1
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Jaemsai B, Palittapongarnpim P, Aiewsakun P. South Asian origin and global transmission history of Mycobacterium tuberculosis lineage 4. mSystems 2025:e0042725. [PMID: 40391891 DOI: 10.1128/msystems.00427-25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2025] [Accepted: 04/17/2025] [Indexed: 05/22/2025] Open
Abstract
The origin and transmission history of Mycobacterium tuberculosis lineage 4 (MTB L4) has been extensively studied. However, different studies yielded different results; thus, the evolutionary history of MTB L4 still remains a subject of debate. Recently, a substantial amount of whole-genome sequencing data of MTB has become available, providing new data from diverse geographical locations worldwide. This study analyzed the most comprehensive global collection of MTB L4 genomes to date (n = 11,154), including new sequences from previously under-represented regions, to re-examine the bacterial evolutionary history. Our results suggest that the bacteria likely emerged and diversified in South Asia during the 12th and 13th centuries and then spread to various Old-World regions and the Americas between the 15th and 16th centuries, before undergoing extensive intercontinental transmissions starting from the 17th century onward. The effective population size of MTB L4 as a whole was estimated to expand steadily throughout its evolutionary history until the mid-20th century when a sharp drop occurred, coinciding with the introduction of antibiotics and significant improvements in human living conditions. Interestingly, this pattern was consistently observed across all major sub-lineages, indicating a broad impact of these factors on MTB L4 as a whole. Altogether, our results offer new refined insights into how anthropological changes might have shaped the bacterial evolutionary history and ultimately its global geographical distribution we observe today.IMPORTANCEContrary to previous studies, our analysis suggests that Mycobacterium tuberculosis lineage 4 (MTB L4) likely emerged and diversified in South Asia during the 12th and 13th centuries. It then spread to both the Americas and other Old-World regions between the 15th and 16th centuries, followed by extensive intercontinental transmissions beginning in the 17th century. These findings suggest that South Asia, one of the main crossroads of historical trade networks, might have played a pivotal role in promoting the early intercontinental spread of MTB L4. The effective population size of all major MTB L4 sub-lineages was inferred to increase steadily until the mid-20th century, after which a decline was observed. This decline coincides with the advent of antibiotics and improved living conditions, suggesting a wide impact of these factors on the entire bacterial population.
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Affiliation(s)
- Bharkbhoom Jaemsai
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Prasit Palittapongarnpim
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Pakorn Aiewsakun
- Department of Microbiology, Faculty of Science, Mahidol University, Ratchathewi District, Bangkok, Thailand
- Pornchai Matangkasombut Center for Microbial Genomics, Department of Microbiology, Faculty of Science, Mahidol University, Bangkok, Thailand
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2
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Goig GA, Windels EM, Loiseau C, Stritt C, Biru L, Borrell S, Brites D, Gagneux S. Ecology, global diversity and evolutionary mechanisms in the Mycobacterium tuberculosis complex. Nat Rev Microbiol 2025:10.1038/s41579-025-01159-w. [PMID: 40133503 DOI: 10.1038/s41579-025-01159-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2025] [Indexed: 03/27/2025]
Abstract
With the COVID-19 pandemic receding, tuberculosis (TB) is again the number one cause of human death to a single infectious agent. TB is caused by bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Recent advances in genome sequencing have provided new insights into the ecology and evolution of the MTBC. This includes the discovery of new phylogenetic lineages within the MTBC, a deeper understanding of the host tropism among the various animal-adapted lineages, enhanced knowledge on the evolutionary dynamics of antimicrobial resistance and transmission, as well as a better grasp of the within-host MTBC diversity. Moreover, advances in long-read sequencing are increasingly highlighting the relevance of structural genomic variation in the MTBC. These findings not only shed new light on the biology and epidemiology of TB, but also give rise to new questions and research avenues. The purpose of this Review is to summarize these new insights and discuss their implications for global TB control.
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Affiliation(s)
- Galo A Goig
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Etthel M Windels
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
- Swiss Institute for Bioinformatics, Lausanne, Switzerland
| | - Chloé Loiseau
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Christoph Stritt
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Loza Biru
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Allschwil, Switzerland.
- University of Basel, Basel, Switzerland.
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3
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Mah JC, Lohmueller KE, Garud NR. Inference of the Demographic Histories and Selective Effects of Human Gut Commensal Microbiota Over the Course of Human History. Mol Biol Evol 2025; 42:msaf010. [PMID: 39838923 PMCID: PMC11824422 DOI: 10.1093/molbev/msaf010] [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: 02/06/2024] [Revised: 11/07/2024] [Accepted: 01/07/2025] [Indexed: 01/23/2025] Open
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their demographic histories and distributions of fitness effects (DFEs) of mutations. Here, we infer the demographic histories and DFEs for amino acid-changing mutations of 39 of the most prevalent and abundant commensal gut microbial species found in Westernized individuals over timescales exceeding human generations. Some species display contractions in population size and others expansions, with several of these events coinciding with several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with differences between accessory and core gene DFEs largely driven by genetic drift. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Together, these findings suggest that gut microbes have distinct demographic and selective histories.
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Affiliation(s)
- Jonathan C Mah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, USA
| | - Kirk E Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Department of Human Genetics, University of California, Los Angeles, USA
| | - Nandita R Garud
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles, USA
- Department of Human Genetics, University of California, Los Angeles, USA
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4
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Gröschel MI, Pérez-Llanos FJ, Diel R, Vargas R, Escuyer V, Musser K, Trieu L, Meissner JS, Knorr J, Klinkenberg D, Kouw P, Homolka S, Samek W, Mathema B, van Soolingen D, Niemann S, Ahuja SD, Farhat MR. Differential rates of Mycobacterium tuberculosis transmission associate with host-pathogen sympatry. Nat Microbiol 2024:10.1038/s41564-024-01758-y. [PMID: 39090390 DOI: 10.1038/s41564-024-01758-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 06/12/2024] [Indexed: 08/04/2024]
Abstract
Several human-adapted Mycobacterium tuberculosis complex (Mtbc) lineages exhibit a restricted geographical distribution globally. These lineages are hypothesized to transmit more effectively among sympatric hosts, that is, those that share the same geographical area, though this is yet to be confirmed while controlling for exposure, social networks and disease risk after exposure. Using pathogen genomic and contact tracing data from 2,279 tuberculosis cases linked to 12,749 contacts from three low-incidence cities, we show that geographically restricted Mtbc lineages were less transmissible than lineages that have a widespread global distribution. Allopatric host-pathogen exposure, in which the restricted pathogen and host are from non-overlapping areas, had a 38% decrease in the odds of infection among contacts compared with sympatric exposures. We measure tenfold lower uptake of geographically restricted lineage 6 strains compared with widespread lineage 4 strains in allopatric macrophage infections. We conclude that Mtbc strain-human long-term coexistence has resulted in differential transmissibility of Mtbc lineages and that this differs by human population.
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Affiliation(s)
- Matthias I Gröschel
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Department of Infectious Diseases and Respiratory Medicine, Charité-Universitätsmedizin Berlin, Berlin, Germany.
- Berlin Institute of Health at Charité-Universitätsmedizin Berlin, Berlin, Germany.
| | - Francy J Pérez-Llanos
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- West German Genome Center, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
- Institute of Human Genetics, The University Hospital of Düsseldorf, Düsseldorf, Germany
| | - Roland Diel
- Institute for Epidemiology, University Medical Hospital Schleswig-Holstein, Kiel, Germany
- Lungenclinic Grosshansdorf, Airway Research Center North (ARCN), Member of the German Center for Lung Research (DZL), Grosshansdorf, Germany
| | - Roger Vargas
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Vincent Escuyer
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Kimberlee Musser
- Wadsworth Center, New York State Department of Health, Albany, NY, USA
| | - Lisa Trieu
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | | | - Jillian Knorr
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Don Klinkenberg
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Peter Kouw
- Department of Tuberculosis, Public Health Service, Amsterdam, The Netherlands
| | - Susanne Homolka
- Diagnostic Mycobacteriology, National and Supranational Reference Center for Mycobacteria, Research Center Borstel, Borstel, Germany
| | - Wojciech Samek
- Department of Electrical Engineering and Computer Science, Technical University Berlin, Berlin, Germany
- Department of Artificial Intelligence, Fraunhofer Heinrich Hertz Institute, Berlin, Germany
| | - Barun Mathema
- Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Dick van Soolingen
- Center for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Stefan Niemann
- Molecular and Experimental Mycobacteriology, Research Center Borstel, Borstel, Germany
- German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Shama Desai Ahuja
- New York City Department of Health and Mental Hygiene, New York, NY, USA
| | - Maha R Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, USA.
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Wodelo W, Wampande EM, Andama A, Kateete DP, Ssekatawa K. Polymorphisms in Immune Genes and Their Association with Tuberculosis Susceptibility: An Analysis of the African Population. Appl Clin Genet 2024; 17:33-46. [PMID: 38567200 PMCID: PMC10986402 DOI: 10.2147/tacg.s457395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Accepted: 03/25/2024] [Indexed: 04/04/2024] Open
Abstract
Tuberculosis remains a global health concern, with substantial mortality rates worldwide. Genetic factors play a significant role in influencing susceptibility to tuberculosis. This review examines the current progress in studying polymorphisms within immune genes associated with tuberculosis susceptibility, focusing on African populations. The roles of various proteins, including Toll-like receptors, Dendritic Cell-Specific Intercellular Adhesion Molecule-3 Grabbing Non-Integrin, vitamin D nuclear receptor, soluble C-type lectins such as surfactant proteins A and D, C-type Lectin Domain Family 4 Member E, and mannose-binding lectin, phagocyte cytokines such as Interleukin-1, Interleukin-6, Interleukin-10, Interleukin-12, and Interleukin-18, and chemokines such as Interleukin-8, monocyte chemoattractant protein 1, Regulated upon activation, normal T-cell expressed and secreted are explored in the context of tuberculosis susceptibility. We also address the potential impact of genetic variants on protein functions, as well as how these findings align with the genetic polymorphisms not associated with tuberculosis. Functional studies in model systems provide insights into the intricate host-pathogen interactions and susceptibility mechanisms. Despite progress, gaps in knowledge remain, highlighting the need for further investigations. This review emphasizes the association of Single Nucleotide Polymorphisms with diverse aspects of tuberculosis pathogenesis, including disease detection and Mycobacterium tuberculosis infection.
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Affiliation(s)
- Wycliff Wodelo
- Department of Immunology and Molecular Biology, School of Biomedical Science, College of Health Science, Makerere University, Kampala, Uganda
| | - Eddie M Wampande
- Department of Immunology and Molecular Biology, School of Biomedical Science, College of Health Science, Makerere University, Kampala, Uganda
- Department of Veterinary Medicine, School of Veterinary Medicine and Animal Resources, College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Alfred Andama
- Department of Medical Microbiology, School of Medicine, College of Health Science, Makerere University, Kampala, Uganda
| | - David Patrick Kateete
- Department of Immunology and Molecular Biology, School of Biomedical Science, College of Health Science, Makerere University, Kampala, Uganda
| | - Kenneth Ssekatawa
- Department of Science, Technical and Vocational Education, Makerere University, Kampala, Uganda
- Africa Center Excellence in Materials Product Development and Nanotechnology (MAPRONANO ACE), Makerere University, Kampala, Uganda
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6
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Silva-Pereira TT, Soler-Camargo NC, Guimarães AMS. Diversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures. Microbiol Spectr 2024; 12:e0228923. [PMID: 38230932 PMCID: PMC10871547 DOI: 10.1128/spectrum.02289-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 12/19/2023] [Indexed: 01/18/2024] Open
Abstract
We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships. In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.
