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Vargová L, Vymazalová K, Horáčková L. A brief history of tuberculosis in the Czech Lands. Tuberculosis (Edinb) 2017; 105:35-48. [DOI: 10.1016/j.tube.2017.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/22/2017] [Accepted: 04/18/2017] [Indexed: 10/19/2022]
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2
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From Evolutionary Advantage to Disease Agents: Forensic Reevaluation of Host-Microbe Interactions and Pathogenicity. Microbiol Spectr 2017; 5. [PMID: 28155809 DOI: 10.1128/microbiolspec.emf-0009-2016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As the "human microbiome era" continues, there is an increasing awareness of our resident microbiota and its indispensable role in our fitness as holobionts. However, the host-microbe relationship is not so clearly defined for some human symbionts. Here we discuss examples of "accidental pathogens," meaning previously nonpathogenic and/or environmental microbes thought to have inadvertently experienced an evolutionary shift toward pathogenicity. For instance, symbionts such as Helicobacter pylori and JC polyomavirus have been shown to have accompanied humans since prehistoric times and are still abundant in extant populations as part of the microbiome. And yet, the relationship between a subgroup of these microbes and their human hosts seems to have changed with time, and they have recently gained notoriety as gastrointestinal and neuropathogens, respectively. On the other hand, environmental microbes such as Legionella spp. have recently experienced a shift in host range and are now a major problem in industrialized countries as a result of artificial ecosystems. Other variables involved in this accidental phenomenon could be the apparent change or reduction in the diversity of human-associated microbiota because of modern medicine and lifestyles. All of this could result in an increased prevalence of accidental pathogens in the form of emerging pathogens.
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Supply P, Brosch R. The Biology and Epidemiology of Mycobacterium canettii. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:27-41. [PMID: 29116628 DOI: 10.1007/978-3-319-64371-7_2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Genome-based insights into the evolution of Mycobacterium tuberculosis and other tuberculosis-causing mycobacteria are constantly increasing. In particular, the recent genomic and functional characterization of several Myocbacterium canettii strains, which are thought to resemble in many aspects the putative common ancestor of the members of the M. tuberculosis complex (MTBC), has consolidated a plausible scenario of the early evolution of tuberculosis-causing mycobacteria, in which the clonal MTBC, comprising numerous key pathogens of mammalian hosts, has evolved from a generalist mycobacterium living in the environment. These studies also have considerably enriched our knowledge on selected molecular events that likely have contributed to the incursion, maintenance and spread of the MTBC members in diverse mammalian hosts. Here, we summarize and discuss recently revealed molecular and evolutionary aspects and emphasize the vast utility of M. canettii strains for identifying the mechanisms that contributed to the global emergence of M. tuberculosis as one of the most important human pathogens.
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Affiliation(s)
- Philip Supply
- Université de Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, UMR 8204 - CIIL - Centre d'Infection et d'Immunité de Lille, F-59000, Lille, France
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, 75724, Paris Cedex 15, France.
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4
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Bañuls AL, Sanou A, Van Anh NT, Godreuil S. Mycobacterium tuberculosis: ecology and evolution of a human bacterium. J Med Microbiol 2015; 64:1261-1269. [PMID: 26385049 DOI: 10.1099/jmm.0.000171] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Some species of the Mycobacterium tuberculosis complex (MTBC), particularly Mycobacterium tuberculosis, which causes human tuberculosis (TB), are the first cause of death linked to a single pathogen worldwide. In the last decades, evolutionary studies have much improved our knowledge on MTBC history and have highlighted its long co-evolution with humans. Its ability to remain latent in humans, the extraordinary proportion of asymptomatic carriers (one-third of the entire human population), the deadly epidemics and the observed increasing level of resistance to antibiotics are proof of its evolutionary success. Many MTBC molecular signatures show not only that these bacteria are a model of adaptation to humans but also that they have influenced human evolution. Owing to the unbalance between the number of asymptomatic carriers and the number of patients with active TB, some authors suggest that infection by MTBC could have a protective role against active TB disease and also against other pathologies. However, it would be inappropriate to consider these infectious pathogens as commensals or symbionts, given the level of morbidity and mortality caused by TB.
