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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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Abstract
The genus Mycobacterium contains several slow-growing human pathogens, including Mycobacterium tuberculosis, Mycobacterium leprae, and Mycobacterium avium. Mycobacterium smegmatis is a nonpathogenic and fast growing species within this genus. In 1990, a mutant of M. smegmatis, designated mc2155, that could be transformed with episomal plasmids was isolated, elevating M. smegmatis to model status as the ideal surrogate for mycobacterial research. Classical bacterial models, such as Escherichia coli, were inadequate for mycobacteria research because they have low genetic conservation, different physiology, and lack the novel envelope structure that distinguishes the Mycobacterium genus. By contrast, M. smegmatis encodes thousands of conserved mycobacterial gene orthologs and has the same cell architecture and physiology. Dissection and characterization of conserved genes, structures, and processes in genetically tractable M. smegmatis mc2155 have since provided previously unattainable insights on these same features in its slow-growing relatives. Notably, tuberculosis (TB) drugs, including the first-line drugs isoniazid and ethambutol, are active against M. smegmatis, but not against E. coli, allowing the identification of their physiological targets. Furthermore, Bedaquiline, the first new TB drug in 40 years, was discovered through an M. smegmatis screen. M. smegmatis has become a model bacterium, not only for M. tuberculosis, but for all other Mycobacterium species and related genera. With a repertoire of bioinformatic and physical resources, including the recently established Mycobacterial Systems Resource, M. smegmatis will continue to accelerate mycobacterial research and advance the field of microbiology.
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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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Sabin S, Morales-Arce AY, Pfeifer SP, Jensen JD. The impact of frequently neglected model violations on bacterial recombination rate estimation: a case study in Mycobacterium canettii and Mycobacterium tuberculosis. G3 (BETHESDA, MD.) 2022; 12:jkac055. [PMID: 35253851 PMCID: PMC9073693 DOI: 10.1093/g3journal/jkac055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Accepted: 02/28/2022] [Indexed: 12/04/2022]
Abstract
Mycobacterium canettii is a causative agent of tuberculosis in humans, along with the members of the Mycobacterium tuberculosis complex. Frequently used as an outgroup to the M. tuberculosis complex in phylogenetic analyses, M. canettii is thought to offer the best proxy for the progenitor species that gave rise to the complex. Here, we leverage whole-genome sequencing data and biologically relevant population genomic models to compare the evolutionary dynamics driving variation in the recombining M. canettii with that in the nonrecombining M. tuberculosis complex, and discuss differences in observed genomic diversity in the light of expected levels of Hill-Robertson interference. In doing so, we highlight the methodological challenges of estimating recombination rates through traditional population genetic approaches using sequences called from populations of microorganisms and evaluate the likely mis-inference that arises owing to a neglect of common model violations including purifying selection, background selection, progeny skew, and population size change. In addition, we compare performance when full within-host polymorphism data are utilized, versus the more common approach of basing analyses on within-host consensus sequences.
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Affiliation(s)
- Susanna Sabin
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Ana Y Morales-Arce
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Susanne P Pfeifer
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA
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Bohr LL, Youngblom MA, Eldholm V, Pepperell CS. Genome reorganization during emergence of host-associated Mycobacterium abscessus. Microb Genom 2021; 7. [PMID: 34874249 PMCID: PMC8767326 DOI: 10.1099/mgen.0.000706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection. Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.
