envelope. Numerous studies show a role for PDIMs in several key steps of M. tuberculosis pathogenesis, with recent studies highlighting its involvement in bacterial virulence, in association with the ESX-1 secretion system. Yet, the mechanisms by which PDIMs help M. tuberculosis to control macrophage phagocytosis, inhibit phagosome acidification and modulate host innate immunity, remain to be fully elucidated.
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Affiliation(s)
- Céline Rens
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Joseph D Chao
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada
| | - Danielle L Sexton
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Elitza I Tocheva
- Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
| | - Yossef Av-Gay
- Division of Infectious Disease, Department of Medicine, The University of British Columbia, Vancouver, Canada.,Department of Microbiology & Immunology, The University of British Columbia, Vancouver, Canada
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13
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Kanabalan RD, Lee LJ, Lee TY, Chong PP, Hassan L, Ismail R, Chin VK. Human tuberculosis and Mycobacterium tuberculosis complex: A review on genetic diversity, pathogenesis and omics approaches in host biomarkers discovery. Microbiol Res 2021; 246:126674. [PMID: 33549960 DOI: 10.1016/j.micres.2020.126674] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 12/09/2020] [Accepted: 12/16/2020] [Indexed: 12/16/2022]
Abstract
Mycobacterium tuberculosis complex (MTBC) refers to a group of mycobacteria encompassing nine members of closely related species that causes tuberculosis in animals and humans. Among the nine members, Mycobacterium tuberculosis (M. tuberculosis) remains the main causative agent for human tuberculosis that results in high mortality and morbidity globally. In general, MTBC species are low in diversity but exhibit distinctive biological differences and phenotypes among different MTBC lineages. MTBC species are likely to have evolved from a common ancestor through insertions/deletions processes resulting in species speciation with different degrees of pathogenicity. The pathogenesis of human tuberculosis is complex and remains poorly understood. It involves multi-interactions or evolutionary co-options between host factors and bacterial determinants for survival of the MTBC. Granuloma formation as a protection or survival mechanism in hosts by MTBC remains controversial. Additionally, MTBC species are capable of modulating host immune response and have adopted several mechanisms to evade from host immune attack in order to survive in humans. On the other hand, current diagnostic tools for human tuberculosis are inadequate and have several shortcomings. Numerous studies have suggested the potential of host biomarkers in early diagnosis of tuberculosis, in disease differentiation and in treatment monitoring. "Multi-omics" approaches provide holistic views to dissect the association of MTBC species with humans and offer great advantages in host biomarkers discovery. Thus, in this review, we seek to understand how the genetic variations in MTBC lead to species speciation with different pathogenicity. Furthermore, we also discuss how the host and bacterial players contribute to the pathogenesis of human tuberculosis. Lastly, we provide an overview of the journey of "omics" approaches in host biomarkers discovery in human tuberculosis and provide some interesting insights on the challenges and directions of "omics" approaches in host biomarkers innovation and clinical implementation.
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Affiliation(s)
- Renuga Devi Kanabalan
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia
| | - Le Jie Lee
- Prima Nexus Sdn. Bhd., Menara CIMB, Jalan Stesen Sentral 2, Kuala Lumpur, Malaysia
| | - Tze Yan Lee
- Perdana University School of Liberal Arts, Science and Technology (PUScLST), Suite 9.2, 9th Floor, Wisma Chase Perdana, Changkat Semantan Damansara Heights, Kuala Lumpur, 50490, Malaysia
| | - Pei Pei Chong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University Lakeside Campus, Subang Jaya, 47500, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia
| | - Rosnah Ismail
- Department of Community Health, Faculty of Medicine, Universiti Kebangsaan Malaysia Medical Centre, Jalan Yaacob Latiff, Bandar Tun Razak, Kuala Lumpur, 56000, Malaysia.
| | - Voon Kin Chin
- Department of Medical Microbiology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang, Selangor, 43400 UPM, Malaysia; Integrative Pharmacogenomics Institute (iPROMISE), Universiti Teknologi MARA, Puncak Alam Campus, Bandar Puncak Alam, Selangor, 42300, Malaysia.
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14
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A sister lineage of the Mycobacterium tuberculosis complex discovered in the African Great Lakes region. Nat Commun 2020; 11:2917. [PMID: 32518235 PMCID: PMC7283319 DOI: 10.1038/s41467-020-16626-6] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 05/13/2020] [Indexed: 02/03/2023] Open
Abstract
The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to have expanded from a common progenitor in Africa. However, the molecular events that accompanied this emergence remain largely unknown. Here, we describe two MTBC strains isolated from patients with multidrug resistant tuberculosis, representing an as-yet-unknown lineage, named Lineage 8 (L8), seemingly restricted to the African Great Lakes region. Using genome-based phylogenetic reconstruction, we show that L8 is a sister clade to the known MTBC lineages. Comparison with other complete mycobacterial genomes indicate that the divergence of L8 preceded the loss of the cobF genome region - involved in the cobalamin/vitamin B12 synthesis - and gene interruptions in a subsequent common ancestor shared by all other known MTBC lineages. This discovery further supports an East African origin for the MTBC and provides additional molecular clues on the ancestral genome reduction associated with adaptation to a pathogenic lifestyle. The human- and animal-adapted lineages of the Mycobacterium tuberculosis complex (MTBC) are thought to be evolved from a common progenitor in Africa. Here, the authors identify two MTBC strains isolated from patients with multidrug-resistant tuberculosis, representing an as-yet-unknown lineage further supporting an East African origin for the MTBC.
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15
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Sapriel G, Brosch R. Shared Pathogenomic Patterns Characterize a New Phylotype, Revealing Transition toward Host-Adaptation Long before Speciation of Mycobacterium tuberculosis. Genome Biol Evol 2020; 11:2420-2438. [PMID: 31368488 PMCID: PMC6736058 DOI: 10.1093/gbe/evz162] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2019] [Indexed: 02/06/2023] Open
Abstract
Tuberculosis remains one of the deadliest infectious diseases of humanity. To better understand the evolutionary history of host-adaptation of tubercle bacilli (MTB), we sought for mycobacterial species that were more closely related to MTB than the previously used comparator species Mycobacterium marinum and Mycobacterium kansasii. Our phylogenomic approach revealed some recently sequenced opportunistic mycobacterial pathogens, Mycobacterium decipiens, Mycobacterium lacus, Mycobacterium riyadhense, and Mycobacterium shinjukuense, to constitute a common clade with MTB, hereafter called MTB-associated phylotype (MTBAP), from which MTB have emerged. Multivariate and clustering analyses of genomic functional content revealed that the MTBAP lineage forms a clearly distinct cluster of species that share common genomic characteristics, such as loss of core genes, shift in dN/dS ratios, and massive expansion of toxin–antitoxin systems. Consistently, analysis of predicted horizontal gene transfer regions suggests that putative functions acquired by MTBAP members were markedly associated with changes in microbial ecology, for example adaption to intracellular stress resistance. Our study thus considerably deepens our view on MTB evolutionary history, unveiling a decisive shift that promoted conversion to host-adaptation among ancestral founders of the MTBAP lineage long before Mycobacterium tuberculosis has adapted to the human host.