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Affiliation(s)
- Anne-Laure Bañuls
- MIVEGEC, UMR CNRS 5290-IRD 224-Université de Montpellier, Montpellier, France.,Laboratory of Tuberculosis, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Adama Sanou
- MIVEGEC, UMR CNRS 5290-IRD 224-Université de Montpellier, Montpellier, France
| | - Nguyen Thi Van Anh
- Laboratory of Tuberculosis, National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Sylvain Godreuil
- INSERM U 1058, Infection by HIV and by Agents with Mucocutaneous Tropism: from Pathogenesis to Prevention, Montpellier, France.,Université Montpellier 1, Montpellier, France.,Centre Hospitalier Régional Universitaire (CHRU) de Montpellier, Département de Bactériologie - Virologie, Montpellier, France
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5
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Boritsch EC, Supply P, Honoré N, Seeman T, Stinear TP, Brosch R. A glimpse into the past and predictions for the future: the molecular evolution of the tuberculosis agent. Mol Microbiol 2014; 93:835-52. [DOI: 10.1111/mmi.12720] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2014] [Indexed: 02/01/2023]
Affiliation(s)
- Eva C. Boritsch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Philip Supply
- INSERM U1019; Lille France
- CNRS UMR 8204; Lille France
- University of Lille Nord de France; Lille France
- Institut Pasteur de Lille; Center for Infection and Immunity of Lille; Lille France
| | - Nadine Honoré
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
| | - Torsten Seeman
- Victorian Bioinformatics Consortium; Monash University; Clayton Victoria Australia
| | - Timothy P. Stinear
- Department of Microbiology and Immunology; University of Melbourne; Parkville Victoria Australia
| | - Roland Brosch
- Institut Pasteur; Unit for Integrated Mycobacterial Pathogenomics; Paris France
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6
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Namouchi A, Karboul A, Fabre M, Gutierrez MC, Mardassi H. Evolution of smooth tubercle Bacilli PE and PE_PGRS genes: evidence for a prominent role of recombination and imprint of positive selection. PLoS One 2013; 8:e64718. [PMID: 23705005 PMCID: PMC3660525 DOI: 10.1371/journal.pone.0064718] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 04/18/2013] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND PE and PE_PGRS are two mycobateria-restricted multigene families encoding membrane associated and secreted proteins that have expanded mainly in the pathogenic species, notably the Mycobacterium tuberculosis complex (MTBC). Several lines of evidence attribute to PE and PE_PGRS genes critical roles in mycobacterial pathogenicity. To get more insight into the nature of these genes, we sought to address their evolutionary trajectories in the group of smooth tubercle bacilli (STB), the putative ancestor of the clonal MTBC. METHODOLOGY/PRINCIPAL FINDINGS By focussing on six polymorphic STB PE/PE_PGRS genes, we demonstrate significant incongruence among single gene genealogies and detect strong signals of recombination using various approaches. Coalescent-based estimation of population recombination and mutation rates (ρ and θ, respectively) indicates that the two mechanisms are of roughly equal importance in generating diversity (ρ/θ = 1.457), a finding in a marked contrast to house keeping genes (HKG) whose evolution is chiefly brought about by mutation (ρ/θ = 0.012). In comparison to HKG, we found 15 times higher mean rate of nonsynonymous substitutions, with strong evidence of positive selection acting on PE_PGRS62 (dN/dS = 1.42), a gene that has previously been shown to be essential for mycobacterial survival in macrophages and granulomas. Imprint of positive selection operating on specific amino acid residues or along branches of PE_PGRS62 phylogenetic tree was further demonstrated using maximum likelihood- and covarion-based approaches, respectively. Strikingly, PE_PGR62 proved highly conserved in present-day MTBC strains. CONCLUSIONS/SIGNIFICANCE Overall the data indicate that, in STB, PE/PE_PGRS genes have undergone a strong diversification process that is speeded up by recombination, with evidence of positive selection. The finding that positive selection involved an essential PE_PGRS gene whose sequence appears to be driven to fixation in present-day MTBC strains lends further support to the critical role of PE/PE_PGRS genes in the evolution of mycobacterial pathogenicity.