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Affiliation(s)
- Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.,Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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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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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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Sabin S, Herbig A, Vågene ÅJ, Ahlström T, Bozovic G, Arcini C, Kühnert D, Bos KI. A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex. Genome Biol 2020; 21:201. [PMID: 32778135 PMCID: PMC7418204 DOI: 10.1186/s13059-020-02112-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Although tuberculosis accounts for the highest mortality from a bacterial infection on a global scale, questions persist regarding its origin. One hypothesis based on modern Mycobacterium tuberculosis complex (MTBC) genomes suggests their most recent common ancestor followed human migrations out of Africa approximately 70,000 years before present. However, studies using ancient genomes as calibration points have yielded much younger dates of less than 6000 years. Here, we aim to address this discrepancy through the analysis of the highest-coverage and highest-quality ancient MTBC genome available to date, reconstructed from a calcified lung nodule of Bishop Peder Winstrup of Lund (b. 1605-d. 1679). RESULTS A metagenomic approach for taxonomic classification of whole DNA content permitted the identification of abundant DNA belonging to the human host and the MTBC, with few non-TB bacterial taxa comprising the background. Genomic enrichment enabled the reconstruction of a 141-fold coverage M. tuberculosis genome. In utilizing this high-quality, high-coverage seventeenth-century genome as a calibration point for dating the MTBC, we employed multiple Bayesian tree models, including birth-death models, which allowed us to model pathogen population dynamics and data sampling strategies more realistically than those based on the coalescent. CONCLUSIONS The results of our metagenomic analysis demonstrate the unique preservation environment calcified nodules provide for DNA. Importantly, we estimate a most recent common ancestor date for the MTBC of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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Affiliation(s)
- Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
- Present address: Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Torbjörn Ahlström
- Department of Archaeology and Ancient History, Lund University, 221 00 Lund, Sweden
| | - Gracijela Bozovic
- Department of Medical Imaging and Clinical Physiology, Skåne University Hospital Lund and Lund University, 221 00 Lund, Sweden
| | - Caroline Arcini
- Arkeologerna, National Historical Museum, 226 60 Lund, Sweden
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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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: 100] [Impact Index Per Article: 25.0] [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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Dordet-Frisoni E, Faucher M, Sagné E, Baranowski E, Tardy F, Nouvel LX, Citti C. Mycoplasma Chromosomal Transfer: A Distributive, Conjugative Process Creating an Infinite Variety of Mosaic Genomes. Front Microbiol 2019; 10:2441. [PMID: 31708906 PMCID: PMC6819513 DOI: 10.3389/fmicb.2019.02441] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 10/10/2019] [Indexed: 11/13/2022] Open
Abstract
The capacity of Mycoplasmas to engage in horizontal gene transfers has recently been highlighted. Despite their small genome, some of these wall-less bacteria are able to exchange multiple, large portions of their chromosome via a conjugative mechanism that does not conform to canonical Hfr/oriT models. To understand the exact features underlying mycoplasma chromosomal transfer (MCT), extensive genomic analyses were performed at the nucleotide level, using individual mating progenies derived from our model organism, Mycoplasma agalactiae. Genome reconstruction showed that MCT resulted in the distributive transfer of multiple chromosomal DNA fragments and generated progenies composed of a variety of mosaic genomes, each being unique. Analyses of macro- and micro-events resulting from MCT revealed that the vast majority of the acquired fragments were unrelated and co-transferred independently from the selection marker, these resulted in up to 17% of the genome being exchanged. Housekeeping and accessory genes were equally affected by MCT, with up to 35 CDSs being gained or lost. This efficient HGT process also created a number of chimeric genes and genetic micro-variations that may impact gene regulation and/or expression. Our study unraveled the tremendous plasticity of M. agalactiae genome and point toward MCT as a major player in diversification and adaptation to changing environments, offering a significant advantage to this minimal pathogen.
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Affiliation(s)
| | - Marion Faucher
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | - Eveline Sagné
- IHAP, INRA, ENVT, Université de Toulouse, Toulouse, France
| | | | - Florence Tardy
- UMR Mycoplasmoses des Ruminants, VetAgro Sup, Laboratoire de Lyon, ANSES, Université de Lyon, Marcy-l'Étoile, France
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Yano H, Suzuki H, Maruyama F, Iwamoto T. The recombination-cold region as an epidemiological marker of recombinogenic opportunistic pathogen Mycobacterium avium. BMC Genomics 2019; 20:752. [PMID: 31623552 PMCID: PMC6798384 DOI: 10.1186/s12864-019-6078-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Accepted: 09/04/2019] [Indexed: 11/10/2022] Open
Abstract
Background The rapid identification of lineage remains a challenge in the genotyping of clinical isolates of recombinogenic pathogens. The chromosome of Mycobacterium avium subsp. hominissuis (MAH), an agent of Mycobacterium avium complex (MAC) lung disease, is often mosaic and is composed of chromosomal segments originating from different lineages. This makes it difficult to infer the MAH lineage in a simple experimental set-up. To overcome this difficulty, we sought to identify chromosomal marker genes containing lineage-specific alleles by genome data mining. Results We conducted genetic population structure analysis, phylogenetic analysis, and a survey of historical recombination using data from 125 global MAH isolates. Six MAH lineages (EA1, EA2, SC1, SC2, SC3, and SC4) were identified in the current dataset. One P-450 gene (locus_tag MAH_0788/MAV_0940) in the recombination-cold region was found to have multiple alleles that could discriminate five lineages. By combining the information about allele type from one additional gene, the six MAH lineages as well as other M. avium subspecies were distinguishable. A recombination-cold region of 116 kb contains an insertion hotspot and is flanked by a mammalian cell-entry protein operon where allelic variants have previously been reported to occur. Hence, we speculate that the acquisition of lineage- or strain-specific insertions has introduced homology breaks in the chromosome, thereby reducing the chance of interlineage recombination. Conclusions The allele types of the newly identified marker genes can be used to predict major lineages of M. avium. The single nucleotide polymorphism typing approach targeting multiallelic loci in recombination-cold regions will facilitate the epidemiological study of MAC, and may also be useful for equivalent studies of other nontuberculous mycobacteria potentially carrying mosaic genomes.