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Affiliation(s)
- Guillaume Sapriel
- UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, CNRS UMR 3525, Paris, France
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16
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Fieweger RA, Wilburn KM, VanderVen BC. Comparing the Metabolic Capabilities of Bacteria in the Mycobacterium tuberculosis Complex. Microorganisms 2019; 7:E177. [PMID: 31216777 PMCID: PMC6617402 DOI: 10.3390/microorganisms7060177] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2019] [Revised: 06/10/2019] [Accepted: 06/15/2019] [Indexed: 02/06/2023] Open
Abstract
Pathogenic mycobacteria are known for their ability to maintain persistent infections in various mammals. The canonical pathogen in this genus is Mycobacterium tuberculosis and this bacterium is particularly successful at surviving and replicating within macrophages. Here, we will highlight the metabolic processes that M. tuberculosis employs during infection in macrophages and compare these findings with what is understood for other pathogens in the M. tuberculosis complex.
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Affiliation(s)
- Rachael A Fieweger
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Kaley M Wilburn
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
| | - Brian C VanderVen
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA.
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17
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Poeta P, Silva V, Guedes A, Eduardo Pereira J, Cláudia Coelho A, Igrejas G. Tuberculosis in the 21th century: Current status of diagnostic methods. Exp Lung Res 2019; 44:352-360. [PMID: 30663432 DOI: 10.1080/01902148.2018.1545880] [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] [Indexed: 10/27/2022]
Abstract
Tuberculosis is an infectious bacterial disease with a high mortality rate worldwide constituting a serious public health problem. The diagnostic methods commonly used by health professionals are slow and expensive and the results may take about sixty days which will cause a delay in administrating the most proper treatment to the patient, as well as increase health care costs and infection transmission possibility. Patients infected simultaneously with human immunodeficiency virus and Mycobacterium tuberculosis are a constant and worrying challenge for the scientific community which will research and develop new methods of diagnosis, new drugs and new therapies. Nowadays there are new tuberculosis diagnosis methods and some of which are already in clinical trial phases. These methods have high sensitivity, but do not replace the microbiological examination for isolation and culture of Mycobacterium spp. However, in clinical practice, microbiological, imaging, clinical and epidemiological data integration provide the best diagnosis and treatment possible. Consequently, throughout this paper, the different methods of diagnosis of human tuberculosis with its advantages and disadvantages will be covered, describing new omics and ultra-fast methods to increase knowledge and obtain a rapid diagnosis of tuberculosis.
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Affiliation(s)
- Patrícia Poeta
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal
| | - Vanessa Silva
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
| | - Andreia Guedes
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal
| | - José Eduardo Pereira
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Ana Cláudia Coelho
- a Department of Veterinary Sciences , University of Trás-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,e CECAV, Centro de Ciência Animal e Veterinária , Universidade de Trás-os-Montes e Alto Douro , Vila Real , Portugal
| | - Gilberto Igrejas
- b Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro , Vila Real , Portugal.,c Functional Genomics and Proteomics Unit , University of Tras-os-Montes and Alto Douro (UTAD) , Vila Real , Portugal.,d Associated Laboratory for Green Chemistry (LAQV-REQUIMTE) , University NOVA of Lisboa , Lisboa , Caparica, Portugal
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18
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Abstract
Humans encounter mycobacterial species due to their ubiquity in different environmental niches. In many individuals, pathogenic mycobacterial species may breach our first-line barrier defenses of the innate immune system and modulate the activation of phagocytes to cause disease of the respiratory tract or the skin and soft tissues, sometimes resulting in disseminated infection. Cutaneous mycobacterial infections may cause a wide range of clinical manifestations, which are divided into four main disease categories: (i) cutaneous manifestations of Mycobacterium tuberculosis infection, (ii) Buruli ulcer caused by Mycobacterium ulcerans and other related slowly growing mycobacteria, (iii) leprosy caused by Mycobacterium leprae and Mycobacterium lepromatosis, and (iv) cutaneous infections caused by rapidly growing mycobacteria. Clinically, cutaneous mycobacterial infections present with widely different clinical presentations, including cellulitis, nonhealing ulcers, subacute or chronic nodular lesions, abscesses, superficial lymphadenitis, verrucous lesions, and other types of findings. Mycobacterial infections of the skin and subcutaneous tissue are associated with important stigma, deformity, and disability. Geography-based environmental exposures influence the epidemiology of cutaneous mycobacterial infections. Cutaneous tuberculosis exhibits different clinical phenotypes acquired through different routes, including via extrinsic inoculation of the tuberculous bacilli and dissemination to the skin from other sites, or represents hypersensitivity reactions to M. tuberculosis infection. In many settings, leprosy remains an important cause of neurological impairment, deformity, limb loss, and stigma. Mycobacterium lepromatosis, a mycobacterial species related to M. leprae, is linked to diffuse lepromatous leprosy of Lucio and Latapí. Mycobacterium ulcerans produces a mycolactone toxin that leads to subcutaneous tissue destruction and immunosuppression, resulting in deep ulcerations that often produce substantial disfigurement and disability. Mycobacterium marinum, a close relative of M. ulcerans, is an important cause of cutaneous sporotrichoid nodular lymphangitic lesions. Among patients with advanced immunosuppression, Mycobacterium kansasii, the Mycobacterium avium-intracellulare complex, and Mycobacterium haemophilum may cause cutaneous or disseminated disease. Rapidly growing mycobacteria, including the Mycobacterium abscessus group, Mycobacterium chelonei, and Mycobacterium fortuitum, are increasingly recognized pathogens in cutaneous infections associated particularly with plastic surgery and cosmetic procedures. Skin biopsies of cutaneous lesions to identify acid-fast staining bacilli and cultures represent the cornerstone of diagnosis. Additionally, histopathological evaluation of skin biopsy specimens may be useful in identifying leprosy, Buruli ulcer, and cutaneous tuberculosis. Molecular assays are useful in some cases. The treatment for cutaneous mycobacterial infections depends on the specific pathogen and therefore requires a careful consideration of antimicrobial choices based on official treatment guidelines.