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Affiliation(s)
- Amine Namouchi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Anis Karboul
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Tunis, Tunisia
| | - Michel Fabre
- Laboratoire de Biologie Clinique, HIA Percy, Clamart, France
| | | | - Helmi Mardassi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development, Institut Pasteur de Tunis, Tunis, Tunisia
- * E-mail:
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7
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Importance of the genetic diversity within the Mycobacterium tuberculosis complex for the development of novel antibiotics and diagnostic tests of drug resistance. Antimicrob Agents Chemother 2012; 56:6080-7. [PMID: 23006760 DOI: 10.1128/aac.01641-12] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Despite being genetically monomorphic, the limited genetic diversity within the Mycobacterium tuberculosis complex (MTBC) has practical consequences for molecular methods for drug susceptibility testing and for the use of current antibiotics and those in clinical trials. It renders some representatives of MTBC intrinsically resistant against one or multiple antibiotics and affects the spectrum and consequences of resistance mutations selected for during treatment. Moreover, neutral or silent changes within genes responsible for drug resistance can cause false-positive results with hybridization-based assays, which have been recently introduced to replace slower phenotypic methods. We discuss the consequences of these findings and propose concrete steps to rigorously assess the genetic diversity of MTBC to support ongoing clinical trials.
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8
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Lee OYC, Wu HHT, Donoghue HD, Spigelman M, Greenblatt CL, Bull ID, Rothschild BM, Martin LD, Minnikin DE, Besra GS. Mycobacterium tuberculosis complex lipid virulence factors preserved in the 17,000-year-old skeleton of an extinct bison, Bison antiquus. PLoS One 2012; 7:e41923. [PMID: 22860031 PMCID: PMC3408397 DOI: 10.1371/journal.pone.0041923] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Accepted: 06/29/2012] [Indexed: 12/22/2022] Open
Abstract
Tracing the evolution of ancient diseases depends on the availability and accessibility of suitable biomarkers in archaeological specimens. DNA is potentially information-rich but it depends on a favourable environment for preservation. In the case of the major mycobacterial pathogens, Mycobacterium tuberculosis and Mycobacterium leprae, robust lipid biomarkers are established as alternatives or complements to DNA analyses. A DNA report, a decade ago, suggested that a 17,000-year-old skeleton of extinct Bison antiquus, from Natural Trap Cave, Wyoming, was the oldest known case of tuberculosis. In the current study, key mycobacterial lipid virulence factor biomarkers were detected in the same two samples from this bison. Fluorescence high-performance liquid chromatography (HPLC) indicated the presence of mycolic acids of the mycobacterial type, but they were degraded and could not be precisely correlated with tuberculosis. However, pristine profiles of C29, C30 and C32 mycocerosates and C27 mycolipenates, typical of the Mycobacterium tuberculosis complex, were recorded by negative ion chemical ionization gas chromatography mass spectrometry of pentafluorobenzyl ester derivatives. These findings were supported by the detection of C34 and C36 phthiocerols, which are usually esterified to the mycocerosates. The existence of Pleistocene tuberculosis in the Americas is confirmed and there are many even older animal bones with well-characterised tuberculous lesions similar to those on the analysed sample. In the absence of any evidence of tuberculosis in human skeletons older than 9,000 years BP, the hypothesis that this disease evolved as a zoonosis, before transfer to humans, is given detailed consideration and discussion.
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Affiliation(s)
- Oona Y-C. Lee
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Houdini H. T. Wu
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Helen D. Donoghue
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Centre for the History of Medicine, University College London, London, United Kingdom
| | - Mark Spigelman
- Centre for Clinical Microbiology (M9), Royal Free Campus, University College London, London, United Kingdom
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Charles L. Greenblatt
- Kuvin Center for the Study of Infectious and Tropical Diseases and Ancient DNA, Hadassah Medical School, Hebrew University, Jerusalem, Israel
| | - Ian D. Bull
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, United Kingdom
| | - Bruce M. Rothschild
- Department of Medicine, Northeast Ohio Medical University, Rootstown, Ohio, United States of America
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - Larry D. Martin
- Biodiversity Institute, University of Kansas, Lawrence, Kansas, United States of America
| | - David E. Minnikin
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
| | - Gurdyal S. Besra
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, United Kingdom
- * E-mail:
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9
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Abstract
Tuberculosis (TB) is a disease of antiquity. Yet TB today still causes more adult deaths than any other single infectious disease. Recent studies show that contrary to the common view postulating an animal origin for TB, Mycobacterium tuberculosis complex (MTBC), the causative agent of TB, emerged as a human pathogen in Africa and colonized the world accompanying the Out-of-Africa migrations of modern humans. More recently, evolutionarily 'modern' lineages of MTBC expanded as a consequence of the global human population increase, and spread throughout the world following waves of exploration, trade and conquest. While epidemiological data suggest that the different phylogenetic lineages of MTBC might have adapted to different human populations, overall, the phylogenetically 'modern' MTBC lineages are more successful in terms of their geographical spread compared with the 'ancient' lineages. Interestingly, the global success of 'modern' MTBC correlates with a hypo-inflammatory phenotype in macrophages, possibly reflecting higher virulence, and a shorter latency in humans. Finally, various human genetic variants have been associated with different MTBC lineages, suggesting an interaction between human genetic diversity and MTBC variation. In summary, the biology and the epidemiology of human TB have been shaped by the long-standing association between MTBC and its human host.