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Affiliation(s)
- Hirokazu Yano
- Graduate School of Life Sciences, Tohoku University, Katahira, Aoba-ku, Sendai, Japan.
| | - Haruo Suzuki
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Fumito Maruyama
- Office of Industry-Academia-Government and Community Collaboration, Hiroshima University, Hiroshima, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan.
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Chiner-Oms Á, Comas I. Large genomics datasets shed light on the evolution of the Mycobacterium tuberculosis complex. INFECTION GENETICS AND EVOLUTION 2019; 72:10-15. [DOI: 10.1016/j.meegid.2019.02.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/21/2019] [Accepted: 02/25/2019] [Indexed: 01/21/2023]
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Chiner-Oms Á, Sánchez-Busó L, Corander J, Gagneux S, Harris SR, Young D, González-Candelas F, Comas I. Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex. SCIENCE ADVANCES 2019; 5:eaaw3307. [PMID: 31448322 PMCID: PMC6691555 DOI: 10.1126/sciadv.aaw3307] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2018] [Accepted: 05/10/2019] [Indexed: 06/10/2023]
Abstract
Models on how bacterial lineages differentiate increase our understanding of early bacterial speciation events and the genetic loci involved. Here, we analyze the population genomics events leading to the emergence of the tuberculosis pathogen. The emergence is characterized by a combination of recombination events involving core pathogenesis functions and purifying selection on early diverging loci. We identify the phoR gene, the sensor kinase of a two-component system involved in virulence, as a key functional player subject to pervasive positive selection after the divergence of the Mycobacterium tuberculosis complex from its ancestor. Previous evidence showed that phoR mutations played a central role in the adaptation of the pathogen to different host species. Now, we show that phoR mutations have been under selection during the early spread of human tuberculosis, during later expansions, and in ongoing transmission events. Our results show that linking pathogen evolution across evolutionary and epidemiological time scales points to past and present virulence determinants.
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Affiliation(s)
- Á. Chiner-Oms
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
| | - L. Sánchez-Busó
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - J. Corander
- Pathogen Genomics, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
- Department of Biostatistics, University of Oslo, 0317 Oslo, Norway
- Helsinki Institute of Information Technology (HIIT), Department of Mathematics and Statistics, University of Helsinki, 00014 Helsinki, Finland
| | - S. Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - S. R. Harris
- Microbiotica, BioData Innovation Centre, Wellcome Genome Campus, Cambridge CB10 1DR, UK
| | - D. Young
- The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - F. González-Candelas
- Unidad Mixta “Infección y Salud Pública” FISABIO-CSISP/Universidad de Valencia, Instituto de Biología Integrativa de Sistemas (ISysBio), Valencia, Spain
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
| | - I. Comas
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
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Saelens JW, Viswanathan G, Tobin DM. Mycobacterial Evolution Intersects With Host Tolerance. Front Immunol 2019; 10:528. [PMID: 30967867 PMCID: PMC6438904 DOI: 10.3389/fimmu.2019.00528] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/27/2019] [Indexed: 12/12/2022] Open
Abstract
Over the past 200 years, tuberculosis (TB) has caused more deaths than any other infectious disease, likely infecting more people than it has at any other time in human history. Mycobacterium tuberculosis (Mtb), the etiologic agent of TB, is an obligate human pathogen that has evolved through the millennia to become an archetypal human-adapted pathogen. This review focuses on the evolutionary framework by which Mtb emerged as a specialized human pathogen and applies this perspective to the emergence of specific lineages that drive global TB burden. We consider how evolutionary pressures, including transmission dynamics, host tolerance, and human population patterns, may have shaped the evolution of diverse mycobacterial genomes.