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19
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Ates LS, Dippenaar A, Sayes F, Pawlik A, Bouchier C, Ma L, Warren RM, Sougakoff W, Majlessi L, van Heijst JWJ, Brossier F, Brosch R. Unexpected Genomic and Phenotypic Diversity of Mycobacterium africanum Lineage 5 Affects Drug Resistance, Protein Secretion, and Immunogenicity. Genome Biol Evol 2018; 10:1858-1874. [PMID: 30010947 PMCID: PMC6071665 DOI: 10.1093/gbe/evy145] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/10/2018] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium africanum consists of Lineages L5 and L6 of the Mycobacterium tuberculosis complex (MTBC) and causes human tuberculosis in specific regions of Western Africa, but is generally not transmitted in other parts of the world. Since M. africanum is evolutionarily closely placed between the globally dispersed Mycobacterium tuberculosis and animal-adapted MTBC-members, these lineages provide valuable insight into M. tuberculosis evolution. Here, we have collected 15 M. africanum L5 strains isolated in France over 4 decades. Illumina sequencing and phylogenomic analysis revealed a previously underappreciated diversity within L5, which consists of distinct sublineages. L5 strains caused relatively high levels of extrapulmonary tuberculosis and included multi- and extensively drug-resistant isolates, especially in the newly defined sublineage L5.2. The specific L5 sublineages also exhibit distinct phenotypic characteristics related to in vitro growth, protein secretion and in vivo immunogenicity. In particular, we identified a PE_PGRS and PPE-MPTR secretion defect specific for sublineage L5.2, which was independent of PPE38. Furthermore, L5 isolates were able to efficiently secrete and induce immune responses against ESX-1 substrates contrary to previous predictions. These phenotypes of Type VII protein secretion and immunogenicity provide valuable information to better link genome sequences to phenotypic traits and thereby understand the evolution of the MTBC.
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Affiliation(s)
- Louis S Ates
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Anzaan Dippenaar
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Fadel Sayes
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Alexandre Pawlik
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Christiane Bouchier
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Laurence Ma
- Department of Genomes and Genetics, Institut Pasteur, Genomics Platform, Paris, France
| | - Robin M Warren
- DST-NRF Centre of Excellence for Biomedical Tuberculosis Research; South African Medical Research Council Centre for Tuberculosis Research; Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Wladimir Sougakoff
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Laleh Majlessi
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
| | - Jeroen W J van Heijst
- Department of Experimental Immunology, Amsterdam UMC, University of Amsterdam, Amsterdam Infection & Immunity Institute, Amsterdam, The Netherlands
| | - Florence Brossier
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
- Sorbonne Universités, INSERM, Centre d'Immunologie et des Maladies Infectieuses, CIMI-Paris, Team 13 (Bacteriology), Paris, France
- Laboratoire de Bactériologie-Hygiène, Centre National de Référence des Mycobactéries (NRC MyRMA), Hôpitaux Universitaires Pitié-Salpêtrière – Charles Foix, Paris, France
| | - Roland Brosch
- Department of Genomes and Genetics, Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, CNRS UMR3525, Paris, France
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20
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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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21
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Gray TA, Derbyshire KM. Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT. Mol Microbiol 2018; 108:601-613. [PMID: 29669186 DOI: 10.1111/mmi.13971] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/14/2018] [Indexed: 12/16/2022]
Abstract
This review discusses a novel form of horizontal gene transfer (HGT) found in mycobacteria called Distributive Conjugal Transfer (DCT). While satisfying the criteria for conjugation, DCT occurs by a mechanism so distinct from oriT-mediated conjugation that it could be considered a fourth category of HGT. DCT involves the transfer of chromosomal DNA between mycobacteria and, most significantly, generates transconjugants with mosaic genomes of the parental strains. Multiple segments of donor chromosomal DNA can be co-transferred regardless of their location or the genetic selection and, as a result, the transconjugant genome contains many donor-derived segments; hence the name DCT. This distinguishing feature of DCT separates it from the other known mechanisms of HGT, which generally result in the introduction of a single, defined segment of DNA into the recipient chromosome (Fig. ). Moreover, these mosaic progeny are generated from a single conjugal event, which provides enormous capacity for rapid adaptation and evolution, again distinguishing it from the three classical modes of HGT. Unsurprisingly, the unusual mosaic products of DCT are generated by a conjugal mechanism that is also unusual. Here, we will describe the unique features of DCT and contrast those to other mechanisms of HGT, both from a mechanistic and an evolutionary perspective. Our focus will be on transfer of chromosomal DNA, as opposed to plasmid mobilization, because DCT mediates transfer of chromosomal DNA and is a chromosomally encoded process.
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Affiliation(s)
- Todd A Gray
- New York State Department of Health, Wadsworth Center, Albany, NY 12201, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
| | - Keith M Derbyshire
- New York State Department of Health, Wadsworth Center, Albany, NY 12201, USA.,Department of Biomedical Sciences, University at Albany, Albany, NY 12201, USA
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22
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DNA Replication Fidelity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1019:247-262. [PMID: 29116639 DOI: 10.1007/978-3-319-64371-7_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Mycobacterium tuberculosis is genetically isolated, with no evidence for horizontal gene transfer or the acquisition of episomal genetic information in the modern evolution of strains of the Mycobacterium tuberculosis complex. When considered in the context of the specific features of the disease M. tuberculosis causes (e.g., transmission via cough aerosol, replication within professional phagocytes, subclinical persistence, and stimulation of a destructive immune pathology), this implies that to understand the mechanisms ensuring preservation of genomic integrity in infecting mycobacterial populations is to understand the source of genetic variation, including the emergence of microdiverse sub-populations that may be linked to the acquisition of drug resistance. In this chapter, we focus on mechanisms involved in maintaining DNA replication fidelity in M. tuberculosis, and consider the potential to target components of the DNA replication machinery as part of novel therapeutic regimens designed to curb the emerging threat of drug-resistance.
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23
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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.
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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
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Abstract
Members of the Mycobacterium tuberculosis complex (MTBC) have evolved causing tuberculosis (TB) in different mammalian hosts. MTBC ecotypes have adapted to diverse animal species, with M. bovis being the most common cause of TB in livestock. Cattle-to-human transmission of M. bovis through ingestion of raw milk was common before introduction of the pasteurization process. TB in humans is mainly caused by M. tuberculosis. This bacterium is considered a genetically clonal pathogen that has coevolved with humans due to its ability to manipulate and subvert the immune response. TB is a major public health problem due to airborne person-to-person transmission of M. tuberculosis. The essential yet unanswered question on the natural history of TB is when M. tuberculosis decides to establish latent infection in the host (resambling the lysogenic cycle of lambda phage) or to cause pulmonary disease (comparable to the lytic cycle of lambda phage). In this latter case, M. tuberculosis kills the host with the aim of achieving transmission to new hosts. Combating the TB epidemic requires stopping transmission. M. bovis BCG, the present vaccine against TB, is derived from M. bovis and only protects against disseminated forms of TB. Thus, a priority in TB research is development of new effective vaccines to prevent pulmonary disease. Attenuated vaccines based on M. tuberculosis as MTBVAC are potential candidates that could contribute to break the TB transmission cycle.