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Affiliation(s)
- Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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7
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. PLoS Pathog 2024; 20:e1012050. [PMID: 38422159 DOI: 10.1371/journal.ppat.1012050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/12/2024] [Accepted: 02/13/2024] [Indexed: 03/02/2024] Open
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2, which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulate Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage-defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2, label preferentially accumulates in dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accrued lactate toxicity via the deleterious buildup of sugar phosphates. The evolved lldD2 variants increase lactate incorporation to pyruvate while altering triose phosphate flux, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX- 1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provides context for the selective advantage of lldD2 mutations in adapting to host stress.
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Affiliation(s)
- Sydney Stanley
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Xin Wang
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Qingyun Liu
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Young Yon Kwon
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Abigail M Frey
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Nathan D Hicks
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Andrew J Vickers
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sheng Hui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, Massachusetts, United States of America
| | - Sarah M Fortune
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, United States of America
- Ragon Institute of MGH, MIT, and Harvard, Cambridge, Massachusetts, United States of America
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, United States of America
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8
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Mah JC, Lohmueller KE, Garud N. Inference of the demographic histories and selective effects of human gut commensal microbiota over the course of human history. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.09.566454. [PMID: 38014007 PMCID: PMC10680615 DOI: 10.1101/2023.11.09.566454] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite the importance of gut commensal microbiota to human health, there is little knowledge about their evolutionary histories, including their population demographic histories and their distributions of fitness effects (DFE) of new mutations. Here, we infer the demographic histories and DFEs of 27 of the most highly prevalent and abundant commensal gut microbial species in North Americans over timescales exceeding human generations using a collection of lineages inferred from a panel of healthy hosts. We find overall reductions in genetic variation among commensal gut microbes sampled from a Western population relative to an African rural population. Additionally, some species in North American microbiomes display contractions in population size and others expansions, potentially occurring at several key historical moments in human history. DFEs across species vary from highly to mildly deleterious, with accessory genes experiencing more drift compared to core genes. Within genera, DFEs tend to be more congruent, reflective of underlying phylogenetic relationships. Taken together, these findings suggest that human commensal gut microbes have distinct evolutionary histories, possibly reflecting the unique roles of individual members of the microbiome.
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Affiliation(s)
- Jonathan C. Mah
- Bioinformatics Interdepartmental Program, University of California, Los Angeles
| | - Kirk E. Lohmueller
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
- Department of Human Genetics, University of California, Los Angeles
| | - Nandita Garud
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
- Department of Human Genetics, University of California, Los Angeles
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9
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Stanley S, Wang X, Liu Q, Kwon YY, Frey AM, Hicks ND, Vickers AJ, Hui S, Fortune SM. Ongoing evolution of the Mycobacterium tuberculosis lactate dehydrogenase reveals the pleiotropic effects of bacterial adaption to host pressure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561592. [PMID: 37873410 PMCID: PMC10592758 DOI: 10.1101/2023.10.09.561592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The bacterial determinants that facilitate Mycobacterium tuberculosis (Mtb) adaptation to the human host environment are poorly characterized. We have sought to decipher the pressures facing the bacterium in vivo by assessing Mtb genes that are under positive selection in clinical isolates. One of the strongest targets of selection in the Mtb genome is lldD2 , which encodes a quinone-dependent L-lactate dehydrogenase (LldD2) that catalyzes the oxidation of lactate to pyruvate. Lactate accumulation is a salient feature of the intracellular environment during infection and lldD2 is essential for Mtb growth in macrophages. We determined the extent of lldD2 variation across a set of global clinical isolates and defined how prevalent mutations modulates Mtb fitness. We show the stepwise nature of lldD2 evolution that occurs as a result of ongoing lldD2 selection in the background of ancestral lineage defining mutations and demonstrate that the genetic evolution of lldD2 additively augments Mtb growth in lactate. Using quinone-dependent antibiotic susceptibility as a functional reporter, we also find that the evolved lldD2 mutations functionally increase the quinone-dependent activity of LldD2. Using 13 C-lactate metabolic flux tracing, we find that lldD2 is necessary for robust incorporation of lactate into central carbon metabolism. In the absence of lldD2 , label preferentially accumulates in methylglyoxal precursors dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P) and is associated with a discernible growth defect, providing experimental evidence for accumulated lactate toxicity via a methylglyoxal pathway that has been proposed previously. The evolved lldD2 variants increase lactate incorporation to pyruvate but also alter flux in the methylglyoxal pathway, suggesting both an anaplerotic and detoxification benefit to lldD2 evolution. We further show that the mycobacterial cell is transcriptionally sensitive to the changes associated with altered lldD2 activity which affect the expression of genes involved in cell wall lipid metabolism and the ESX-1 virulence system. Together, these data illustrate a multifunctional role of LldD2 that provide context for the selective advantage of lldD2 mutations in adapting to host stress.
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10
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Vargas R, Luna MJ, Freschi L, Marin M, Froom R, Murphy KC, Campbell EA, Ioerger TR, Sassetti CM, Farhat MR. Phase variation as a major mechanism of adaptation in Mycobacterium tuberculosis complex. Proc Natl Acad Sci U S A 2023; 120:e2301394120. [PMID: 37399390 PMCID: PMC10334774 DOI: 10.1073/pnas.2301394120] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Accepted: 05/03/2023] [Indexed: 07/05/2023] Open
Abstract
Phase variation induced by insertions and deletions (INDELs) in genomic homopolymeric tracts (HT) can silence and regulate genes in pathogenic bacteria, but this process is not characterized in MTBC (Mycobacterium tuberculosis complex) adaptation. We leverage 31,428 diverse clinical isolates to identify genomic regions including phase-variants under positive selection. Of 87,651 INDEL events that emerge repeatedly across the phylogeny, 12.4% are phase-variants within HTs (0.02% of the genome by length). We estimated the in-vitro frameshift rate in a neutral HT at 100× the neutral substitution rate at [Formula: see text] frameshifts/HT/year. Using neutral evolution simulations, we identified 4,098 substitutions and 45 phase-variants to be putatively adaptive to MTBC (P < 0.002). We experimentally confirm that a putatively adaptive phase-variant alters the expression of espA, a critical mediator of ESX-1-dependent virulence. Our evidence supports the hypothesis that phase variation in the ESX-1 system of MTBC can act as a toggle between antigenicity and survival in the host.
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Affiliation(s)
- Roger Vargas
- Center for Computational Biomedicine, Harvard Medical School, Boston, MA02115
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Michael J. Luna
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Luca Freschi
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Maximillian Marin
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
| | - Ruby Froom
- Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY10065
- Laboratory of Host-Pathogen Biology, The Rockefeller University, New York, NY10065
| | - Kenan C. Murphy
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | | | - Thomas R. Ioerger
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX77843
| | - Christopher M. Sassetti
- Department of Microbiology and Physiological Systems, University of Massachusetts Chan Medical School, Worcester, MA01655
| | - Maha Reda Farhat
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA02115
- Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA02114
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11
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van Doren TP. Biocultural perspectives of infectious diseases and demographic evolution: Tuberculosis and its comorbidities through history. Evol Anthropol 2022; 32:100-117. [PMID: 36436141 DOI: 10.1002/evan.21970] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 06/09/2022] [Accepted: 11/11/2022] [Indexed: 11/28/2022]
Abstract
Anthropologists recognize the importance of conceptualizing health in the context of the mutually evolving nature of biology and culture through the biocultural approach, but biocultural anthropological perspectives of infectious diseases and their impacts on humans (and vice versa) through time are relatively underrepresented. Tuberculosis (TB) has been a constant companion of humans for thousands of years and has heavily influenced population health in almost every phase of cultural and demographic evolution. TB in human populations has been dramatically influenced by behavior, demographic and epidemiological shifts, and other comorbidities through history. This paper critically discusses TB and some of its major comorbidities through history within a biocultural framework to show how transitions in human demography and culture affected the disease-scape of TB. In doing so, I address the potential synthesis of biocultural and epidemiological transition theory to better comprehend the mutual evolution of infectious diseases and humans.
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12
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Soler-Camargo NC, Silva-Pereira TT, Zimpel CK, Camacho MF, Zelanis A, Aono AH, Patané JS, Dos Santos AP, Guimarães AMS. The rate and role of pseudogenes of the Mycobacterium tuberculosis complex. Microb Genom 2022; 8. [PMID: 36250787 DOI: 10.1099/mgen.0.000876] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Whole-genome sequence analyses have significantly contributed to the understanding of virulence and evolution of the Mycobacterium tuberculosis complex (MTBC), the causative pathogens of tuberculosis. Most MTBC evolutionary studies are focused on single nucleotide polymorphisms and deletions, but rare studies have evaluated gene content, whereas none has comprehensively evaluated pseudogenes. Accordingly, we describe an extensive study focused on quantifying and predicting possible functions of MTBC and Mycobacterium canettii pseudogenes. Using NCBI's PGAP-detected pseudogenes, we analysed 25 837 pseudogenes from 158 MTBC and M. canetii strains and combined transcriptomics and proteomics of M. tuberculosis H37Rv to gain insights about pseudogenes' expression. Our results indicate significant variability concerning rate and conservancy of in silico predicted pseudogenes among different ecotypes and lineages of tuberculous mycobacteria and pseudogenization of important virulence factors and genes of the metabolism and antimicrobial resistance/tolerance. We show that in silico predicted pseudogenes contribute considerably to MTBC genetic diversity at the population level. Moreover, the transcription machinery of M. tuberculosis can fully transcribe most pseudogenes, indicating intact promoters and recent pseudogene evolutionary emergence. Proteomics of M. tuberculosis and close evaluation of mutational lesions driving pseudogenization suggest that few in silico predicted pseudogenes are likely capable of neofunctionalization, nonsense mutation reversal, or phase variation, contradicting the classical definition of pseudogenes. Such findings indicate that genome annotation should be accompanied by proteomics and protein function assays to improve its accuracy. While indels and insertion sequences are the main drivers of the observed mutational lesions in these species, population bottlenecks and genetic drift are likely the evolutionary processes acting on pseudogenes' emergence over time. Our findings unveil a new perspective on MTBC's evolution and genetic diversity.