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Affiliation(s)
- Joseph W. Saelens
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - Gopinath Viswanathan
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
| | - David M. Tobin
- Department of Molecular Genetics and Microbiology, Duke University School of Medicine, Durham, NC, United States
- Department of Immunology, Duke University School of Medicine, Durham, NC, United States
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15
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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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16
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Yano H, Iwamoto T, Nishiuchi Y, Nakajima C, Starkova DA, Mokrousov I, Narvskaya O, Yoshida S, Arikawa K, Nakanishi N, Osaki K, Nakagawa I, Ato M, Suzuki Y, Maruyama F. Population Structure and Local Adaptation of MAC Lung Disease Agent Mycobacterium avium subsp. hominissuis. Genome Biol Evol 2018; 9:2403-2417. [PMID: 28957464 PMCID: PMC5622343 DOI: 10.1093/gbe/evx183] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/08/2017] [Indexed: 12/11/2022] Open
Abstract
Mycobacterium avium subsp. hominissuis (MAH) is one of the most common nontuberculous mycobacterial species responsible for chronic lung disease in humans. Despite increasing worldwide incidence, little is known about the genetic mechanisms behind the population evolution of MAH. To elucidate the local adaptation mechanisms of MAH, we assessed genetic population structure, the mutual homologous recombination, and gene content for 36 global MAH isolates, including 12 Japanese isolates sequenced in the present study. We identified five major MAH lineages and found that extensive mutual homologous recombination occurs among them. Two lineages (MahEastAsia1 and MahEastAsia2) were predominant in the Japanese isolates. We identified alleles unique to these two East Asian lineages in the loci responsible for trehalose biosynthesis (treS and mak) and in one mammalian cell entry operon, which presumably originated from as yet undiscovered mycobacterial lineages. Several genes and alleles unique to East Asian strains were located in the fragments introduced via recombination between East Asian lineages, suggesting implication of recombination in local adaptation. These patterns of MAH genomes are consistent with the signature of distribution conjugative transfer, a mode of sexual reproduction reported for other mycobacterial species.
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Affiliation(s)
- Hirokazu Yano
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan.,Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Tomotada Iwamoto
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Yukiko Nishiuchi
- Toneyama Institute for Tuberculosis Research, Osaka City University Medical School, Osaka, Japan
| | - Chie Nakajima
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | | | - Igor Mokrousov
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Olga Narvskaya
- St. Petersburg Pasteur Institute, St. Petersburg, Russia
| | - Shiomi Yoshida
- Clinical Research Center, National Hospital Organization, Kinki-Chuo Chest Medical Center, Osaka, Japan
| | - Kentaro Arikawa
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Noriko Nakanishi
- Department of Infectious Diseases, Kobe Institute of Health, Kobe, Japan
| | - Ken Osaki
- TOMY Digital Biology Co. Ltd, Taito-Ku, Tokyo, Japan
| | - Ichiro Nakagawa
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Manabu Ato
- Department of Immunology, National Institute of Infectious Diseases, Shinjuku-Ku, Tokyo, Japan
| | - Yasuhiko Suzuki
- Division of Bioresources, Hokkaido University Research Center for Zoonosis Control, Sapporo, Japan.,The Global Station for Zoonosis Control, Hokkaido University Global Institution for Collaborative Research and Education, Sapporo, Japan
| | - Fumito Maruyama
- Department of Microbiology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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17
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Hall JPJ, Brockhurst MA, Harrison E. Sampling the mobile gene pool: innovation via horizontal gene transfer in bacteria. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0424. [PMID: 29061896 DOI: 10.1098/rstb.2016.0424] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/05/2017] [Indexed: 12/26/2022] Open
Abstract
In biological systems, evolutionary innovations can spread not only from parent to offspring (i.e. vertical transmission), but also 'horizontally' between individuals, who may or may not be related. Nowhere is this more apparent than in bacteria, where novel ecological traits can spread rapidly within and between species through horizontal gene transfer (HGT). This important evolutionary process is predominantly a by-product of the infectious spread of mobile genetic elements (MGEs). We will discuss the ecological conditions that favour the spread of traits by HGT, the evolutionary and social consequences of sharing traits, and how HGT is shaped by inherent conflicts between bacteria and MGEs.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'.