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Laencina L, Dubois V, Le Moigne V, Viljoen A, Majlessi L, Pritchard J, Bernut A, Piel L, Roux AL, Gaillard JL, Lombard B, Loew D, Rubin EJ, Brosch R, Kremer L, Herrmann JL, Girard-Misguich F. Identification of genes required for Mycobacterium abscessus growth in vivo with a prominent role of the ESX-4 locus. Proc Natl Acad Sci U S A 2018; 115:E1002-E1011. [PMID: 29343644 PMCID: PMC5798338 DOI: 10.1073/pnas.1713195115] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mycobacterium abscessus, a rapidly growing mycobacterium (RGM) and an opportunistic human pathogen, is responsible for a wide spectrum of clinical manifestations ranging from pulmonary to skin and soft tissue infections. This intracellular organism can resist the bactericidal defense mechanisms of amoebae and macrophages, an ability that has not been observed in other RGM. M. abscessus can up-regulate several virulence factors during transient infection of amoebae, thereby becoming more virulent in subsequent respiratory infections in mice. Here, we sought to identify the M. abscessus genes required for replication within amoebae. To this end, we constructed and screened a transposon (Tn) insertion library of an M. abscessus subspecies massiliense clinical isolate for attenuated clones. This approach identified five genes within the ESX-4 locus, which in M. abscessus encodes an ESX-4 type VII secretion system that exceptionally also includes the ESX conserved EccE component. To confirm the screening results and to get further insight into the contribution of ESX-4 to M. abscessus growth and survival in amoebae and macrophages, we generated a deletion mutant of eccB4 that encodes a core structural element of ESX-4. This mutant was less efficient at blocking phagosomal acidification than its parental strain. Importantly, and in contrast to the wild-type strain, it also failed to damage phagosomes and showed reduced signs of phagosome-to-cytosol contact, as demonstrated by a combination of cellular and immunological assays. This study attributes an unexpected and genuine biological role to the underexplored mycobacterial ESX-4 system and its substrates.
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Affiliation(s)
- Laura Laencina
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Violaine Dubois
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Vincent Le Moigne
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Albertus Viljoen
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Laleh Majlessi
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, 75015 Paris, France
| | - Justin Pritchard
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Audrey Bernut
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
| | - Laura Piel
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
| | - Anne-Laure Roux
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
| | - Jean-Louis Gaillard
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
| | - Bérengère Lombard
- Laboratoire de spectrométrie de masse protéomique, Institut Curie, Paris Science and Letters Research University, 75248 Paris, France
| | - Damarys Loew
- Laboratoire de spectrométrie de masse protéomique, Institut Curie, Paris Science and Letters Research University, 75248 Paris, France
| | - Eric J Rubin
- Department of Immunology and Infectious Disease, Harvard T.H. Chan School of Public Health, Boston, MA 02115
| | - Roland Brosch
- Unité de Pathogénomique Mycobactérienne, Institut Pasteur, 75015 Paris, France
| | - Laurent Kremer
- Institut de Recherche en Infectiologie de Montpellier, Université de Montpellier, CNRS UMR 9004, 34293 Montpellier, France
- INSERM, Institut de Recherche en Infectiologie de Montpellier, 34293 Montpellier, France
| | - Jean-Louis Herrmann
- Université de Versailles Saint Quentin en Yvelines, INSERM UMR1173, 78000 Versailles, France;
- Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Ile de France Ouest, Ambroise Paré, Boulogne and Raymond Poincaré, 92380 Garches, France
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Horizontal acquisition of a hypoxia-responsive molybdenum cofactor biosynthesis pathway contributed to Mycobacterium tuberculosis pathoadaptation. PLoS Pathog 2017; 13:e1006752. [PMID: 29176894 PMCID: PMC5720804 DOI: 10.1371/journal.ppat.1006752] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 12/07/2017] [Accepted: 11/13/2017] [Indexed: 12/16/2022] Open
Abstract
The unique ability of the tuberculosis (TB) bacillus, Mycobacterium tuberculosis, to persist for long periods of time in lung hypoxic lesions chiefly contributes to the global burden of latent TB. We and others previously reported that the M. tuberculosis ancestor underwent massive episodes of horizontal gene transfer (HGT), mostly from environmental species. Here, we sought to explore whether such ancient HGT played a part in M. tuberculosis evolution towards pathogenicity. We were interested by a HGT-acquired M. tuberculosis-specific gene set, namely moaA1-D1, which is involved in the biosynthesis of the molybdenum cofactor. Horizontal acquisition of this gene set was striking because homologues of these moa genes are present all across the Mycobacterium genus, including in M. tuberculosis. Here, we discovered that, unlike their paralogues, the moaA1-D1 genes are strongly induced under hypoxia. In vitro, a M. tuberculosis moaA1-D1-null mutant has an impaired ability to respire nitrate, to enter dormancy and to survive in oxygen-limiting conditions. Conversely, heterologous expression of moaA1-D1 in the phylogenetically closest non-TB mycobacterium, Mycobacterium kansasii, which lacks these genes, improves its capacity to respire nitrate and grants it with a marked ability to survive oxygen depletion. In vivo, the M. tuberculosis moaA1-D1-null mutant shows impaired survival in hypoxic granulomas in C3HeB/FeJ mice, but not in normoxic lesions in C57BL/6 animals. Collectively, our results identify a novel pathway required for M. tuberculosis resistance to host-imposed stress, namely hypoxia, and provide evidence that ancient HGT bolstered M. tuberculosis evolution from an environmental species towards a pervasive human-adapted pathogen. Mycobacterium tuberculosis, the etiological agent of tuberculosis (TB), can persist for years and even decades in the lungs of its human host. Here we report that a unique M. tuberculosis gene cluster involved in the synthesis of the molybdenum cofactor, a cofactor for several oxidoreductases including the nitrate reductase, allows this major pathogen to respire nitrate and to persist in a dormant state under hypoxia, a stress condition encountered in lung TB lesions. Strikingly the M. tuberculosis ancestor, which most likely was an environmental harmless bacterium, acquired this gene cluster, together with its hypoxia-responsive transcriptional regulator, horizontally from neighboring bacteria. Our results uncover a key step in M. tuberculosis evolution towards pathogenicity.