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Affiliation(s)
- Sebastien Gagneux
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland.
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10
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Djelouadji Z, Raoult D, Drancourt M. Palaeogenomics of Mycobacterium tuberculosis: epidemic bursts with a degrading genome. THE LANCET. INFECTIOUS DISEASES 2011; 11:641-50. [DOI: 10.1016/s1473-3099(11)70093-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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11
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Koeck JL, Fabre M, Simon F, Daffé M, Garnotel E, Matan AB, Gérôme P, Bernatas JJ, Buisson Y, Pourcel C. Clinical characteristics of the smooth tubercle bacilli 'Mycobacterium canettii' infection suggest the existence of an environmental reservoir. Clin Microbiol Infect 2010; 17:1013-9. [PMID: 20831613 DOI: 10.1111/j.1469-0691.2010.03347.x] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Over a 3-year follow-up, 30 out of the 318 unique Mycobacterium tuberculosis complex isolates recovered in the Republic of Djibouti had a smooth-type morphology and were Niacine-negative, the characteristics of 'Mycobacterium canettii' strains. Unlike M. tuberculosis, 'M. canettii' grew on nutrient-poor media at 30°C, and possessed characteristic lipids. They were isolated from respiratory and extra-respiratory sites from patients with typical forms of tuberculosis. Most cases resolved with antibiotic therapy but in two human immunodeficiency virus-positive patients 'M. canettii' infection led to septicaemia and death. No cases of human-to-human transmission were observed. The proportion of tuberculosis cases caused by 'M. canettii' was higher among French patients than among Djiboutian patients. Patients with 'M. canettii' were significantly younger than those with tuberculosis caused by other M. tuberculosis complex strains. Smooth tubercle bacilli could be misidentified as non-tuberculous mycobacteria and appear to be limited to the Horn of Africa. Their characteristics are consistent with the existence of non-human sources of infection.
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Affiliation(s)
- J-L Koeck
- Laboratoire de biologie clinique, HIA Robert Picqué, Bordeaux, France
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12
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Fabre M, Hauck Y, Soler C, Koeck JL, van Ingen J, van Soolingen D, Vergnaud G, Pourcel C. Molecular characteristics of "Mycobacterium canettii" the smooth Mycobacterium tuberculosis bacilli. INFECTION GENETICS AND EVOLUTION 2010; 10:1165-73. [PMID: 20692377 DOI: 10.1016/j.meegid.2010.07.016] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2010] [Revised: 07/19/2010] [Accepted: 07/20/2010] [Indexed: 10/19/2022]
Abstract
Since the first discovery of the smooth tubercle (SmTB) bacilli "Mycobacterium canettii" less than 60 isolates have been reported, all but one originating from a limited geographical location, the Horn of Africa. In spite of its rarity, the SmTB lineage deserves special attention. Previous investigations suggested that SmTB isolates represent an ancestral lineage of the Mycobacterium tuberculosis complex (MTBC) and that consequently they might provide essential clues on the origin and evolution of the MTBC. There is evidence that unlike the rest of the MTBC, SmTB strains recombine chromosomal sequences with a yet unknown Mycobacterium species. This behavior contributes to the much larger genetic heterogeneity observed in the SmTB isolates compared to the other members of the MTBC. We have collected 59 SmTB isolates of which 14 were newly recovered since previous reports, and performed extensive phenotypical and genotypical characterization. We take advantage of these investigations to review the current knowledge of "M. canettii". Their characteristics and the apparent lack of human to human transmission are consistent with the previously proposed existence of non-human sources of infection. SmTB strains show remarkably common features together with secondary and taxonomically minor genetic differences such as the presence or absence of the CRISPR (Clustered Regularly Interspersed Palindromic Repeat) locus (usually called Direct Repeat or DR region) or number of IS sequences. Multiple Locus Variable number of tandem repeat Analysis (MLVA) and DR region analyses reveal one predominant clone, one minor clone and a number of more distantly related strains. This suggests that the two most frequent clones may represent successfully emerging lineages.