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Affiliation(s)
- Naila Cristina Soler-Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil
| | - Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, College of Veterinary Medicine, University of São Paulo, São Paulo, SP, Brazil
| | - Maurício F Camacho
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - André Zelanis
- Functional Proteomics Laboratory, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | - Alexandre H Aono
- Center of Molecular Biology and Genetic Engineering, University of Campinas, Campinas, SP, Brazil.,Institute of Science and Technology, Federal University of São Paulo (UNIFESP), São José dos Campos, SP, Brazil
| | | | | | - Ana Marcia Sá Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, SP, Brazil.,Department of Comparative Pathobiology, College of Veterinary Medicine, Purdue University
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13
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Smith TM, Youngblom MA, Kernien JF, Mohamed MA, Fry SS, Bohr LL, Mortimer TD, O'Neill MB, Pepperell CS. Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis. eLife 2022; 11:e78454. [PMID: 35726854 PMCID: PMC9213004 DOI: 10.7554/elife.78454] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/15/2022] [Indexed: 12/30/2022] Open
Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (M. tb), is a leading cause of death due to infectious disease. TB is not traditionally associated with biofilms, but M. tb biofilms are linked with drug and immune tolerance and there is increasing recognition of their contribution to the recalcitrance of TB infections. Here, we used M. tb experimental evolution to investigate this complex phenotype and identify candidate loci controlling biofilm formation. We identified novel candidate loci, adding to our understanding of the genetic architecture underlying M. tb biofilm development. Under selective pressure to grow as a biofilm, regulatory mutations rapidly swept to fixation and were associated with changes in multiple traits, including extracellular matrix production, cell size, and growth rate. Genetic and phenotypic paths to enhanced biofilm growth varied according to the genetic background of the parent strain, suggesting that epistatic interactions are important in M. tb adaptation to changing environments.
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Affiliation(s)
| | - Madison A Youngblom
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - John F Kernien
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Mohamed A Mohamed
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Sydney S Fry
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
| | - Lindsey L Bohr
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Microbiology Doctoral Training Program, University of Wisconsin-MadisonMadisonUnited States
| | - Tatum D Mortimer
- Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public HealthBostonUnited States
| | - Mary B O'Neill
- Laboratoire de Biochimie (LBC), Chimie Biologie et Innovation, ESPCI Paris, PSL UniversitéParisFrance
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
- Department of Medicine (Infectious Diseases), School of Medicine and Public Health, University of Wisconsin-MadisonMadisonUnited States
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14
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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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15
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Dong Y, Feng Y, Ou X, Liu C, Fan W, Zhao Y, Hu Y, Zhou X. Genomic analysis of diversity, biogeography, and drug resistance in Mycobacterium bovis. Transbound Emerg Dis 2022; 69:e2769-e2778. [PMID: 35695307 DOI: 10.1111/tbed.14628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 05/16/2022] [Accepted: 06/08/2022] [Indexed: 11/29/2022]
Abstract
Mycobacterium bovis is the cause of bovine tuberculosis, and it can also cause disease in humans, with symptoms similar to those caused by Mycobacterium tuberculosis. However, our understanding of its genomic diversity, biogeography, and drug resistance remains incomplete. We performed a comparative and phylogenetic analysis of 3,228 M. bovis genomes from 24 countries. Following drug susceptibility testing, we applied a bacterial genome-wide association study to capture associations between genomic variation and drug resistance in 74 newly isolated strains from China. The data show that the cattle-adapted M. bovis were divided into six lineages with a strong phylogeographical population structure. Lineage 1 and Lineage 6 are the most widespread globally, while others show a strong geographical restriction. 17.39% of M. bovis isolates were resistant to at least one drug in China. Furthermore, we identify genomic variations associated with an increased risk of resistance acquisition. This study furthers our knowledge of M. bovis diversity, biogeography, and drug resistance and will facilitate more deeply informed genomic tracking and surveillance to minimize its threat to human health, as a cause of zoonotic tuberculosis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuhui Dong
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
| | - Yuqing Feng
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xichao Ou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Chunfa Liu
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Weixing Fan
- National Reference Laboroatory for Animal Tuberculosis, China Animal Health and Epidemiology Center, Qingdao, 266032, China
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Yongfei Hu
- State Key Laboratory of Animal Nutrition, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xiangmei Zhou
- Key Laboratory of Animal Epidemiology and Zoonosis, Ministry of Agriculture, National Animal Transmissible Spongiform Encephalopathy Laboratory, College of Veterinary Medicine, China Agricultural University, Beijing, 100193, China
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16
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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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17
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Chiner-Oms Á, López MG, Moreno-Molina M, Furió V, Comas I. Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection. Proc Natl Acad Sci U S A 2022; 119:e2113600119. [PMID: 35452305 PMCID: PMC9173582 DOI: 10.1073/pnas.2113600119] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 02/17/2022] [Indexed: 12/20/2022] Open
Abstract
Genetic differences between different Mycobacterium tuberculosis complex (MTBC) strains determine their ability to transmit within different host populations, their latency times, and their drug resistance profiles. Said differences usually emerge through de novo mutations and are maintained or discarded by the balance of evolutionary forces. Using a dataset of ∼5,000 strains representing global MTBC diversity, we determined the past and present selective forces that have shaped the current variability observed in the pathogen population. We identified regions that have evolved under changing types of selection since the time of the MTBC common ancestor. Our approach highlighted striking differences in the genome regions relevant for host–pathogen interaction and, in particular, suggested an adaptive role for the sensor protein of two-component systems. In addition, we applied our approach to successfully identify potential determinants of resistance to drugs administered as second-line tuberculosis treatments.
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Affiliation(s)
- Álvaro Chiner-Oms
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | - Mariana G. López
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | | | - Victoria Furió
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
| | - Iñaki Comas
- Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, 46010, Spain
- CIBER en Epidemiología y Salud Pública, Valencia, Spain
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18
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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: 0.8] [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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19
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Lima DAR, Zimpel CK, Patané JS, Silva-Pereira TT, Etges RN, Rodrigues RA, Dávila AMR, Ikuta CY, Ferreira Neto JS, Guimarães AMS, Araújo FR. Genomic analysis of an outbreak of bovine tuberculosis in a man-made multi-host species system: A call for action on wildlife in Brazil. Transbound Emerg Dis 2021; 69:e580-e591. [PMID: 34633756 DOI: 10.1111/tbed.14343] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from eight species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Using a previously sequenced dataset of 71 M. bovis genomes from cattle, we found no recent transmission events between nearby farms and the park based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.
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Affiliation(s)
- Daiane A R Lima
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Cristina K Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - José S Patané
- Center for Bioinformatics and Computational Biology, Butantan Institute, São Paulo, São Paulo, Brazil
| | - Taiana Tainá Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Rodrigo N Etges
- Livestock and Rural Development, Secretary of Agriculture, Porto Alegre, Rio Grande do Sul, Brazil
| | - Rudielle A Rodrigues
- Department of Veterinary Medicine, Graduate Program in Veterinary Sciences, School of Veterinary Medicine, Federal University of Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | - Alberto M R Dávila
- Computational and Systems Biology Laboratory and Graduate Program on Biodiversity and Health, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - José S Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Ana Marcia S Guimarães
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, São Paulo, Brazil
| | - Flábio R Araújo
- Embrapa Beef Cattle, Campo Grande, Mato Grosso do Sul, Brazil
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20
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Castro RAD, Borrell S, Gagneux S. The within-host evolution of antimicrobial resistance in Mycobacterium tuberculosis. FEMS Microbiol Rev 2021; 45:fuaa071. [PMID: 33320947 PMCID: PMC8371278 DOI: 10.1093/femsre/fuaa071] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Accepted: 12/11/2020] [Indexed: 12/12/2022] Open
Abstract
Tuberculosis (TB) has been responsible for the greatest number of human deaths due to an infectious disease in general, and due to antimicrobial resistance (AMR) in particular. The etiological agents of human TB are a closely-related group of human-adapted bacteria that belong to the Mycobacterium tuberculosis complex (MTBC). Understanding how MTBC populations evolve within-host may allow for improved TB treatment and control strategies. In this review, we highlight recent works that have shed light on how AMR evolves in MTBC populations within individual patients. We discuss the role of heteroresistance in AMR evolution, and review the bacterial, patient and environmental factors that likely modulate the magnitude of heteroresistance within-host. We further highlight recent works on the dynamics of MTBC genetic diversity within-host, and discuss how spatial substructures in patients' lungs, spatiotemporal heterogeneity in antimicrobial concentrations and phenotypic drug tolerance likely modulates the dynamics of MTBC genetic diversity in patients during treatment. We note the general characteristics that are shared between how the MTBC and other bacterial pathogens evolve in humans, and highlight the characteristics unique to the MTBC.
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Affiliation(s)
- Rhastin A D Castro
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sonia Borrell
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Socinstrasse 57, 4051 Basel, Basel, Switzerland
- University of Basel, Petersplatz 1, 4001 Basel, Basel, Switzerland
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21
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Deaconescu AM. Mfd - at the crossroads of bacterial DNA repair, transcriptional regulation and molecular evolvability. Transcription 2021; 12:156-170. [PMID: 34674614 PMCID: PMC8632110 DOI: 10.1080/21541264.2021.1982628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/06/2021] [Accepted: 09/14/2021] [Indexed: 12/21/2022] Open
Abstract
For survival, bacteria need to continuously evolve and adapt to complex environments, including those that may impact the integrity of the DNA, the repository of genetic information to be passed on to future generations. The multiple factors of DNA repair share the substrate on which they operate with other key cellular machineries, principally those of replication and transcription, implying a high degree of coordination of DNA-based activities. In this review, I focus on progress made in the understanding of the protein factors operating at the crossroads of these three fundamental processes, with emphasis on the mutation frequency decline protein (Mfd, aka TRCF). Although Mfd research has a rich history that goes back in time for more than half a century, recent reports hint that much remains to be uncovered. I argue that besides being a transcription-repair coupling factor (TRCF), Mfd is also a global regulator of transcription and a pro-mutagenic factor, and that the way it interfaces with transcription, replication and nucleotide excision repair makes it an attractive candidate for the development of strategies to curb molecular evolution, hence, antibiotic resistance.