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Ready Experimental Translocation of Mycobacterium canettii Yields Pulmonary Tuberculosis. Infect Immun 2017; 85:IAI.00507-17. [PMID: 28923895 DOI: 10.1128/iai.00507-17] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 09/14/2017] [Indexed: 11/20/2022] Open
Abstract
Mycobacterium canettii, which has a smooth colony morphology, is the tuberculous organism retaining the most genetic traits from the putative last common ancestor of the rough-morphology Mycobacterium tuberculosis complex. To explore whether M. canettii can infect individuals by the oral route, mice were fed phosphate-buffered saline or 106M. canettii mycobacteria and sacrificed over a 28-day experiment. While no M. canettii was detected in negative controls, M. canettii-infected mice yielded granuloma-like lesions for 4/4 lungs at days 14 and 28 postinoculation (p.i.) and positive PCR detection of M. canettii for 5/8 mesenteric lymph nodes at days 1 and 3 p.i. and 5/6 pooled stools collected from day 1 to day 28 p.i. Smooth M. canettii colonies grew from 68% of lungs and 36% of spleens and cervical lymph nodes but fewer than 20% of axillary lymph nodes, livers, brown fat samples, kidneys, or blood samples throughout the 28-day experiment. Ready translocation in mice after digestive tract challenge demonstrates the potential of ingested M. canettii organisms to relocate to distant organs and lungs. The demonstration of this relocation supports the possibility that populations may be infected by environmental M. canettii.
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Shaping the niche in macrophages: Genetic diversity of the M. tuberculosis complex and its consequences for the infected host. Int J Med Microbiol 2017; 308:118-128. [PMID: 28969988 DOI: 10.1016/j.ijmm.2017.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/12/2022] Open
Abstract
Pathogenic mycobacteria of the Mycobacterium tuberculosis complex (MTBC) have co-evolved with their individual hosts and are able to transform the hostile environment of the macrophage into a permissive cellular habitat. The impact of MTBC genetic variability has long been considered largely unimportant in TB pathogenesis. Members of the MTBC can now be distinguished into three major phylogenetic groups consisting of 7 phylogenetic lineages and more than 30 so called sub-lineages/subgroups. MTBC genetic diversity indeed influences the transmissibility and virulence of clinical MTBC isolates as well as the immune response and the clinical outcome. Here we review the genetic diversity and epidemiology of MTBC strains and describe the current knowledge about the host immune response to infection with MTBC clinical isolates using human and murine experimental model systems in vivo and in vitro. We discuss the role of innate cytokines in detail and portray two in our group recently developed approaches to characterize the intracellular niches of MTBC strains. Characterizing the niches and deciphering the strategies of MTBC strains to transform an antibacterial effector cell into a permissive cellular habitat offers the opportunity to identify strain- and lineage-specific key factors which may represent targets for novel antimicrobial or host directed therapies for tuberculosis.
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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Abstract
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.
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Jankute M, Nataraj V, Lee OYC, Wu HHT, Ridell M, Garton NJ, Barer MR, Minnikin DE, Bhatt A, Besra GS. The role of hydrophobicity in tuberculosis evolution and pathogenicity. Sci Rep 2017; 7:1315. [PMID: 28465507 PMCID: PMC5431016 DOI: 10.1038/s41598-017-01501-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/29/2017] [Indexed: 12/24/2022] Open
Abstract
The evolution of tubercle bacilli parallels a route from environmental Mycobacterium kansasii, through intermediate "Mycobacterium canettii", to the modern Mycobacterium tuberculosis complex. Cell envelope outer membrane lipids change systematically from hydrophilic lipooligosaccharides and phenolic glycolipids to hydrophobic phthiocerol dimycocerosates, di- and pentaacyl trehaloses and sulfoglycolipids. Such lipid changes point to a hydrophobic phenotype for M. tuberculosis sensu stricto. Using Congo Red staining and hexadecane-aqueous buffer partitioning, the hydrophobicity of rough morphology M. tuberculosis and Mycobacterium bovis strains was greater than smooth "M. canettii" and M. kansasii. Killed mycobacteria maintained differential hydrophobicity but defatted cells were similar, indicating that outer membrane lipids govern overall hydrophobicity. A rough M. tuberculosis H37Rv ΔpapA1 sulfoglycolipid-deficient mutant had significantly diminished Congo Red uptake though hexadecane-aqueous buffer partitioning was similar to H37Rv. An M. kansasii, ΔMKAN27435 partially lipooligosaccharide-deficient mutant absorbed marginally more Congo Red dye than the parent strain but was comparable in partition experiments. In evolving from ancestral mycobacteria, related to "M. canettii" and M. kansasii, modern M. tuberculosis probably became more hydrophobic by increasing the proportion of less polar lipids in the outer membrane. Importantly, such a change would enhance the capability for aerosol transmission, affecting virulence and pathogenicity.
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Affiliation(s)
- Monika Jankute
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Vijayashankar Nataraj
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malin Ridell
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Natalie J Garton
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Apoorva Bhatt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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Affiliation(s)
- Timothy P Stinear
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC 3000, Australia
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75015 Paris, France.
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Cvetkovikj I, Mrenoshki S, Krstevski K, Djadjovski I, Angjelovski B, Popova Z, Janevski A, Dodovski A, Cvetkovikj A. Bovine Tuberculosis in the Republic of Macedonia: Postmortem, Microbiological and Molecular Study in Slaughtered Reactor Cattle. MACEDONIAN VETERINARY REVIEW 2017. [DOI: 10.1515/macvetrev-2016-0097] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Abstract
Bovine tuberculosis is a chronic infectious disease in cattle caused mainly by Mycobacterium bovis and to a lesser extent by Mycobacterium caprae. The other members of the Mycobacterium tuberculosis complex (MTBC) can also cause the disease in domestic and wild animals and all of them have a zoonotic potential. The main purpose of the study was to determine the presence and distribution of the tuberculous lesions in reactor cattle, and to isolate and identify the causative agents of bovine tuberculosis in the Republic of Macedonia. Lymph nodes and affected organs from 188 reactor cattle slaughtered due to a positive intradermal comparative cervical tuberculin test were analyzed by detection of tuberculous lesions, followed by isolation and molecular identification of the isolated mycobacteria. The isolation was performed on selective media - Lowenstein Jensen with glycerol, Lowenstein Jensen without glycerol and Stonebrink medium supplemented with pyruvate. The molecular identification of the MTBC members was performed by analysis of the Regions of difference (RD1, RD9 and RD4) and detection of single nucleotide polymorphisms in the lepA gene for Mycobacterium caprae. Typical tuberculous lesions were detected in 62 animals (33.0%) and the lesions were most prevalent in the mediastinal lymph nodes (47.5%). The isolated mycobacteria in the MTBC were identified as Mycobacterium bovis and Mycobacterium caprae and were found in both animals with visible lesions (82.2%) and animals without visible lesions (27.7%). The slaughterhouse postmortem examinations and laboratory investigations should be included on regular bases in order to improve the National eradication program.