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Affiliation(s)
- James P J Hall
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Michael A Brockhurst
- Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield S10 2TN, UK
| | - Ellie Harrison
- P3 Institute, Department of Animal and Plant Sciences, Arthur Willis Environment Centre, University of Sheffield, 1 Maxfield Avenue, Sheffield S10 1AE, UK
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18
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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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19
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20
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Evolution of virulence in the Mycobacterium tuberculosis complex. Curr Opin Microbiol 2018; 41:68-75. [DOI: 10.1016/j.mib.2017.11.021] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 10/27/2017] [Accepted: 11/04/2017] [Indexed: 01/16/2023]
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21
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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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22
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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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23
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The transjugation machinery of Thermus thermophilus: Identification of TdtA, an ATPase involved in DNA donation. PLoS Genet 2017; 13:e1006669. [PMID: 28282376 PMCID: PMC5365140 DOI: 10.1371/journal.pgen.1006669] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Revised: 03/24/2017] [Accepted: 03/04/2017] [Indexed: 11/19/2022] Open
Abstract
In addition to natural competence, some Thermus thermophilus strains show a high rate of DNA transfer via direct cell-to-cell contact. The process is bidirectional and follows a two-step model where the donor cell actively pushes out DNA and the recipient cell employs the natural competence system to take up the DNA, in a hybrid transformation-dependent conjugation process (transjugation). While the DNA uptake machinery is well known as in other bacterial species that undergo transformation, the pushing step of transjugation remains to be characterized. Here we have searched for hypothetical DNA translocases putatively involved in the pushing step of transjugation. Among candidates encoded by T. thermophilus HB27, the TdtA protein was found to be required for DNA pushing but not for DNA pulling during transjugation, without affecting other cellular processes. Purified TdtA shows ATPase activity and oligomerizes as hexamers with a central opening that can accommodate double-stranded DNA. The tdtA gene was found to belong to a mobile 14 kbp-long DNA element inserted within the 3′ end of a tRNA gene, flanked by 47 bp direct repeats. The insertion also encoded a homolog of bacteriophage site-specific recombinases and actively self-excised from the chromosome at high frequency to form an apparently non-replicative circular form. The insertion also encoded a type II restriction endonuclease and a NurA-like nuclease, whose activities were required for efficient transjugation. All these data support that TdtA belongs to a new type of Integrative and Conjugative Element which promotes the generalized and efficient transfer of genetic traits that could facilitate its co-selection among bacterial populations. Transjugation is a new type of horizontal gene transfer process in which a donor cell pushes out genomic DNA upon cell contact and a recipient cell pulls this DNA inside by natural transformation. Here we describe TdtA, a DNA translocase of the pushing system of T. thermophilus, which is encoded within ICEth1, a new class of Integrative and Conjugative Element whose presence leads to generalized cell-to-cell transfer of any gene marker, circumventing the Argonaute surveillance system that controls access of extracellular DNA acquired by transformation.
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24
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Vandelannoote K, Meehan CJ, Eddyani M, Affolabi D, Phanzu DM, Eyangoh S, Jordaens K, Portaels F, Mangas K, Seemann T, Marsollier L, Marion E, Chauty A, Landier J, Fontanet A, Leirs H, Stinear TP, de Jong BC. Multiple Introductions and Recent Spread of the Emerging Human Pathogen Mycobacterium ulcerans across Africa. Genome Biol Evol 2017; 9:414-426. [PMID: 28137745 PMCID: PMC5381664 DOI: 10.1093/gbe/evx003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/18/2017] [Indexed: 12/21/2022] Open
Abstract
Buruli ulcer (BU) is an insidious neglected tropical disease. Cases are reported around the world but the rural regions of West and Central Africa are most affected. How BU is transmitted and spreads has remained a mystery, even though the causative agent, Mycobacterium ulcerans, has been known for more than 70 years. Here, using the tools of population genomics, we reconstruct the evolutionary history of M. ulcerans by comparing 165 isolates spanning 48 years and representing 11 endemic countries across Africa. The genetic diversity of African M. ulcerans was found to be restricted due to the bacterium's slow substitution rate coupled with its relatively recent origin. We identified two specific M. ulcerans lineages within the African continent, and inferred that M. ulcerans lineage Mu_A1 existed in Africa for several hundreds of years, unlike lineage Mu_A2, which was introduced much more recently, approximately during the 19th century. Additionally, we observed that specific M. ulcerans epidemic Mu_A1 clones were introduced during the same time period in the three hydrological basins that were well covered in our panel. The estimated time span of the introduction events coincides with the Neo-imperialism period, during which time the European colonial powers divided the African continent among themselves. Using this temporal association, and in the absence of a known BU reservoir or-vector on the continent, we postulate that the so-called "Scramble for Africa" played a significant role in the spread of the disease across the continent.