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Affiliation(s)
- Alexandra M. Deaconescu
- CONTACT Alexandra M. Deaconescu Molecular Biology, Cell Biology and Biochemistry, Laboratories of Molecular Medicine, Brown University, 70 Ship St. G-E4, Providence, RI02903, USA
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22
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Menardo F, Gagneux S, Freund F. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis. Mol Biol Evol 2021; 38:290-306. [PMID: 32667991 PMCID: PMC8480183 DOI: 10.1093/molbev/msaa179] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Kingman coalescent and its developments are often considered among the most important advances in population genetics of the last decades. Demographic inference based on coalescent theory has been used to reconstruct the population dynamics and evolutionary history of several species, including Mycobacterium tuberculosis (MTB), an important human pathogen causing tuberculosis. One key assumption of the Kingman coalescent is that the number of descendants of different individuals does not vary strongly, and violating this assumption could lead to severe biases caused by model misspecification. Individual lineages of MTB are expected to vary strongly in reproductive success because 1) MTB is potentially under constant selection due to the pressure of the host immune system and of antibiotic treatment, 2) MTB undergoes repeated population bottlenecks when it transmits from one host to the next, and 3) some hosts show much higher transmission rates compared with the average (superspreaders). Here, we used an approximate Bayesian computation approach to test whether multiple-merger coalescents (MMC), a class of models that allow for large variation in reproductive success among lineages, are more appropriate models to study MTB populations. We considered 11 publicly available whole-genome sequence data sets sampled from local MTB populations and outbreaks and found that MMC had a better fit compared with the Kingman coalescent for 10 of the 11 data sets. These results indicate that the null model for analyzing MTB outbreaks should be reassessed and that past findings based on the Kingman coalescent need to be revisited.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sébastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Fabian Freund
- Department of Plant Biodiversity and Breeding Informatics, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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23
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Pérez-González J, Carranza J, Martínez R, Benítez-Medina JM. Host Genetic Diversity and Infectious Diseases. Focus on Wild Boar, Red Deer and Tuberculosis. Animals (Basel) 2021; 11:1630. [PMID: 34072907 PMCID: PMC8229303 DOI: 10.3390/ani11061630] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/19/2021] [Accepted: 05/28/2021] [Indexed: 12/16/2022] Open
Abstract
Host genetic diversity tends to limit disease spread in nature and buffers populations against epidemics. Genetic diversity in wildlife is expected to receive increasing attention in contexts related to disease transmission and human health. Ungulates such as wild boar (Sus scrofa) and red deer (Cervus elaphus) are important zoonotic hosts that can be precursors to disease emergence and spread in humans. Tuberculosis is a zoonotic disease with relevant consequences and can present high prevalence in wild boar and red deer populations. Here, we review studies on the genetic diversity of ungulates and determine to what extent these studies consider its importance on the spread of disease. This assessment also focused on wild boar, red deer, and tuberculosis. We found a disconnection between studies treating genetic diversity and those dealing with infectious diseases. Contrarily, genetic diversity studies in ungulates are mainly concerned with conservation. Despite the existing disconnection between studies on genetic diversity and studies on disease emergence and spread, the knowledge gathered in each discipline can be applied to the other. The bidirectional applications are illustrated in wild boar and red deer populations from Spain, where TB is an important threat for wildlife, livestock, and humans.
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Affiliation(s)
- Javier Pérez-González
- Biology and Ethology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain
| | - Juan Carranza
- Wildlife Research Unit (UIRCP), University of Córdoba, 14071 Córdoba, Spain;
| | - Remigio Martínez
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
| | - José Manuel Benítez-Medina
- Infectious Pathology Unit, Veterinary Faculty, University of Extremadura, 10003 Cáceres, Spain; (R.M.); (J.M.B.-M.)
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24
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Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau. Proc Natl Acad Sci U S A 2021; 118:2017831118. [PMID: 33879609 DOI: 10.1073/pnas.2017831118] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
During its global dispersal, Mycobacterium tuberculosis (Mtb) has encountered varied geographic environments and host populations. Although local adaptation seems to be a plausible model for describing long-term host-pathogen interactions, genetic evidence for this model is lacking. Here, we analyzed 576 whole-genome sequences of Mtb strains sampled from different regions of high-altitude Tibet. Our results show that, after sequential introduction of a few ancestral strains, the Tibetan Mtb population diversified locally while maintaining strict separation from the Mtb populations on the lower altitude plain regions of China. The current population structure and estimated past population dynamics suggest that the modern Beijing sublineage strains, which expanded over most of China and other global regions, did not show an expansion advantage in Tibet. The mutations in the Tibetan strains showed a higher proportion of A > G/T > C transitions than strains from the plain regions, and genes encoding DNA repair enzymes showed evidence of positive selection. Moreover, the long-term Tibetan exclusive selection for truncating mutations in the thiol-oxidoreductase encoding sseA gene suggests that Mtb was subjected to local selective pressures associated with oxidative stress. Collectively, the population genomics of Mtb strains in the relatively isolated population of Tibet provides genetic evidence that Mtb has adapted to local environments.
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25
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Abstract
The dN/dS ratio provides evidence of adaptation or functional constraint in protein-coding genes by quantifying the relative excess or deficit of amino acid-replacing versus silent nucleotide variation. Inexpensive sequencing promises a better understanding of parameters, such as dN/dS, but analyzing very large data sets poses a major statistical challenge. Here, I introduce genomegaMap for estimating within-species genome-wide variation in dN/dS, and I apply it to 3,979 genes across 10,209 tuberculosis genomes to characterize the selection pressures shaping this global pathogen. GenomegaMap is a phylogeny-free method that addresses two major problems with existing approaches: 1) It is fast no matter how large the sample size and 2) it is robust to recombination, which causes phylogenetic methods to report artefactual signals of adaptation. GenomegaMap uses population genetics theory to approximate the distribution of allele frequencies under general, parent-dependent mutation models. Coalescent simulations show that substitution parameters are well estimated even when genomegaMap’s simplifying assumption of independence among sites is violated. I demonstrate the ability of genomegaMap to detect genuine signatures of selection at antimicrobial resistance-conferring substitutions in Mycobacterium tuberculosis and describe a novel signature of selection in the cold-shock DEAD-box protein A gene deaD/csdA. The genomegaMap approach helps accelerate the exploitation of big data for gaining new insights into evolution within species.
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Affiliation(s)
- Daniel J Wilson
- Big Data Institute, Nuffield Department of Population Health, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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26
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Menardo F, Rutaihwa LK, Zwyer M, Borrell S, Comas I, Conceição EC, Coscolla M, Cox H, Joloba M, Dou HY, Feldmann J, Fenner L, Fyfe J, Gao Q, García de Viedma D, Garcia-Basteiro AL, Gygli SM, Hella J, Hiza H, Jugheli L, Kamwela L, Kato-Maeda M, Liu Q, Ley SD, Loiseau C, Mahasirimongkol S, Malla B, Palittapongarnpim P, Rakotosamimanana N, Rasolofo V, Reinhard M, Reither K, Sasamalo M, Silva Duarte R, Sola C, Suffys P, Batista Lima KV, Yeboah-Manu D, Beisel C, Brites D, Gagneux S. Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim. F1000Res 2021; 10:60. [PMID: 33732436 PMCID: PMC7921886 DOI: 10.12688/f1000research.28318.2] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Background: Lineage 1 (L1) and 3 (L3) are two lineages of the Mycobacterium tuberculosis complex (MTBC) causing tuberculosis (TB) in humans. L1 and L3 are prevalent around the rim of the Indian Ocean, the region that accounts for most of the world's new TB cases. Despite their relevance for this region, L1 and L3 remain understudied. Methods: We analyzed 2,938 L1 and 2,030 L3 whole genome sequences originating from 69 countries. We reconstructed the evolutionary history of these two lineages and identified genes under positive selection. Results: We found a strongly asymmetric pattern of migration from South Asia toward neighboring regions, highlighting the historical role of South Asia in the dispersion of L1 and L3. Moreover, we found that several genes were under positive selection, including genes involved in virulence and resistance to antibiotics. For L1 we identified signatures of local adaptation at the esxH locus, a gene coding for a secreted effector that targets the human endosomal sorting complex, and is included in several vaccine candidates. Conclusions: Our study highlights the importance of genetic diversity in the MTBC, and sheds new light on two of the most important MTBC lineages affecting humans.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Liliana K Rutaihwa
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Michaela Zwyer
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sonia Borrell
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, Valencia, Spain
| | - Emilyn Costa Conceição
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil.,Instituto Nacional de Infectologia Evandro Chagas, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | | | - Helen Cox
- Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Moses Joloba
- Department of Medical Microbiology, Makerere University, Kampala, Uganda
| | - Horng-Yunn Dou
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institute, Zhunan, Taiwan
| | - Julia Feldmann
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lukas Fenner
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Institute for Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Janet Fyfe
- Victorian Infectious Diseases Reference Laboratory, Melbourne, Australia
| | - Qian Gao
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Darío García de Viedma
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.,CIBER Enfermedades Respiratorias, Madrid, Spain.,Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Madrid, Spain
| | - Alberto L Garcia-Basteiro
- Barcelona Institute for Global Health, Barcelona, Spain.,Centro de Investigação em Saúde de Manhiça, Maputo, Mozambique
| | - Sebastian M Gygli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Jerry Hella
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | - Hellen Hiza
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Levan Jugheli
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Lujeko Kamwela
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | | | - Qingyun Liu
- Institute of Medical Microbiology, School of Basic Medical Science of Fudan University, Shanghai, China
| | - Serej D Ley
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Papua New Guinea Institute of Medical Research, Goroka, Papua New Guinea
| | - Chloe Loiseau
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Surakameth Mahasirimongkol
- Department of Microbiology, Mahidol University, Bangkok, Thailand.,National Science and Technology Development Agency, Bangkok, Thailand
| | - Bijaya Malla
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Prasit Palittapongarnpim
- Department of Microbiology, Mahidol University, Bangkok, Thailand.,National Science and Technology Development Agency, Bangkok, Thailand
| | | | | | - Miriam Reinhard
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Klaus Reither
- University of Basel, Basel, Switzerland.,Department of Medicine, Swiss Tropical and Public Health Institute, Basel, Switzerland
| | - Mohamed Sasamalo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Ifakara Health Institute, Bagamoyo, Tanzania
| | - Rafael Silva Duarte
- Instituto de Microbiologia, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Christophe Sola
- Université Paris-Saclay, Paris, France.,INSERM-Université de Paris, Paris, France
| | - Philip Suffys
- Laboratório de Biologia Molecular Aplicada a Micobactérias, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Karla Valeria Batista Lima
- Centro de Ciências Biológicas e da Saúde, Universidade do Estado do Pará, Belém, Brazil.,Instituto Evandro Chagas, Ananindeua, Brazil
| | - Dorothy Yeboah-Manu
- Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Christian Beisel
- Department of Biosystems Science and Engineering, ETH Zürich, Basel, Switzerland
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
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27
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Wibberg D, Price-Carter M, Rückert C, Blom J, Möbius P. Complete Genome Sequence of Ovine Mycobacterium avium subsp. paratuberculosis Strain JIII-386 (MAP-S/type III) and Its Comparison to MAP-S/type I, MAP-C, and M. avium Complex Genomes. Microorganisms 2020; 9:microorganisms9010070. [PMID: 33383865 PMCID: PMC7823733 DOI: 10.3390/microorganisms9010070] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 12/21/2020] [Accepted: 12/24/2020] [Indexed: 02/07/2023] Open
Abstract
Mycobacterium avium (M. a.) subsp. paratuberculosis (MAP) is a worldwide-distributed obligate pathogen in ruminants causing Johne’s disease. Due to a lack of complete subtype III genome sequences, there is not yet conclusive information about genetic differences between strains of cattle (MAP-C, type II) and sheep (MAP-S) type, and especially between MAP-S subtypes I, and III. Here we present the complete, circular genome of MAP-S/type III strain JIII-386 (DE) closed by Nanopore-technology and its comparison with MAP-S/type I closed genome of strain Telford (AUS), MAP-S/type III draft genome of strain S397 (U.S.), twelve closed MAP-C strains, and eight closed M.-a.-complex-strains. Structural comparative alignments revealed clearly the mosaic nature of MAP, emphasized differences between the subtypes and the higher diversity of MAP-S genomes. The comparison of various genomic elements including transposases and genomic islands provide new insights in MAP genomics. MAP type specific phenotypic features may be attributed to genes of known large sequence polymorphisms (LSPSs) regions I–IV and deletions #1 and #2, confirmed here, but could also result from identified frameshifts or interruptions of various virulence-associated genes (e.g., mbtC in MAP-S). Comprehensive core and pan genome analysis uncovered unique genes (e.g., cytochromes) and genes probably acquired by horizontal gene transfer in different MAP-types and subtypes, but also emphasized the highly conserved and close relationship, and the complex evolution of M.-a.-strains.