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Affiliation(s)
- Iskra Cvetkovikj
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Slavcho Mrenoshki
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Kiril Krstevski
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Igor Djadjovski
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Branko Angjelovski
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Zagorka Popova
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Aleksandar Janevski
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Aleksandar Dodovski
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
| | - Aleksandar Cvetkovikj
- Veterinary Institute, Faculty of Veterinary Medicine , Ss. Cyril and Methodius University in Skopje , Lazar Pop Trajkov 5-7, 1000 Skopje , Macedonia (the former Yugoslav Republic of)
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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Supply P, Brosch R. The Biology and Epidemiology of Mycobacterium canettii. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:27-41. [PMID: 29116628 DOI: 10.1007/978-3-319-64371-7_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Genome-based insights into the evolution of Mycobacterium tuberculosis and other tuberculosis-causing mycobacteria are constantly increasing. In particular, the recent genomic and functional characterization of several Myocbacterium canettii strains, which are thought to resemble in many aspects the putative common ancestor of the members of the M. tuberculosis complex (MTBC), has consolidated a plausible scenario of the early evolution of tuberculosis-causing mycobacteria, in which the clonal MTBC, comprising numerous key pathogens of mammalian hosts, has evolved from a generalist mycobacterium living in the environment. These studies also have considerably enriched our knowledge on selected molecular events that likely have contributed to the incursion, maintenance and spread of the MTBC members in diverse mammalian hosts. Here, we summarize and discuss recently revealed molecular and evolutionary aspects and emphasize the vast utility of M. canettii strains for identifying the mechanisms that contributed to the global emergence of M. tuberculosis as one of the most important human pathogens.
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Affiliation(s)
- Philip Supply
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724, Paris Cedex 15, France.
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Ates LS, Brosch R. Discovery of the type VII ESX-1 secretion needle? Mol Microbiol 2016; 103:7-12. [PMID: 27859892 DOI: 10.1111/mmi.13579] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/11/2016] [Indexed: 01/03/2023]
Abstract
Mycobacterium tuberculosis, the etiological agent of human tuberculosis, harbours five ESAT-6/type VII secretion (ESX/T7S) systems. The first esx gene clusters were identified during the genome-sequencing project of M. tuberculosis H37Rv. Follow-up studies revealed additional genes playing important roles in ESX/T7S systems. Among the latter genes, one can find those that encode Pro-Glu (PE) and Pro-Pro-Glu (PPE) proteins as well as a gene cluster that is encoded >260 kb upstream of the esx-1 locus and encodes ESX-1 secretion-associated proteins EspA (Rv3616c), EspC (Rv3615c) and EspD (Rv3614c). The espACD cluster has been suggested to have an important function in ESX-1 secretion since EspA-EspC and EsxA-EsxB are mutually co-dependent on each other for secretion. However, the molecular mechanism of this co-dependence and interaction between the substrates remained unknown. In this issue of Molecular Microbiology, Lou and colleagues show that EspC forms high-molecular weight polymerization complexes that resemble selected components of type II, III and/or IV secretion systems of Gram-negative bacteria. Indeed, EspC-multimeric complexes form filamentous structures that could well represent a secretion needle of ESX-1 type VII secretion systems. This exciting observation opens new avenues for research to discover and characterize ESX/T7S components and elucidates the co-dependence of EsxA/B secretion with EspA/C.
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Affiliation(s)
- Louis S Ates
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724 Paris Cedex 15, France
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39
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Abstract
Mycobacterium tuberculosis uses sophisticated secretion systems, named 6 kDa early secretory antigenic target (ESAT6) protein family secretion (ESX) systems (also known as type VII secretion systems), to export a set of effector proteins that helps the pathogen to resist or evade the host immune response. Since the discovery of the esx loci during the M. tuberculosis H37Rv genome project, structural biology, cell biology and evolutionary analyses have advanced our knowledge of the function of these systems. In this Review, we highlight the intriguing roles that these studies have revealed for ESX systems in bacterial survival and pathogenicity during infection with M. tuberculosis. Furthermore, we discuss the diversity of ESX systems that has been described among mycobacteria and selected non-mycobacterial species. Finally, we consider how our knowledge of ESX systems might be applied to the development of novel strategies for the treatment and prevention of disease.
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Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria. Proc Natl Acad Sci U S A 2016; 113:9876-81. [PMID: 27528665 DOI: 10.1073/pnas.1604921113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force of bacterial diversification and evolution. For tuberculosis-causing mycobacteria, the impact of HGT in the emergence and distribution of dominant lineages remains a matter of debate. Here, by using fluorescence-assisted mating assays and whole genome sequencing, we present unique experimental evidence of chromosomal DNA transfer between tubercle bacilli of the early-branching Mycobacterium canettii clade. We found that the obtained recombinants had received multiple donor-derived DNA fragments in the size range of 100 bp to 118 kbp, fragments large enough to contain whole operons. Although the transfer frequency between M. canettii strains was low and no transfer could be observed among classical Mycobacterium tuberculosis complex (MTBC) strains, our study provides the proof of concept for genetic exchange in tubercle bacilli. This outstanding, now experimentally validated phenomenon presumably played a key role in the early evolution of the MTBC toward pathogenicity. Moreover, our findings also provide important information for the risk evaluation of potential transfer of drug resistance and fitness mutations among clinically relevant mycobacterial strains.
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41
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Lillebaek T, Norman A, Rasmussen EM, Marvig RL, Folkvardsen DB, Andersen ÅB, Jelsbak L. Substantial molecular evolution and mutation rates in prolonged latent Mycobacterium tuberculosis infection in humans. Int J Med Microbiol 2016; 306:580-585. [PMID: 27296510 DOI: 10.1016/j.ijmm.2016.05.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 05/27/2016] [Accepted: 05/27/2016] [Indexed: 01/10/2023] Open
Abstract
The genome of Mycobacterium tuberculosis (Mtb) of latently infected individuals may hold the key to understanding the processes that lead to reactivation and progression to clinical disease. We report here analysis of pairs of Mtb isolates from putative prolonged latent TB cases. We identified two confirmed cases, and used whole genome sequencing to investigate the mutational processes that occur over decades in latent Mtb. We found an estimated mutation rate between 0.2 and 0.3 over 33 years, suggesting that latent Mtb accumulates mutations at rates similar to observations from cases of active disease.
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Affiliation(s)
- Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, DK-2300 Copenhagen, Denmark.
| | - Anders Norman
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Rasmus L Marvig
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark
| | - Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, DK-2300 Copenhagen, Denmark
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, DK-2100 Copenhagen, Denmark
| | - Lars Jelsbak
- Department of Systems Biology, Technical University of Denmark, DK-2800 Lyngby, Denmark.