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Affiliation(s)
- Michel Fabre
- Laboratoire de biologie clinique, HIA Percy, Clamart, France
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13
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Stone AC, Wilbur AK, Buikstra JE, Roberts CA. Tuberculosis and leprosy in perspective. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 140 Suppl 49:66-94. [PMID: 19890861 DOI: 10.1002/ajpa.21185] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Two of humankind's most socially and psychologically devastating diseases, tuberculosis and leprosy, have been the subject of intensive paleopathological research due to their antiquity, a presumed association with human settlement and subsistence patterns, and their propensity to leave characteristic lesions on skeletal and mummified remains. Despite a long history of medical research and the development of effective chemotherapy, these diseases remain global health threats even in the 21st century, and as such, their causative agents Mycobacterium tuberculosis and M. leprae, respectively, have recently been the subject of molecular genetics research. The new genome-level data for several mycobacterial species have informed extensive phylogenetic analyses that call into question previously accepted theories concerning the origins and antiquity of these diseases. Of special note is the fact that all new models are in broad agreement that human TB predated that in other animals, including cattle and other domesticates, and that this disease originated at least 35,000 years ago and probably closer to 2.6 million years ago. In this work, we review current phylogenetic and biogeographic models derived from molecular biology and explore their implications for the global development of TB and leprosy, past and present. In so doing, we also briefly review the skeletal evidence for TB and leprosy, explore the current status of these pathogens, critically consider current methods for identifying ancient mycobacterial DNA, and evaluate coevolutionary models.
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Affiliation(s)
- Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.
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14
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Wilbur AK, Farnbach AW, Knudson KJ, Buikstra JE. Diet, tuberculosis, and the paleopathological record. CURRENT ANTHROPOLOGY 2009; 49:963-77; discussion 977-91. [PMID: 19391442 DOI: 10.1086/592434] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Osseous manifestation of infectious disease is of paramount importance to paleopathologists seeking to interpret ancient health, but the relationships among infectious agent exposure, development of disease, and skeletal involvement are complex. The outcome of an exposure strongly depends on multiple factors, including ecology, diet, nutrition, immune function, and the genetics of pathogen and host. Mycobacterial diseases are often studied in ancient remains but also are especially influenced by these factors; individual and population differences in severity and course are apparent following onset of active disease. The osteological record for these diseases represents the complex interplay of host and pathogen characteristics influencing within- and among-individual skeletal lesion prevalence and distribution. However, many of these characteristics may be assessed independently through the archaeological record. Here, we explore the contributions of dietary protein and iron to immune function, particularly the course and outcome of infection with Mycobacterium tuberculosis. We emphasize how nutrition may influence the dissemination of bacilli to the skeleton and subsequent formation of diagnostic lesions. We then generate models and hypotheses informed by this interplay and apply them to four prehistoric New World areas. Finally, discrepancies between our expectations and the observed record are explored as a basis for new hypotheses.
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Affiliation(s)
- A K Wilbur
- Center for Bioarchaeological Research, School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287, USA.