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Affiliation(s)
- Daniel Wibberg
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Marian Price-Carter
- AgResearch, Hopkirk Research Institute, Grasslands Research Centre, Palmerston North 4442, New Zealand;
| | - Christian Rückert
- Center for Biotechnology (CeBiTec), Bielefeld University, 33501 Bielefeld, Germany; (D.W.); (C.R.)
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Gießen, D-35390 Gießen, Germany;
| | - Petra Möbius
- Friedrich-Loeffler-Institut/Federal Research Institute for Animal Health, Institute of Molecular Pathogenesis, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-(0)3641-8042280
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28
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Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination. Appl Environ Microbiol 2020; 87:AEM.02002-20. [PMID: 33097502 DOI: 10.1128/aem.02002-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Accepted: 10/14/2020] [Indexed: 01/14/2023] Open
Abstract
Genomic data reveal single-nucleotide polymorphisms (SNPs) that may carry information about the evolutionary history of bacteria. However, it remains unclear what inferences about selection can be made from genomic SNP data. Bacterial species are often sampled during epidemic outbreaks or within hosts during the course of chronic infections. SNPs obtained from genomic analysis of these data are not necessarily fixed. Treating them as fixed during analysis by using measures such as the ratio of nonsynonymous to synonymous evolutionary changes (dN/dS) may lead to incorrect inferences about the strength and direction of selection. In this study, we consider data from a range of whole-genome sequencing studies of bacterial pathogens and explore patterns of nonsynonymous variation to assess whether evidence of selection can be identified by investigating SNP counts alone across multiple WGS studies. We visualize these SNP data in ways that highlight their relationship to neutral baseline expectations. These neutral expectations are based on a simple model of mutation, from which we simulate SNP accumulation to investigate how SNP counts are distributed under alternative assumptions about positive and negative selection. We compare these patterns with empirical SNP data and illustrate the general difficulty of detecting positive selection from SNP data. Finally, we consider whether SNP counts observed at the between-host population level differ from those observed at the within-host level and find some evidence that suggests that dynamics across these two scales are driven by different underlying processes.IMPORTANCE Identifying selection from SNP data obtained from whole-genome sequencing studies is challenging. Some current measures used to identify and quantify selection acting on genomes rely on fixed differences; thus, these are inappropriate for SNP data where variants are not fixed. With the increase in whole-genome sequencing studies, it is important to consider SNP data in the context of evolutionary processes. How SNPs are counted and analyzed can help in understanding mutation accumulation and trajectories of strains. We developed a tool for identifying possible evidence of selection and for comparative analysis with other SNP data. We propose a model that provides a rule-of-thumb guideline and two new visualization techniques that can be used to interpret and compare SNP data. We quantify the expected proportion of nonsynonymous SNPs in coding regions under neutrality and demonstrate its use in identifying evidence of positive and negative selection from simulations and empirical data.
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29
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Morales-Arce AY, Sabin SJ, Stone AC, Jensen JD. The population genomics of within-host Mycobacterium tuberculosis. Heredity (Edinb) 2020; 126:1-9. [PMID: 33060846 DOI: 10.1038/s41437-020-00377-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/02/2020] [Accepted: 10/03/2020] [Indexed: 11/09/2022] Open
Abstract
Recent progress in genomic sequencing from patient samples has allowed for the first detailed insight into the within-host genetic diversity of Mycobacterium tuberculosis (M.TB), revealing remarkably low levels of variation. While this has often been attributed to low mutation rates, other factors have been described, including resistance evolution (i.e., selective sweeps), widespread purifying and background selection, and, more recently, progeny skew. Here we review recent findings pertaining to the processes governing the evolutionary dynamics of M.TB, discuss their implications for improving our understanding of this important human pathogen, and make recommendations for future work. Significantly, this emerging evolutionary framework involving the joint estimation of demographic, selective, and reproductive processes is forming a new paradigm for the study of within-host pathogen evolution that will be widely applicable across organisms.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.
| | - Susanna J Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA. .,School of Life Sciences, Arizona State University, Tempe, AZ, USA.
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30
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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: 36] [Impact Index Per Article: 7.2] [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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31
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Zimpel CK, Patané JSL, Guedes ACP, de Souza RF, Silva-Pereira TT, Camargo NCS, de Souza Filho AF, Ikuta CY, Neto JSF, Setubal JC, Heinemann MB, Guimaraes AMS. Global Distribution and Evolution of Mycobacterium bovis Lineages. Front Microbiol 2020; 11:843. [PMID: 32477295 PMCID: PMC7232559 DOI: 10.3389/fmicb.2020.00843] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
Mycobacterium bovis is the main causative agent of zoonotic tuberculosis in humans and frequently devastates livestock and wildlife worldwide. Previous studies suggested the existence of genetic groups of M. bovis strains based on limited DNA markers (a.k.a. clonal complexes), and the evolution and ecology of this pathogen has been only marginally explored at the global level. We have screened over 2,600 publicly available M. bovis genomes and newly sequenced four wildlife M. bovis strains, gathering 1,969 genomes from 23 countries and at least 24 host species, including humans, to complete a phylogenomic analyses. We propose the existence of four distinct global lineages of M. bovis (Lb1, Lb2, Lb3, and Lb4) underlying the current disease distribution. These lineages are not fully represented by clonal complexes and are dispersed based on geographic location rather than host species. Our data divergence analysis agreed with previous studies reporting independent archeological data of ancient M. bovis (South Siberian infected skeletons at ∼2,000 years before present) and indicates that extant M. bovis originated between 715 and 3,556 years BP, with later emergence in the New World and Oceania, likely influenced by trades among countries.
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Affiliation(s)
- Cristina Kraemer Zimpel
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Salvatore L Patané
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Laboratory of Cellular Cycle, Butantan Institute, São Paulo, Brazil
| | - Aureliano Coelho Proença Guedes
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Robson F de Souza
- Laboratory of Protein Structure and Evolution, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Taiana T Silva-Pereira
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Naila C Soler Camargo
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil.,Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Antônio F de Souza Filho
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Cássia Y Ikuta
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - José Soares Ferreira Neto
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - João Carlos Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil.,Biocomplexity Institute of Virginia Tech, Blacksburg, VA, United States
| | - Marcos Bryan Heinemann
- Department of Preventive Veterinary Medicine and Animal Health, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Ana Marcia Sa Guimaraes
- Laboratory of Applied Research in Mycobacteria, Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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32
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Liu Q, Wei J, Li Y, Wang M, Su J, Lu Y, López MG, Qian X, Zhu Z, Wang H, Gan M, Jiang Q, Fu YX, Takiff HE, Comas I, Li F, Lu X, Fortune SM, Gao Q. Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments. SCIENCE ADVANCES 2020; 6:eaba4901. [PMID: 32524000 PMCID: PMC7259932 DOI: 10.1126/sciadv.aba4901] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Accepted: 03/25/2020] [Indexed: 05/12/2023]
Abstract
Mycobacterium tuberculosis (Mtb) infection results in a spectrum of clinical and histopathologic manifestations. It has been proposed that the environmental and immune pressures associated with different contexts of infection have different consequences for the associated bacterial populations, affecting drug susceptibility and the emergence of resistance. However, there is little concrete evidence for this model. We prospectively collected sputum samples from 18 newly diagnosed and treatment-naïve patients with tuberculosis and sequenced 795 colony-derived Mtb isolates. Mutant accumulation rates varied considerably between different bacilli isolated from the same individual, and where high rates of mutation were observed, the mutational spectrum was consistent with reactive oxygen species-induced mutagenesis. Elevated bacterial mutation rates were identified in isolates from HIV-negative but not HIV-positive individuals, suggesting that they were immune-driven. These results support the model that mutagenesis of Mtb in vivo is modulated by the host environment, which could drive the emergence of variants associated with drug resistance in a host-dependent manner.
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Affiliation(s)
- Qingyun Liu
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
| | - Jianhao Wei
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yawei Li
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Mei Wang
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Jun Su
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Yonghui Lu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mariana G. López
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
| | - Xueqin Qian
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Zhaoqin Zhu
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Haiying Wang
- Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Mingyun Gan
- Molecular Medical Center, Children’s Hospital of Fudan University, Shanghai, China
| | - Qi Jiang
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Yun-Xin Fu
- Department of Biostatistics and Human Genetics Center, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Howard E. Takiff
- Integrated Mycobacterial Pathogenomics Unit, Institut Pasteur, Paris, France
- Nanshan Center for Chronic Disease Control, Shenzhen, China
| | - Iñaki Comas
- Tuberculosis Genomic Unit, Instituto de Biomedicina de Valencia (IBV-CSIC), Valencia, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
| | - Feng Li
- Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Xuemei Lu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- CAS Center for Excellence in Animal Evolution and Genetics, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China
| | - Sarah M. Fortune
- Department of Immunology and Infectious Diseases, Harvard T. H. Chan School of Public Health, Boston, MA 02115, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Qian Gao
- Shanghai Public Health Clinical Center, Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Medical College and School of Basic Medical Sciences, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
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33
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Morales-Arce AY, Harris RB, Stone AC, Jensen JD. Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution. Evolution 2020; 74:992-1001. [PMID: 32233086 DOI: 10.1111/evo.13954] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/08/2020] [Indexed: 12/28/2022]
Abstract
The within-host evolutionary dynamics of tuberculosis (TB) remain unclear, and underlying biological characteristics render standard population genetic approaches based upon the Wright-Fisher model largely inappropriate. In addition, the compact genome combined with an absence of recombination is expected to result in strong purifying selection effects. Thus, it is imperative to establish a biologically relevant evolutionary framework incorporating these factors in order to enable an accurate study of this important human pathogen. Further, such a model is critical for inferring fundamental evolutionary parameters related to patient treatment, including mutation rates and the severity of infection bottlenecks. We here implement such a model and infer the underlying evolutionary parameters governing within-patient evolutionary dynamics. Results demonstrate that the progeny skew associated with the clonal nature of TB severely reduces genetic diversity and that the neglect of this parameter in previous studies has led to significant mis-inference of mutation rates. As such, our results suggest an underlying de novo mutation rate that is considerably faster than previously inferred, and a progeny distribution differing significantly from Wright-Fisher assumptions. This inference represents a more appropriate evolutionary null model, against which the periodic effects of positive selection, associated with drug-resistance for example, may be better assessed.