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42
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Franco-Paredes C, Rodriguez-Morales AJ. Unsolved matters in leprosy: a descriptive review and call for further research. Ann Clin Microbiol Antimicrob 2016; 15:33. [PMID: 27209077 PMCID: PMC4875741 DOI: 10.1186/s12941-016-0149-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Accepted: 05/11/2016] [Indexed: 10/25/2022] Open
Abstract
Leprosy, a chronic mycobacterial infection caused by Mycobacterium leprae, is an infectious disease that has ravaged human societies throughout millennia. This ancestral pathogen causes disfiguring cutaneous lesions, peripheral nerve injury, ostearticular deformity, limb loss and dysfunction, blindness and stigma. Despite ongoing efforts in interrupting leprosy transmission, large numbers of new cases are persistently identified in many endemic areas. Moreover, at the time of diagnosis, most newly identified cases have considerable neurologic disability. Many challenges remain in our understanding of the epidemiology of leprosy including: (a) the precise mode and route of transmission; (b) the socioeconomic, environmental, and behavioral factors that promote its transmission; and
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Affiliation(s)
- Carlos Franco-Paredes
- Infectious Diseases Clinic, Phoebe Putney Memorial Hospital, 507 3rd Avenue, Albany, GA, 31721, USA. .,Hospital Infantil de México, Federico Gómez, Mexico D.F., Mexico.
| | - Alfonso J Rodriguez-Morales
- Public Health and Infection Research Group, Faculty of Health Sciences, Universidad Tecnológica de Pereira, Pereira, Risaralda, Colombia
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Majlessi L, Brosch R. Mycobacterium tuberculosis Meets the Cytosol: The Role of cGAS in Anti-mycobacterial Immunity. Cell Host Microbe 2016; 17:733-5. [PMID: 26067600 DOI: 10.1016/j.chom.2015.05.017] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
The intracellular fate of Mycobacterium tuberculosis is a subject of long debate. In this issue of Cell Host & Microbe, three independent studies reveal the detection of cytosolic mycobacterial DNA by the nucleotidyltransferase cGAS, emphasizing the concept of cytosolic access by M. tuberculosis and its role in balancing immune-protection and immune-pathogenesis.
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Affiliation(s)
- Laleh Majlessi
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, 25 rue du Dr. Roux, Paris 75015, France.
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Kaufmann E, Spohr C, Battenfeld S, De Paepe D, Holzhauser T, Balks E, Homolka S, Reiling N, Gilleron M, Bastian M. BCG Vaccination Induces Robust CD4+ T Cell Responses to Mycobacterium tuberculosis Complex–Specific Lipopeptides in Guinea Pigs. THE JOURNAL OF IMMUNOLOGY 2016; 196:2723-32. [DOI: 10.4049/jimmunol.1502307] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/12/2016] [Indexed: 01/11/2023]
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46
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pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence. Nat Microbiol 2016; 1:15019. [PMID: 27571976 DOI: 10.1038/nmicrobiol.2015.19] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/19/2015] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is a major, globally spread, aerosol-transmitted human pathogen, thought to have evolved by clonal expansion from a Mycobacterium canettii-like progenitor. In contrast, extant M. canettii strains are rare, genetically diverse, and geographically restricted mycobacteria of only marginal epidemiological importance. Here, we show that the contrasting evolutionary success of these two groups is linked to loss of lipooligosaccharide biosynthesis and subsequent morphotype changes. Spontaneous smooth-to-rough M. canettii variants were found to be mutated in the polyketide-synthase-encoding pks5 locus and deficient in lipooligosaccharide synthesis, a phenotype restored by complementation. Importantly, these rough variants showed an altered host-pathogen interaction and increased virulence in cellular- and animal-infection models. In one variant, lipooligosaccharide deficiency occurred via homologous recombination between two pks5 genes and removal of the intervening acyltransferase-encoding gene. The resulting single pks5 configuration is similar to that fixed in M. tuberculosis, which is known to lack lipooligosaccharides. Our results suggest that pks5-recombination-mediated bacterial surface remodelling increased virulence, driving evolution from putative generalist mycobacteria towards professional pathogens of mammalian hosts.
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47
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Dumas E, Christina Boritsch E, Vandenbogaert M, Rodríguez de la Vega RC, Thiberge JM, Caro V, Gaillard JL, Heym B, Girard-Misguich F, Brosch R, Sapriel G. Mycobacterial Pan-Genome Analysis Suggests Important Role of Plasmids in the Radiation of Type VII Secretion Systems. Genome Biol Evol 2016; 8:387-402. [PMID: 26748339 PMCID: PMC4779608 DOI: 10.1093/gbe/evw001] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
In mycobacteria, various type VII secretion systems corresponding to different ESX (ESAT-6 secretory) types, are contributing to pathogenicity, iron acquisition, and/or conjugation. In addition to the known chromosomal ESX loci, the existence of plasmid-encoded ESX systems was recently reported. To investigate the potential role of ESX-encoding plasmids on mycobacterial evolution, we analyzed a large representative collection of mycobacterial genomes, including both chromosomal and plasmid-borne sequences. Data obtained for chromosomal ESX loci confirmed the previous five classical ESX types and identified a novel mycobacterial ESX-4-like type, termed ESX-4-bis. Moreover, analysis of the plasmid-encoded ESX loci showed extensive diversification, with at least seven new ESX profiles, identified. Three of them (ESX-P clusters 1–3) were found in multiple plasmids, while four corresponded to singletons. Our phylogenetic and gene-order-analyses revealed two main groups of ESX types: 1) ancestral types, including ESX-4 and ESX-4-like systems from mycobacterial and non-mycobacterial actinobacteria and 2) mycobacteria-specific ESX systems, including ESX-1-2-3-5 systems and the plasmid-encoded ESX types. Synteny analysis revealed that ESX-P systems are part of phylogenetic groups that derived from a common ancestor, which diversified and resulted in the different ESX types through extensive gene rearrangements. A converging body of evidence, derived from composition bias-, phylogenetic-, and synteny analyses points to a scenario in which ESX-encoding plasmids have been a major driving force for acquisition and diversification of type VII systems in mycobacteria, which likely played (and possibly still play) important roles in the adaptation to new environments and hosts during evolution of mycobacterial pathogenesis.