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15
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Hershberg R, Lipatov M, Small PM, Sheffer H, Niemann S, Homolka S, Roach JC, Kremer K, Petrov DA, Feldman MW, Gagneux S. High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography. PLoS Biol 2009; 6:e311. [PMID: 19090620 PMCID: PMC2602723 DOI: 10.1371/journal.pbio.0060311] [Citation(s) in RCA: 406] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2008] [Accepted: 10/31/2008] [Indexed: 12/15/2022] Open
Abstract
Mycobacterium tuberculosis infects one third of the human world population and kills someone every 15 seconds. For more than a century, scientists and clinicians have been distinguishing between the human- and animal-adapted members of the M. tuberculosis complex (MTBC). However, all human-adapted strains of MTBC have traditionally been considered to be essentially identical. We surveyed sequence diversity within a global collection of strains belonging to MTBC using seven megabase pairs of DNA sequence data. We show that the members of MTBC affecting humans are more genetically diverse than generally assumed, and that this diversity can be linked to human demographic and migratory events. We further demonstrate that these organisms are under extremely reduced purifying selection and that, as a result of increased genetic drift, much of this genetic diversity is likely to have functional consequences. Our findings suggest that the current increases in human population, urbanization, and global travel, combined with the population genetic characteristics of M. tuberculosis described here, could contribute to the emergence and spread of drug-resistant tuberculosis. Tuberculosis remains a worldwide public health emergency. The emergence of drug-resistant forms of tuberculosis in many parts of the world is threatening to make this important human disease incurable. Even though many resources are being invested into the development of new tuberculosis control tools, we still do not know the extent of genetic diversity in tuberculosis bacteria, nor do we understand the evolutionary forces that shape this diversity. To address these questions, we studied a large collection of human tuberculosis strains using DNA sequencing. We found that strains originating in different parts of the world are more genetically diverse than previously recognized. Our results also suggest that much of this diversity has functional consequences and could affect the efficacy of new tuberculosis diagnostics, drugs, and vaccines. Furthermore, we found that the global diversity in tuberculosis strains can be linked to the ancient human migrations out of Africa, as well as to more recent movements that followed the increases of human populations in Europe, India, and China during the past few hundred years. Taken together, our findings suggest that the evolutionary characteristics of tuberculosis bacteria could synergize with the effects of increasing globalization and human travel to enhance the global spread of drug-resistant tuberculosis. DNA sequence analysis of a global collection ofM. tuberculosis strains reveals high functional diversity, severely reduced selective constraint, and global spread through both ancient and recent human migrations.
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Affiliation(s)
- Ruth Hershberg
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Mikhail Lipatov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Peter M Small
- Institute for Systems Biology, Seattle, Washington, United States of America
- Bill and Melinda Gates Foundation, Seattle, Washington, United States of America
| | - Hadar Sheffer
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Stefan Niemann
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Susanne Homolka
- Forschungszentrum Borstel, National Reference Center for Mycobacteria, Borstel, Germany
| | - Jared C Roach
- Seattle Children's Hospital Research Institute, Seattle, Washington, United States of America
| | - Kristin Kremer
- Mycobacteria Reference Unit (CIb-LIS), National Institute of Public Health and the Environment, Bilthoven, The Netherlands
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Marcus W Feldman
- Department of Biology, Stanford University, Stanford, California, United States of America
| | - Sebastien Gagneux
- Institute for Systems Biology, Seattle, Washington, United States of America
- MRC National Institute for Medical Research, London, United Kingdom
- * To whom correspondence should be addressed. E-mail:
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16
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Achtman M. Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens. Annu Rev Microbiol 2008; 62:53-70. [PMID: 18785837 DOI: 10.1146/annurev.micro.62.081307.162832] [Citation(s) in RCA: 307] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Genetically monomorphic bacteria contain so little sequence diversity that sequencing a few gene fragments yields little or no information. As a result, our understanding of their evolutionary patterns presents greater technical challenges than exist for genetically diverse microbes. These challenges are now being met by analyses at the genomic level for diverse types of genetic variation, the most promising of which are single nucleotide polymorphisms. Many of the most virulent bacterial pathogens are genetically monomorphic, and understanding their evolutionary and phylogeographic patterns will help our understanding of the effects of infectious disease on human history.
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Affiliation(s)
- Mark Achtman
- Environmental Research Institute, University College Cork, Cork, Ireland.