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Affiliation(s)
- Ana Y Morales-Arce
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Rebecca B Harris
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA
| | - Anne C Stone
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Human Evolution and Social Change, Arizona State University, Tempe, Arizona, USA
| | - Jeffrey D Jensen
- Center for Evolution and Medicine, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
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34
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Loiseau C, Menardo F, Aseffa A, Hailu E, Gumi B, Ameni G, Berg S, Rigouts L, Robbe-Austerman S, Zinsstag J, Gagneux S, Brites D. An African origin for Mycobacterium bovis. Evol Med Public Health 2020; 2020:49-59. [PMID: 32211193 PMCID: PMC7081938 DOI: 10.1093/emph/eoaa005] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 12/24/2019] [Accepted: 01/24/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND AND OBJECTIVES Mycobacterium bovis and Mycobacterium caprae are two of the most important agents of tuberculosis in livestock and the most important causes of zoonotic tuberculosis in humans. However, little is known about the global population structure, phylogeography and evolutionary history of these pathogens. METHODOLOGY We compiled a global collection of 3364 whole-genome sequences from M.bovis and M.caprae originating from 35 countries and inferred their phylogenetic relationships, geographic origins and age. RESULTS Our results resolved the phylogenetic relationship among the four previously defined clonal complexes of M.bovis, and another eight newly described here. Our phylogeographic analysis showed that M.bovis likely originated in East Africa. While some groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world. CONCLUSIONS AND IMPLICATIONS Our results allow a better understanding of the global population structure of M.bovis and its evolutionary history. This knowledge can be used to define better molecular markers for epidemiological investigations of M.bovis in settings where whole-genome sequencing cannot easily be implemented. LAY SUMMARY During the last few years, analyses of large globally representative collections of whole-genome sequences (WGS) from the human-adapted Mycobacterium tuberculosis complex (MTBC) lineages have enhanced our understanding of the global population structure, phylogeography and evolutionary history of these pathogens. In contrast, little corresponding data exists for M. bovis, the most important agent of tuberculosis in livestock. Using whole-genome sequences of globally distributed M. bovis isolates, we inferred the genetic relationships among different M. bovis genotypes distributed around the world. The most likely origin of M. bovis is East Africa according to our inferences. While some M. bovis groups remained restricted to East and West Africa, others have subsequently dispersed to different parts of the world driven by cattle movements.
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Affiliation(s)
- Chloé Loiseau
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Fabrizio Menardo
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Abraham Aseffa
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Elena Hailu
- Mycobacterial Diseases Directorate, Armauer Hansen Research Centre, Addis Ababa, Ethiopia
| | - Balako Gumi
- Department of Animal Science and Range Management, Bule Hora University, Bule Hora Town, Ethiopia
| | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University, Addis Ababa, Ethiopia
| | - Stefan Berg
- Bacteriology Department, Animal & Plant Health Agency (APHA), Weybridge, Surrey, UK
| | - Leen Rigouts
- Mycobacteriology Unit, Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Collection of Mycobacterial Cultures (BCCM/ITM), Institute of Tropical Medicine, Antwerp, Belgium
- Department of Biomedical Sciences, Antwerp University, Antwerp, Belgium
| | - Suelee Robbe-Austerman
- Diagnostic Bacteriology and Pathology Laboratory, National Veterinary Services Laboratories, United States Department of Agriculture, Ames, IA, USA
| | - Jakob Zinsstag
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Daniela Brites
- Molecular Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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35
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Mulholland CV, Shockey AC, Aung HL, Cursons RT, O'Toole RF, Gautam SS, Brites D, Gagneux S, Roberts SA, Karalus N, Cook GM, Pepperell CS, Arcus VL. Dispersal of Mycobacterium tuberculosis Driven by Historical European Trade in the South Pacific. Front Microbiol 2019; 10:2778. [PMID: 31921003 PMCID: PMC6915100 DOI: 10.3389/fmicb.2019.02778] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 11/14/2019] [Indexed: 12/30/2022] Open
Abstract
Mycobacterium tuberculosis (Mtb) is a globally distributed bacterial pathogen whose population structure has largely been shaped by the activities of its obligate human host. Oceania was the last major global region to be reached by Europeans and is the last region for which the dispersal and evolution of Mtb remains largely unexplored. Here, we investigated the evolutionary history of the Euro-American L4.4 sublineage and its dispersal to the South Pacific. Using a phylodynamics approach and a dataset of 236 global Mtb L4.4 genomes we have traced the origins and dispersal of L4.4 strains to New Zealand. These strains are predominantly found in indigenous Māori and Pacific people and we identify a clade of European, likely French, origin that is prevalent in indigenous populations in both New Zealand and Canada. Molecular dating suggests the expansion of European trade networks in the early 19th century drove the dispersal of this clade to the South Pacific. We also identify historical and social factors within the region that have contributed to the local spread and expansion of these strains, including recent Pacific migrations to New Zealand and the rapid urbanization of Māori in the 20th century. Our results offer new insight into the expansion and dispersal of Mtb in the South Pacific and provide a striking example of the role of historical European migrations in the global dispersal of Mtb.
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Affiliation(s)
- Claire V Mulholland
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
| | - Abigail C Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Htin L Aung
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Ray T Cursons
- School of Science, University of Waikato, Hamilton, New Zealand
| | - Ronan F O'Toole
- School of Medicine, University of Tasmania, Hobart, TAS, Australia.,School of Molecular Sciences, La Trobe University, Melbourne, VIC, Australia
| | - Sanjay S Gautam
- School of Medicine, University of Tasmania, Hobart, TAS, Australia
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | | | | | - Gregory M Cook
- Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand.,Department of Microbiology and Immunology, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | - Caitlin S Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States.,Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Vickery L Arcus
- School of Science, University of Waikato, Hamilton, New Zealand.,Maurice Wilkins Centre for Molecular Biodiscovery, The University of Auckland, Auckland, New Zealand
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36
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Minias A, Minias P, Czubat B, Dziadek J. Purifying Selective Pressure Suggests the Functionality of a Vitamin B12 Biosynthesis Pathway in a Global Population of Mycobacterium tuberculosis. Genome Biol Evol 2019; 10:2326-2337. [PMID: 30060031 PMCID: PMC6363050 DOI: 10.1093/gbe/evy153] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/27/2018] [Indexed: 12/20/2022] Open
Abstract
Mycobacterium tuberculosis is one of the deadliest and most challenging pathogens to study in current microbiological research. One of the issues that remains to be resolved is the importance of cobalamin in the metabolism of M. tuberculosis. The functionality of a vitamin B12 biosynthesis pathway in M. tuberculosis is under dispute, and the ability of this pathogen to scavenge vitamin B12 from the host is unknown. Here, we quantified the ratios of nonsynonymous and synonymous nucleotide substitution rates (dN/dS) in the genes involved in vitamin B12 biosynthesis and transport and in genes encoding cobalamin-dependent enzymes in nearly four thousand strains of M. tuberculosis. We showed that purifying selection is the dominant force acting on cobalamin-related genes at the levels of individual codons, genes and groups of genes. We conclude that cobalamin-related genes may not be essential but are adaptive for M. tuberculosis in clinical settings. Furthermore, the cobalamin biosynthesis pathway is likely to be functional in this species.
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Affiliation(s)
- Alina Minias
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
| | - Piotr Minias
- Department of Biodiversity Studies and Bioeducation, Faculty of Biology and Environmental Protection University of Łódź, Łódź, Poland
| | - Bożena Czubat
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland.,Department of Biochemistry and Cell Biology, Faculty of Biology and Agriculture, University of Rzeszów, Rzeszów, Poland
| | - Jarosław Dziadek
- Laboratory of Genetics and Physiology of Mycobacterium, Institute of Medical Biology, Polish Academy of Sciences, Łódź, Poland
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37
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Menardo F, Duchêne S, Brites D, Gagneux S. The molecular clock of Mycobacterium tuberculosis. PLoS Pathog 2019; 15:e1008067. [PMID: 31513651 PMCID: PMC6759198 DOI: 10.1371/journal.ppat.1008067] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 09/24/2019] [Accepted: 09/03/2019] [Indexed: 12/20/2022] Open
Abstract
The molecular clock and its phylogenetic applications to genomic data have changed how we study and understand one of the major human pathogens, Mycobacterium tuberculosis (MTB), the etiologic agent of tuberculosis. Genome sequences of MTB strains sampled at different times are increasingly used to infer when a particular outbreak begun, when a drug-resistant clone appeared and expanded, or when a strain was introduced into a specific region. Despite the growing importance of the molecular clock in tuberculosis research, there is a lack of consensus as to whether MTB displays a clocklike behavior and about its rate of evolution. Here we performed a systematic study of the molecular clock of MTB on a large genomic data set (6,285 strains), covering different epidemiological settings and most of the known global diversity. We found that sampling times below 15-20 years were often insufficient to calibrate the clock of MTB. For data sets where such calibration was possible, we obtained a clock rate between 1x10-8 and 5x10-7 nucleotide changes per-site-per-year (0.04-2.2 SNPs per-genome-per-year), with substantial differences between clades. These estimates were not strongly dependent on the time of the calibration points as they changed only marginally when we used epidemiological isolates (sampled in the last 40 years) or three ancient DNA samples (about 1,000 years old) to calibrate the tree. Additionally, the uncertainty and the discrepancies in the results of different methods were sometimes large, highlighting the importance of using different methods, and of considering carefully their assumptions and limitations.
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Affiliation(s)
- Fabrizio Menardo
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastian Duchêne
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, Australia
| | - Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
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38
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O'Neill MB, Shockey A, Zarley A, Aylward W, Eldholm V, Kitchen A, Pepperell CS. Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia. Mol Ecol 2019; 28:3241-3256. [PMID: 31066139 PMCID: PMC6660993 DOI: 10.1111/mec.15120] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 04/18/2019] [Accepted: 04/23/2019] [Indexed: 12/29/2022]
Abstract
Mycobacterium tuberculosis (M.tb) is a globally distributed, obligate pathogen of humans that can be divided into seven clearly defined lineages. An emerging consensus places the origin and global dispersal of M.tb within the past 6,000 years: identifying how the ancestral clone of M.tb spread and differentiated within this timeframe is important for identifying the ecological drivers of the current pandemic. We used Bayesian phylogeographic inference to reconstruct the migratory history of M.tb in Africa and Eurasia and to investigate lineage specific patterns of spread from a geographically diverse sample of 552 M.tb genomes. Applying evolutionary rates inferred with ancient M.tb genome calibration, we estimated the timing of major events in the migratory history of the pathogen. Inferred timings contextualize M.tb dispersal within historical phenomena that altered patterns of connectivity throughout Africa and Eurasia: trans-Indian Ocean trade in spices and other goods, the Silk Road and its predecessors, the expansion of the Roman Empire, and the European Age of Exploration. We found that Eastern Africa and Southeast Asia have been critical in the dispersal of M.tb. Our results further reveal that M.tb populations have grown through range expansion, as well as in situ, and delineate the independent evolutionary trajectories of bacterial subpopulations underlying the current pandemic.