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Affiliation(s)
- Emilie Dumas
- INSERM U1173, UFR Simone Weil, Versailles-Saint-en-Quentin University, Saint-Quentin-en-Yvelines 78180, France
| | - Eva Christina Boritsch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724, Paris Cedex 15, France
| | - Mathias Vandenbogaert
- Institut Pasteur, Genotyping of Pathogens and Public Health, 75724, Paris Cedex 15, France
| | | | - Jean-Michel Thiberge
- Institut Pasteur, Genotyping of Pathogens and Public Health, 75724, Paris Cedex 15, France
| | - Valerie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, 75724, Paris Cedex 15, France
| | - Jean-Louis Gaillard
- INSERM U1173, UFR Simone Weil, Versailles-Saint-en-Quentin University, Saint-Quentin-en-Yvelines 78180, France AP-HP, Hôpital Ambroise Paré, Service De Microbiologie Et Hygiène, Boulogne-Billancourt, France
| | - Beate Heym
- INSERM U1173, UFR Simone Weil, Versailles-Saint-en-Quentin University, Saint-Quentin-en-Yvelines 78180, France AP-HP, Hôpital Ambroise Paré, Service De Microbiologie Et Hygiène, Boulogne-Billancourt, France
| | - Fabienne Girard-Misguich
- INSERM U1173, UFR Simone Weil, Versailles-Saint-en-Quentin University, Saint-Quentin-en-Yvelines 78180, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724, Paris Cedex 15, France
| | - Guillaume Sapriel
- INSERM U1173, UFR Simone Weil, Versailles-Saint-en-Quentin University, Saint-Quentin-en-Yvelines 78180, France UMR 8212, LSCE, Versailles-Saint-Quentin University, Saint-Quentin-en-Yvelines 78180, France Atelier De Bio-Informatique. Institut De Systématique, Evolution, Biodiversité, ISYEB, UMR 7205, CNRS, MNHN, UPMC, EPHE. Muséum National D'histoire Naturelle, Cedex 05, Paris 75231, France
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48
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Comas I, Hailu E, Kiros T, Bekele S, Mekonnen W, Gumi B, Tschopp R, Ameni G, Hewinson RG, Robertson BD, Goig GA, Stucki D, Gagneux S, Aseffa A, Young D, Berg S. Population Genomics of Mycobacterium tuberculosis in Ethiopia Contradicts the Virgin Soil Hypothesis for Human Tuberculosis in Sub-Saharan Africa. Curr Biol 2015; 25:3260-6. [PMID: 26687624 PMCID: PMC4691238 DOI: 10.1016/j.cub.2015.10.061] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/26/2015] [Accepted: 10/28/2015] [Indexed: 02/06/2023]
Abstract
Colonial medical reports claimed that tuberculosis (TB) was largely unknown in Africa prior to European contact, providing a "virgin soil" for spread of TB in highly susceptible populations previously unexposed to the disease [1, 2]. This is in direct contrast to recent phylogenetic models which support an African origin for TB [3-6]. To address this apparent contradiction, we performed a broad genomic sampling of Mycobacterium tuberculosis in Ethiopia. All members of the M. tuberculosis complex (MTBC) arose from clonal expansion of a single common ancestor [7] with a proposed origin in East Africa [3, 4, 8]. Consistent with this proposal, MTBC lineage 7 is almost exclusively found in that region [9-11]. Although a detailed medical history of Ethiopia supports the view that TB was rare until the 20(th) century [12], over the last century Ethiopia has become a high-burden TB country [13]. Our results provide further support for an African origin for TB, with some genotypes already present on the continent well before European contact. Phylogenetic analyses reveal a pattern of serial introductions of multiple genotypes into Ethiopia in association with human migration and trade. In place of a "virgin soil" fostering the spread of TB in a previously naive population, we propose that increased TB mortality in Africa was driven by the introduction of European strains of M. tuberculosis alongside expansion of selected indigenous strains having biological characteristics that carry a fitness benefit in the urbanized settings of post-colonial Africa.
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Affiliation(s)
- Iñaki Comas
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain; CIBER (Centros de Investigación Biomédica en Red) in Epidemiology and Public Health, Instituto de Salud Carlos III, Madrid 28029, Spain.
| | - Elena Hailu
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Teklu Kiros
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Shiferaw Bekele
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Wondale Mekonnen
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Balako Gumi
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Rea Tschopp
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia; Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, PO Box 1176, Addis Ababa, Ethiopia
| | - R Glyn Hewinson
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK
| | - Brian D Robertson
- Center for Molecular Bacteriology and Infection, Department of Medicine, Flowers Building, South Kensington, Imperial College London, London SW7 2AZ, UK
| | - Galo A Goig
- Genomics and Health Unit, FISABIO Public Health, Valencia 46020, Spain
| | - David Stucki
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel 4002, and University of Basel, Basel 4003, Switzerland
| | - Abraham Aseffa
- Armauer Hansen Research Institute, PO Box 1005, Addis Ababa, Ethiopia
| | - Douglas Young
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Stefan Berg
- Bovine TB Research Group, Animal and Plant Health Agency, Surrey KT15 3NB, UK.
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49
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Slama N, Jamet S, Frigui W, Pawlik A, Bottai D, Laval F, Constant P, Lemassu A, Cam K, Daffé M, Brosch R, Eynard N, Quémard A. The changes in mycolic acid structures caused byhadCmutation have a dramatic effect on the virulence ofMycobacterium tuberculosis. Mol Microbiol 2015; 99:794-807. [DOI: 10.1111/mmi.13266] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/02/2015] [Indexed: 01/13/2023]
Affiliation(s)
- Nawel Slama
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Stevie Jamet
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Wafa Frigui
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Alexandre Pawlik
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Daria Bottai
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Françoise Laval
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Patricia Constant
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Anne Lemassu
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Kaymeuang Cam
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Mamadou Daffé
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Nathalie Eynard
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
| | - Annaïk Quémard
- Département Tuberculose & Biologie des Infections; Institut de Pharmacologie et de Biologie Structurale - UMR5089; Centre National de la Recherche Scientifique; Toulouse France
- Institut de Pharmacologie et de Biologie Structurale; Université de Toulouse; Université Paul Sabatier; Toulouse France
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Revisiting the role of phospholipases C in virulence and the lifecycle of Mycobacterium tuberculosis. Sci Rep 2015; 5:16918. [PMID: 26603639 PMCID: PMC4658479 DOI: 10.1038/srep16918] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 10/22/2015] [Indexed: 12/02/2022] Open
Abstract
Mycobacterium tuberculosis, the agent of human tuberculosis has developed
different virulence mechanisms and virulence-associated tools during its evolution
to survive and multiply inside the host. Based on previous reports and by analogy
with other bacteria, phospholipases C (PLC) of M. tuberculosis were thought
to be among these tools. To get deeper insights into the function of PLCs, we
investigated their putative involvement in the intracellular lifestyle of M.
tuberculosis, with emphasis on phagosomal rupture and virulence, thereby
re-visiting a research theme of longstanding interest. Through the construction and
use of an M. tuberculosis H37Rv PLC-null mutant (ΔPLC) and
control strains, we found that PLCs of M. tuberculosis were not required for
induction of phagosomal rupture and only showed marginal, if any, impact on
virulence of M. tuberculosis in the cellular and mouse infection models used
in this study. In contrast, we found that PLC-encoding genes were strongly
upregulated under phosphate starvation and that PLC-proficient M.
tuberculosis strains survived better than ΔPLC mutants under
conditions where phosphatidylcholine served as sole phosphate source, opening new
perspectives for studies on the role of PLCs in the lifecycle of M.
tuberculosis.
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