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Affiliation(s)
- Koen Vandelannoote
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Evolutionary Ecology Group University of Antwerp, Antwerp, Belgium
| | - Conor J. Meehan
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Miriam Eddyani
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | | | | | - Sara Eyangoh
- Service de Mycobactériologie, Centre Pasteur du Cameroun, Yaoundé, Cameroun
| | - Kurt Jordaens
- Evolutionary Ecology Group University of Antwerp, Antwerp, Belgium
- Invertebrates Section, Royal Museum for Central Africa, Tervuren, Belgium
| | - Françoise Portaels
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Kirstie Mangas
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Torsten Seemann
- Victorian Life Sciences Computation Initiative University of Melbourne, Victoria, Australia
| | | | - Estelle Marion
- CRCNA Inserm U892 CNRS 6299, CHU & Université d’Angers, Angers, France
| | | | - Jordi Landier
- Service de Mycobactériologie, Centre Pasteur du Cameroun, Yaoundé, Cameroun
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
| | - Arnaud Fontanet
- Emerging Diseases Epidemiology Unit, Institut Pasteur, Paris, France
| | - Herwig Leirs
- Evolutionary Ecology Group University of Antwerp, Antwerp, Belgium
| | - Timothy P. Stinear
- Department of Microbiology and Immunology, University of Melbourne, Victoria, Australia
| | - Bouke C. de Jong
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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25
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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: 35] [Impact Index Per Article: 5.0] [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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26
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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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27
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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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28
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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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29
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Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. Trends Microbiol 2016; 24:637-648. [PMID: 27068531 DOI: 10.1016/j.tim.2016.03.007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/13/2016] [Accepted: 03/15/2016] [Indexed: 01/29/2023]
Abstract
Antimicrobial resistance (AMR) threats are typically represented by bacteria capable of extensive horizontal gene transfer (HGT). One clear exception is Mycobacterium tuberculosis (Mtb). It is an obligate human pathogen with limited genetic diversity and a low mutation rate which lacks any evidence for HGT. Such features should, in principle, reduce its ability to rapidly evolve AMR. We identify key features in its biology and epidemiology that allow it to overcome its low adaptive potential. We focus in particular on its innate resistance to drugs, its unusual life cycle, including an often extensive latent phase, and its ability to shelter from exposure to antimicrobial drugs within cavities it induces in the lungs.
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30
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Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics 2016; 17:118. [PMID: 26884275 PMCID: PMC4756508 DOI: 10.1186/s12864-016-2448-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/08/2016] [Indexed: 11/16/2022] Open
Abstract
Background In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). Results Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal ‘patchwork’ architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. Conclusion Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2448-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Sapriel
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,Laboratoire des Sciences du Climat et de l'Environnement, LSCE, UMR8212, Université de Versailles St. Quentin - CEA - CNRS, Saint-Aubin, France. .,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France.
| | - Julie Konjek
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | - Laurent Bouri
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Lise Frézal
- Institut of Biology of the Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris, Cedex 05, France.
| | | | - Emilie Dumas
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | | | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | | | | | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Jean-Louis Herrmann
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Raymond Poincaré, Service de Microbiologie et Hygiène, Garches, France.
| | - Jean-Louis Gaillard
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Beate Heym
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Thierry Wirth
- Laboratoire de Biologie intégrative des populations, Evolution moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 16 rue Buffon, F-75231, Paris, Cedex 05, France.
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31
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Aboubaker Osman D, Bouzid F, Canaan S, Drancourt M. Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens. Front Public Health 2016; 3:283. [PMID: 26793699 PMCID: PMC4707939 DOI: 10.3389/fpubh.2015.00283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Smooth tubercle bacilli (STB) including “Mycobacterium canettii” are members of the Mycobacterium tuberculosis complex (MTBC), which cause non-contagious tuberculosis in human. This group comprises <100 isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa, and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes, which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Republic of Djibouti
| | - Feriel Bouzid
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille, France
| | - Stéphane Canaan
- Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université , Marseille , France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095 , Marseille , France
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32
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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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