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Affiliation(s)
- Mary B. O'Neill
- Laboratory of GeneticsUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Present address:
Unit of Human Evolutionary GeneticsInstitut PasteurParisFrance
| | - Abigail Shockey
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Alex Zarley
- Department of GeographyUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - William Aylward
- Department of Classical and Ancient Near Eastern StudiesUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Vegard Eldholm
- Infection Control and Environmental HealthNorwegian Institute of Public HealthOsloNorway
| | - Andrew Kitchen
- Department of AnthropologyUniversity of IowaIowa CityIAUSA
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and ImmunologyUniversity of Wisconsin‐MadisonMadisonWIUSA
- Department of MedicineUniversity of Wisconsin‐MadisonMadisonWIUSA
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39
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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: 17] [Impact Index Per Article: 2.8] [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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40
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Shockey AC, Dabney J, Pepperell CS. Effects of Host, Sample, and in vitro Culture on Genomic Diversity of Pathogenic Mycobacteria. Front Genet 2019; 10:477. [PMID: 31214242 PMCID: PMC6558051 DOI: 10.3389/fgene.2019.00477] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Accepted: 05/03/2019] [Indexed: 12/16/2022] Open
Abstract
Mycobacterium tuberculosis (M. tb), an obligate human pathogen and the etiological agent of tuberculosis (TB), remains a major threat to global public health. Comparative genomics has been invaluable for monitoring the emergence and spread of TB and for gaining insight into adaptation of M. tb. Most genomic studies of M. tb are based on single bacterial isolates that have been cultured for several weeks in vitro. However, in its natural human host, M. tb comprises complex, in some cases massive bacterial populations that diversify over the course of infection and cannot be wholly represented by a single genome. Recently, enrichment via hybridization capture has been used as a rapid diagnostic tool for TB, circumventing culturing protocols and enabling the recovery of M. tb genomes directly from sputum. This method has further applicability to the study of M. tb adaptation, as it enables a higher resolution and more direct analysis of M. tb genetic diversity within hosts with TB. Here we analyzed genomic material from M. tb and Mycobacterium bovis populations captured directly from sputum and from cultured samples using metagenomic and Pool-Seq approaches. We identified effects of sampling, patient, and sample type on bacterial genetic diversity. Bacterial genetic diversity was more variable and on average higher in sputum than in culture samples, suggesting that manipulation in the laboratory reshapes the bacterial population. Using outlier analyses, we identified candidate bacterial genetic loci mediating adaptation to these distinct environments. The study of M. tb in its natural human host is a powerful tool for illuminating host pathogen interactions and understanding the bacterial genetic underpinnings of virulence.
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Affiliation(s)
- Abigail C. Shockey
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
| | - Jesse Dabney
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, United Kingdom
| | - Caitlin S. Pepperell
- Department of Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
- Department of Medicine, Division of Infectious Diseases, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, United States
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41
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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: 24] [Impact Index Per Article: 4.0] [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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42
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Ramaiah A, Nayak S, Rakshit S, Manson AL, Abeel T, Shanmugam S, Sahoo PN, John AJUK, Sundaramurthi JC, Narayanan S, D'Souza G, von Hoegen P, Ottenhoff THM, Swaminathan S, Earl AM, Vyakarnam A. Evidence for Highly Variable, Region-Specific Patterns of T-Cell Epitope Mutations Accumulating in Mycobacterium tuberculosis Strains. Front Immunol 2019; 10:195. [PMID: 30814998 PMCID: PMC6381025 DOI: 10.3389/fimmu.2019.00195] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/23/2019] [Indexed: 01/26/2023] Open
Abstract
Vaccines that confer protection through induction of adaptive T-cell immunity rely on understanding T-cell epitope (TCE) evolution induced by immune escape. This is poorly understood in tuberculosis (TB), an ancient, chronic disease, where CD4 T-cell immunity is of recognized importance. We probed 905 functionally validated, curated human CD4 T cell epitopes in 79 Mycobacterium tuberculosis (Mtb) whole genomes from India. This screen resulted in identifying 64 mutated epitopes in these strains initially using a computational pipeline and subsequently verified by single nucleotide polymorphism (SNP) analysis. SNP based phylogeny revealed the 79 Mtb strains to cluster to East African Indian (EAI), Central Asian Strain (CAS), and Beijing (BEI) lineages. Eighty-nine percent of the mutated T-cell epitopes (mTCEs) identified in the 79 Mtb strains from India has not previously been reported. These mTCEs were encoded by genes with high nucleotide diversity scores including seven mTCEs encoded by six antigens in the top 10% of rapidly divergent Mtb genes encoded by these strains. Using a T cell functional assay readout, we demonstrate 62% of mTCEs tested to significantly alter CD4 T-cell IFNγ and/or IL2 secretion with associated changes in predicted HLA-DR binding affinity: the gain of function mutations displayed higher predicted HLA-DR binding affinity and conversely mutations resulting in loss of function displayed lower predicted HLA-DR binding affinity. Most mutated antigens belonged to the cell wall/cell processes, and, intermediary metabolism and respiration families though all known Mtb proteins encoded mutations. Analysis of the mTCEs in an SNP database of 5,310 global Mtb strains identified 82% mTCEs to be significantly more prevalent in Mtb strains isolated from India, including 36 mTCEs identified exclusively in strains from India. These epitopes had a significantly higher predicted binding affinity to HLA-DR alleles that were highly prevalent in India compared to HLA-DR alleles rare in India, highlighting HLA-DR maybe an important driver of these mutations. This first evidence of region-specific TCE mutations potentially employed by Mtb to escape host immunity has important implications for TB vaccine design.
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Affiliation(s)
- Arunachalam Ramaiah
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Soumya Nayak
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | - Srabanti Rakshit
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | | | - Thomas Abeel
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | | | - Pravat Nalini Sahoo
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
| | | | | | - Sujatha Narayanan
- National Institute for Research in Tuberculosis (ICMR), Chennai, India
| | - George D'Souza
- Department of Pulmonary Medicine, St. John's Research Institute, Bangalore, India
| | | | - Tom H. M. Ottenhoff
- Department of Infectious Diseases, Leiden University Medical Center, Leiden, Netherlands
| | | | - Ashlee M. Earl
- Broad Institute of MIT and Harvard, Cambridge, MA, United States
| | - Annapurna Vyakarnam
- Centre for Infectious Disease Research, Indian Institute of Science, Bangalore, India
- Department of Infectious Diseases, Faculty of Life Sciences & Medicine, School of Immunology and Microbial Sciences, King's College London, London, United Kingdom
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43
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Liu Q, Ma A, Wei L, Pang Y, Wu B, Luo T, Zhou Y, Zheng HX, Jiang Q, Gan M, Zuo T, Liu M, Yang C, Jin L, Comas I, Gagneux S, Zhao Y, Pepperell CS, Gao Q. China's tuberculosis epidemic stems from historical expansion of four strains of Mycobacterium tuberculosis. Nat Ecol Evol 2018; 2:1982-1992. [PMID: 30397300 PMCID: PMC6295914 DOI: 10.1038/s41559-018-0680-6] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 08/28/2018] [Indexed: 12/18/2022]
Abstract
A small number of high-burden countries account for the majority of tuberculosis cases worldwide. Detailed data are lacking from these regions. To explore the evolutionary history of Mycobacterium tuberculosis in China-the country with the third highest tuberculosis burden-we analysed a countrywide collection of 4,578 isolates. Little genetic diversity was detected, with 99.4% of the bacterial population belonging to lineage 2 and three sublineages of lineage 4. The deeply rooted phylogenetic positions and geographic restriction of these four genotypes indicate that their populations expanded in situ following a small number of introductions to China. Coalescent analyses suggest that these bacterial subpopulations emerged in China around 1,000 years ago, and expanded in parallel from the twelfth century onwards, and that the whole population peaked in the late eighteenth century. More recently, sublineage L2.3, which is indigenous to China and exhibited relatively high transmissibility and extensive global dissemination, came to dominate the population dynamics of M. tuberculosis in China. Our results indicate that historical expansion of four M. tuberculosis strains shaped the current tuberculosis epidemic in China, and highlight the long-term genetic continuity of the indigenous M. tuberculosis population.
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Affiliation(s)
- Qingyun Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Aijing Ma
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lanhai Wei
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Yu Pang
- National Tuberculosis Clinical Laboratory, Beijing Key Laboratory for Drug Resistance Tuberculosis Research, Beijing Tuberculosis and Thoracic Tumor Research Institute, Beijing Chest Hospital, Capital Medical University, Beijing, China
| | - Beibei Wu
- The Institute of TB Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Tao Luo
- West China School of Basic Medical Sciences and Forensic Medicines, Sichuan University, Chengdu, China
| | - Yang Zhou
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hong-Xiang Zheng
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Qi Jiang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Mingyu Gan
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Shenzhen Center for Chronic Disease Control, Shenzhen, China
| | - Tianyu Zuo
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Mei Liu
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
| | - Chongguang Yang
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Li Jin
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences and Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Iñaki Comas
- Institute of Biomedicine of Valencia, CSIC and CIBER in Epidemiology and Public Health, Valencia, Spain
| | - Sebastien Gagneux
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- University of Basel, Basel, Switzerland
| | - Yanlin Zhao
- National Center for Tuberculosis Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.
| | - Caitlin S Pepperell
- Department of Medicine, Division of Infectious Diseases, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI, USA.
| | - Qian Gao
- Key Laboratory of Medical Molecular Virology, Ministry of Education and Health, School of Basic Medical Sciences, Shanghai Public Health Clinical Center, Fudan University, Shanghai, China.
- Shenzhen Center for Chronic Disease Control, Shenzhen, China.
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44
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Wangari IM, Trauer J, Stone L. Modelling heterogeneity in host susceptibility to tuberculosis and its effect on public health interventions. PLoS One 2018; 13:e0206603. [PMID: 30427891 PMCID: PMC6235601 DOI: 10.1371/journal.pone.0206603] [Citation(s) in RCA: 5] [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: 02/16/2018] [Accepted: 10/16/2018] [Indexed: 11/25/2022] Open
Abstract
A tuberculosis (TB) model that accounts for heterogeneity in host susceptibility to tuberculosis is proposed, with the aim of investigating the implications this may have for the effectiveness of public health interventions. The model examines the possibility that recovered individuals treated from active TB and individuals treated with preventive therapy acquire different levels of immunity. This contrasts with recent studies that assume the two cohorts acquire the same level of immunity, and therefore both groups are reinfected at the same rate. The analysis presented here examines the impact of this assumption when designing intervention strategies. Comparison of reinfection rates between cohorts treated with preventive therapy and recovered individuals who were previously treated for active TB provides important epidemiological insights. It is found that the reinfection rate of the cohort treated with preventive therapy is the one that plays the key role in qualitative changes in TB dynamics. By contrast, the reinfection rate of recovered individuals (previously treated from active TB) plays a minor role. Moreover, the study shows that preventive treatment of individuals during early latency is always beneficial regardless of the level of susceptibility to reinfection. Further, if patients have greater immunity following treatment for late latent infection, then treatment is again beneficial. However, if susceptibility increases following treatment for late latent infection, the effect of treatment depends on the epidemiological setting. That is: (i) in (very) low burden settings, the effect on reactivation predominates and the burden declines with treatment; (ii) in moderate to high burden settings the effect of reinfection predominates and burden increases with treatment. The effect is most dominant between the two reinfection thresholds, RT2 and RT1, respectively associated with individuals being treated with preventive therapy and individuals with untreated late latent TB infection.