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Cagliani R, Fumagalli M, Riva S, Pozzoli U, Comi GP, Menozzi G, Bresolin N, Sironi M. The signature of long-standing balancing selection at the human defensin beta-1 promoter. Genome Biol 2008; 9:R143. [PMID: 18817538 PMCID: PMC2592704 DOI: 10.1186/gb-2008-9-9-r143] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2008] [Revised: 05/21/2008] [Accepted: 09/25/2008] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Defensins, small endogenous peptides with antimicrobial activity, are pivotal components of the innate immune response. A large cluster of defensin genes is located on human chromosome 8p; among them the beta defensin 1 (DEFB1) promoterhas been extensively studied since discovery that specific polymorphisms and haplotypes associate with asthma and atopy, susceptibility to severe sepsis, as well as HIV and Candida infection predisposition. RESULTS Here, we characterize the sequence variation and haplotype structure of the DEFB1 promoter region in six human populations. In all of them, we observed high levels of nucleotide variation, an excess of intermediate-frequency alleles, reduced population differentiation and a genealogy with common haplotypes separated by deep branches. Indeed, a significant departure from the expectation of evolutionary neutrality was observed in all populations and the possibility that this is due to demographic history alone was ruled out. Also, we verified that the selection signature is restricted to the promoter region and not due to a linked balanced polymorphism. A phylogeny-based estimation indicated that the two major haplotype clades separated around 4.5 million years ago, approximately the time when the human and chimpanzee lineages split. CONCLUSION Altogether, these features represent strong molecular signatures of long-term balancing selection, a process that is thought to be extremely rare outside major histocompatibility complex genes. Our data indicate that the DEFB1 promoter region carries functional variants and support previous hypotheses whereby alleles predisposing to atopic disorders are widespread in modern societies because they conferred resistance to pathogens in ancient settings.
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Affiliation(s)
- Rachele Cagliani
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Matteo Fumagalli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
- Bioengineering Department, Politecnico di Milano, Pzza L. da Vinci, 32, 20133 Milan, Italy
| | - Stefania Riva
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Uberto Pozzoli
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Giacomo P Comi
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, Via F. Sforza 35, 20100 Milan, Italy
| | - Giorgia Menozzi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
| | - Nereo Bresolin
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
- Dino Ferrari Centre, Department of Neurological Sciences, University of Milan, IRCCS Ospedale Maggiore Policlinico, Mangiagalli and Regina Elena Foundation, Via F. Sforza 35, 20100 Milan, Italy
| | - Manuela Sironi
- Scientific Institute IRCCS E. Medea, Bioinformatic Lab, Via don L. Monza 20, 23842 Bosisio Parini (LC), Italy
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Ernst JD, Trevejo-Nuñez G, Banaiee N. Genomics and the evolution, pathogenesis, and diagnosis of tuberculosis. J Clin Invest 2007; 117:1738-45. [PMID: 17607348 PMCID: PMC1904327 DOI: 10.1172/jci31810] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Tuberculosis kills nearly 2 million people annually, and current approaches to tuberculosis control are expensive, have limited efficacy, and are vulnerable to being overcome by extensively drug-resistant strains of Mycobacterium tuberculosis. Determination of the genome sequence of M. tuberculosis has revolutionized tuberculosis research, contributed to major advances in the understanding of the evolution and pathogenesis of M. tuberculosis, and facilitated development of new diagnostic tests with increased specificity for tuberculosis. In this review, we describe some of the major progress in tuberculosis research that has resulted from knowledge of the genome sequence and note some of the problems that remain unsolved.
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Affiliation(s)
- Joel D Ernst
- Department of Medicine, Division of Infectious Diseases, New York University School of Medicine, New York, NY 10016, USA.
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McEvoy CRE, Falmer AA, Gey van Pittius NC, Victor TC, van Helden PD, Warren RM. The role of IS6110 in the evolution of Mycobacterium tuberculosis. Tuberculosis (Edinb) 2007; 87:393-404. [PMID: 17627889 DOI: 10.1016/j.tube.2007.05.010] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Revised: 05/15/2007] [Accepted: 05/22/2007] [Indexed: 10/23/2022]
Abstract
Members of the Mycobacterium tuberculosis complex contain the transposable element IS6110 which, due to its high numerical and positional polymorphism, has become a widely used marker in epidemiological studies. Here, we review the evidence that IS6110 is not simply a passive or 'junk' DNA sequence, but that, through its transposable activity, it is able to generate genotypic variation that translates into strain-specific phenotypic variation. We also speculate on the role that this variation has played in the evolution of M. tuberculosis and conclude that the presence of a moderate IS6110 copy number within the genome may provide the pathogen with a selective advantage that has aided its virulence.
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Affiliation(s)
- Christopher R E McEvoy
- DST/NRF Centre of Excellence in Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Brisse S, Supply P, Brosch R, Vincent V, Gutierrez MC. "A re-evaluation of M. prototuberculosis": continuing the debate. PLoS Pathog 2006; 2:e95. [PMID: 17009866 PMCID: PMC1579240 DOI: 10.1371/journal.ppat.0020095] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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