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Affiliation(s)
- Isaac Mwangi Wangari
- Mathematical Sciences, School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
- * E-mail:
| | - James Trauer
- School of Public Health and Preventive Medicine, Monash University, Melbourne 3004, Australia
| | - Lewi Stone
- Mathematical Sciences, School of Science, Royal Melbourne Institute of Technology, Melbourne, Victoria, Australia
- Biomathematics Unit, Department of Zoology, Faculty of Life Sciences, Tel Aviv University, Israel
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45
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Folkvardsen DB, Norman A, Andersen ÅB, Rasmussen EM, Lillebaek T, Jelsbak L. A Major Mycobacterium tuberculosis outbreak caused by one specific genotype in a low-incidence country: Exploring gene profile virulence explanations. Sci Rep 2018; 8:11869. [PMID: 30089859 PMCID: PMC6082827 DOI: 10.1038/s41598-018-30363-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 07/10/2018] [Indexed: 12/30/2022] Open
Abstract
Denmark, a tuberculosis low burden country, still experiences significant active Mycobacterium tuberculosis (Mtb) transmission, especially with one specific genotype named Cluster 2/1112-15 (C2), the most prevalent lineage in Scandinavia. In addition to environmental factors, antibiotic resistance, and human genetics, there is increasing evidence that Mtb strain variation plays a role for the outcome of infection and disease. In this study, we explore the reasons for the success of the C2 genotype by analysing strain specific polymorphisms identified through whole genome sequencing of all C2 isolates identified in Denmark between 1992 and 2014 (n = 952), and the demographic distribution of C2. Of 234 non-synonymous (NS) monomorphic SNPs found in C2 in comparison with Mtb reference strain H37Rv, 23 were in genes previously reported to be involved in Mtb virulence. Of these 23 SNPs, three were specific for C2 including a NS mutation in a gene associated with hyper-virulence. We show that the genotype is readily transmitted to different ethnicities and is also found outside Denmark. Our data suggest that strain specific virulence factor variations are important for the success of the C2 genotype. These factors, likely in combination with poor TB control, seem to be the main drivers of C2 success.
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Affiliation(s)
- Dorte Bek Folkvardsen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark.
| | - Anders Norman
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
| | - Åse Bengård Andersen
- Department of Infectious Diseases, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
- Research Unit for Infectious Diseases, Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Erik Michael Rasmussen
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Troels Lillebaek
- International Reference Laboratory of Mycobacteriology, Statens Serum Institut, Copenhagen, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kgs. Lyngby, Denmark
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46
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Holt KE, McAdam P, Thai PVK, Thuong NTT, Ha DTM, Lan NN, Lan NH, Nhu NTQ, Hai HT, Ha VTN, Thwaites G, Edwards DJ, Nath AP, Pham K, Ascher DB, Farrar J, Khor CC, Teo YY, Inouye M, Caws M, Dunstan SJ. Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 2018; 50:849-856. [PMID: 29785015 PMCID: PMC6143168 DOI: 10.1038/s41588-018-0117-9] [Citation(s) in RCA: 143] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 03/22/2018] [Indexed: 12/19/2022]
Abstract
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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Affiliation(s)
- Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia.
| | - Paul McAdam
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Phan Vuong Khac Thai
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Dang Thi Minh Ha
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Ngoc Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | - Nguyen Huu Lan
- Pham Ngoc Thach Hospital for Tuberculosis and Lung Disease, Ho Chi Minh City, Vietnam
| | | | - Hoang Thanh Hai
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vu Thi Ngoc Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - David J Edwards
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Artika P Nath
- Department of Microbiology and Immunology, University of Melbourne, Parkville, Victoria, Australia
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
| | - Kym Pham
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
| | - David B Ascher
- Department of Biochemistry and Molecular Biology, Bio 21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Jeremy Farrar
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine, Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK
| | - Chiea Chuen Khor
- Genome Institute of Singapore, Singapore, Singapore
- Singapore Eye Research Institute, Singapore, Singapore
| | - Yik Ying Teo
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Michael Inouye
- Systems Genomics Lab, Baker Heart and Diabetes Institute, Melbourne, Victoria, Australia
- Department of Clinical Pathology, University of Melbourne, Parkville, Victoria, Australia
- Department of Public Health and Primary Care, University of Cambridge, Strangeways Research Laboratories, Cambridge, UK
| | - Maxine Caws
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
- Birat-Nepal Medical Trust, Kathmandu, Nepal
| | - Sarah J Dunstan
- Peter Doherty Institute for Infection and Immunity, University of Melbourne, Parkville, Victoria, Australia.
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47
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Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam. Nat Genet 2018. [PMID: 29785015 DOI: 10.1038/s41588-018-0117-9.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
To examine the transmission dynamics of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients in Ho Chi Minh City, Vietnam, we sequenced the whole genomes of 1,635 isolates and compared these with 3,144 isolates from elsewhere. The data identify an underlying burden of disease caused by the endemic Mtb lineage 1 associated with the activation of long-term latent infection, and a threefold higher burden associated with the more recently introduced Beijing lineage and lineage 4 Mtb strains. We find that Beijing lineage Mtb is frequently transferred between Vietnam and other countries, and detect higher levels of transmission of Beijing lineage strains within this host population than the endemic lineage 1 Mtb. Screening for parallel evolution of Beijing lineage-associated SNPs in other Mtb lineages as a signal of positive selection, we identify an alteration in the ESX-5 type VII-secreted protein EsxW, which could potentially contribute to the enhanced transmission of Beijing lineage Mtb in Vietnamese and other host populations.
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48
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Last AR, Pickering H, Roberts CH, Coll F, Phelan J, Burr SE, Cassama E, Nabicassa M, Seth-Smith HMB, Hadfield J, Cutcliffe LT, Clarke IN, Mabey DCW, Bailey RL, Clark TG, Thomson NR, Holland MJ. Population-based analysis of ocular Chlamydia trachomatis in trachoma-endemic West African communities identifies genomic markers of disease severity. Genome Med 2018; 10:15. [PMID: 29482619 PMCID: PMC5828069 DOI: 10.1186/s13073-018-0521-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Accepted: 02/13/2018] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Chlamydia trachomatis (Ct) is the most common infectious cause of blindness and bacterial sexually transmitted infection worldwide. Ct strain-specific differences in clinical trachoma suggest that genetic polymorphisms in Ct may contribute to the observed variability in severity of clinical disease. METHODS Using Ct whole genome sequences obtained directly from conjunctival swabs, we studied Ct genomic diversity and associations between Ct genetic polymorphisms with ocular localization and disease severity in a treatment-naïve trachoma-endemic population in Guinea-Bissau, West Africa. RESULTS All Ct sequences fall within the T2 ocular clade phylogenetically. This is consistent with the presence of the characteristic deletion in trpA resulting in a truncated non-functional protein and the ocular tyrosine repeat regions present in tarP associated with ocular tissue localization. We have identified 21 Ct non-synonymous single nucleotide polymorphisms (SNPs) associated with ocular localization, including SNPs within pmpD (odds ratio, OR = 4.07, p* = 0.001) and tarP (OR = 0.34, p* = 0.009). Eight synonymous SNPs associated with disease severity were found in yjfH (rlmB) (OR = 0.13, p* = 0.037), CTA0273 (OR = 0.12, p* = 0.027), trmD (OR = 0.12, p* = 0.032), CTA0744 (OR = 0.12, p* = 0.041), glgA (OR = 0.10, p* = 0.026), alaS (OR = 0.10, p* = 0.032), pmpE (OR = 0.08, p* = 0.001) and the intergenic region CTA0744-CTA0745 (OR = 0.13, p* = 0.043). CONCLUSIONS This study demonstrates the extent of genomic diversity within a naturally circulating population of ocular Ct and is the first to describe novel genomic associations with disease severity. These findings direct investigation of host-pathogen interactions that may be important in ocular Ct pathogenesis and disease transmission.
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Affiliation(s)
- A. R. Last
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - H. Pickering
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - C. h. Roberts
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - F. Coll
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - J. Phelan
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - S. E. Burr
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Disease Control and Elimination Theme, Medical Research Council Unit The Gambia, Fajara, Gambia
| | - E. Cassama
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - M. Nabicassa
- Programa Nacional de Saúde de Visão, Ministério de Saúde Publica, Bissau, Guinea-Bissau
| | - H. M. B. Seth-Smith
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
- Clinical Microbiology, Universitätsspital Basel, Basel, Switzerland
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland
| | - J. Hadfield
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - L. T. Cutcliffe
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - I. N. Clarke
- Molecular Microbiology Group, University of Southampton Medical School, Southampton, UK
| | - D. C. W. Mabey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - R. L. Bailey
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - T. G. Clark
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Department of Infectious Diseases Epidemiology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
| | - N. R. Thomson
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
- Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK
| | - M. J. Holland
- Clinical Research Department, London School of Hygiene and Tropical Medicine, Keppel Street, London, UK
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49
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50
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Queirós J, Alves PC, Vicente J, Gortázar C, de la Fuente J. Genome-wide associations identify novel candidate loci associated with genetic susceptibility to tuberculosis in wild boar. Sci Rep 2018; 8:1980. [PMID: 29386541 PMCID: PMC5792637 DOI: 10.1038/s41598-018-20158-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 01/12/2018] [Indexed: 12/23/2022] Open
Abstract
Tuberculosis (TB) affects a wide range of host species worldwide. Understanding host-pathogen co-evolution remains a global challenge owing to complex interactions among host genetic factors, pathogen traits and environmental conditions. We used an endemic wild boar population that had undergone a huge increase in Mycobacterium bovis infection prevalence, from 45% in 2002/06 to 83% in 2009/12, to understand the effects of host genetics on host TB outcomes and disease dynamics. Host genomic variation was characterized using a high-density single nucleotide polymorphism (SNP) array, while host TB phenotype was assessed using both gross pathology and mycobacterial culture. Two complementary genome-wide association (GWAS) analyses were conducted: (i) infected-uninfected; and (ii) 2002/06–2009/12. The SNPs with the highest allelic frequency differences between time-periods and TB outcomes were identified and validated in a large dataset. In addition, we quantified the expression levels of some of their closest genes. These analyses highlighted various SNPs (i.e. rs81465339, rs81394585, rs81423166) and some of the closest genes (i.e. LOC102164072, BDNF/NT-3, NTRK2, CDH8, IGSF21) as candidates for host genetic susceptibility. In addition to TB-driven selection, our findings outline the putative role of demographic events in shaping genomic variation in natural populations and how population crashes and drift may impact host genetic susceptibility to TB over time.
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Affiliation(s)
- João Queirós
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal. .,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal. .,SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.
| | - Paulo Célio Alves
- Centro de Investigacão em Biodiversidade e Recursos Genéticos (CIBIO)/InBio Laboratório Associado, Universidade do Porto, Campus Agrário de Vairão, R. Monte-Crasto, 4485-661, Vairão, Portugal.,Departamento de Biologia, Faculdade de Ciências da Universidade do Porto (FCUP), Rua do Campo Alegre s/n, 4169-007, Porto, Portugal.,Wildlife Biology Program, University of Montana, Missoula, MT, 59812, USA
| | - Joaquín Vicente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - Christian Gortázar
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain
| | - José de la Fuente
- SaBio, Instituto de Investigación en Recursos Cinegéticos IREC (CSIC-UCLM-JCCM), Ronda de Toledo s/n, 13071, Ciudad Real, Spain.,Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
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