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Brites D, Gagneux S. The Nature and Evolution of Genomic Diversity in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:1-26. [DOI: 10.1007/978-3-319-64371-7_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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102
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Al-Saeedi M, Al-Hajoj S. Diversity and evolution of drug resistance mechanisms in Mycobacterium tuberculosis. Infect Drug Resist 2017; 10:333-342. [PMID: 29075131 PMCID: PMC5648319 DOI: 10.2147/idr.s144446] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
Despite the efficacy of antibiotics to protect humankind against many deadly pathogens, such as Mycobacterium tuberculosis, nothing can prevent the emergence of drug-resistant strains. Several mechanisms facilitate drug resistance in M. tuberculosis including compensatory evolution, epistasis, clonal interference, cell wall integrity, efflux pumps, and target mimicry. In this study, we present recent findings relevant to these mechanisms, which can enable the discovery of new drug targets and subsequent development of novel drugs for treatment of drug-resistant M. tuberculosis.
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Affiliation(s)
- Mashael Al-Saeedi
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
| | - Sahal Al-Hajoj
- Department of Infection and Immunity, Mycobacteriology Research Section, King Faisal Specialist Hospital and Research Center, Riyadh, Saudi Arabia
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103
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Drug development against tuberculosis: Past, present and future. ACTA ACUST UNITED AC 2017; 64:252-275. [DOI: 10.1016/j.ijtb.2017.03.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/15/2017] [Indexed: 12/29/2022]
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104
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Abstract
The tuberculosis agent Mycobacterium tuberculosis has undergone a long and selective evolution toward human infection and represents one of the most widely spread pathogens due to its efficient aerosol-mediated human-to-human transmission. With the availability of more and more genome sequences, the evolutionary trajectory of this obligate pathogen becomes visible, which provides us with new insights into the molecular events governing evolution of the bacterium and its ability to accumulate drug-resistance mutations. In this review, we summarize recent developments in mycobacterial research related to this matter that are important for a better understanding of the current situation and future trends and developments in the global epidemiology of tuberculosis, as well as for possible public health intervention possibilities.
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105
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Abstract
Tuberculosis (TB) remains the most deadly bacterial infectious disease worldwide. Its treatment and control are threatened by increasing numbers of multidrug-resistant (MDR) or nearly untreatable extensively drug-resistant (XDR) strains. New concepts are therefore urgently needed to understand the factors driving the TB epidemics and the spread of different strain populations, especially in association with drug resistance. Classical genotyping and, more recently, whole-genome sequencing (WGS) revealed that the world population of tubercle bacilli is more diverse than previously thought. Several major phylogenetic lineages can be distinguished, which are associated with their sympatric host population. Distinct clonal (sub)populations can even coexist within infected patients. WGS is now used as the ultimate approach for differentiating clinical isolates and for linking phenotypic to genomic variation from lineage to strain levels. Multiple lines of evidence indicate that the genetic diversity of TB strains translates into pathobiological consequences, and key molecular mechanisms probably involved in differential pathoadaptation of some main lineages have recently been identified. Evidence also accumulates on molecular mechanisms putatively fostering the emergence and rapid expansion of particular MDR and XDR strain groups in some world regions. However, further integrative studies will be needed for complete elucidation of the mechanisms that allow the pathogen to infect its host, acquire multidrug resistance, and transmit so efficiently. Such knowledge will be key for the development of the most effective new diagnostics, drugs, and vaccination strategies.
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106
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Chisholm RH, Tanaka MM. The emergence of latent infection in the early evolution of Mycobacterium tuberculosis. Proc Biol Sci 2017; 283:rspb.2016.0499. [PMID: 27194699 DOI: 10.1098/rspb.2016.0499] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 04/19/2016] [Indexed: 01/09/2023] Open
Abstract
Mycobacterium tuberculosis has an unusual natural history in that the vast majority of its human hosts enter a latent state that is both non-infectious and devoid of any symptoms of disease. From the pathogen perspective, it seems counterproductive to relinquish reproductive opportunities to achieve a détente with the host immune response. However, a small fraction of latent infections reactivate to the disease state. Thus, latency has been argued to provide a safe harbour for future infections which optimizes the persistence of M. tuberculosis in human populations. Yet, if a pathogen begins interactions with humans as an active disease without latency, how could it begin to evolve latency properties without incurring an immediate reproductive disadvantage? We address this question with a mathematical model. Results suggest that the emergence of tuberculosis latency may have been enabled by a mechanism akin to cryptic genetic variation in that detrimental latency properties were hidden from natural selection until their expression became evolutionarily favoured.
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Affiliation(s)
- Rebecca H Chisholm
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia Evolution and Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
| | - Mark M Tanaka
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney 2052, Australia Evolution and Ecology Research Centre, University of New South Wales, Sydney 2052, Australia
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107
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Dunsirn MM, Thoden JB, Gilbert M, Holden HM. Biochemical Investigation of Rv3404c from Mycobacterium tuberculosis. Biochemistry 2017; 56:3818-3825. [PMID: 28665588 DOI: 10.1021/acs.biochem.7b00506] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The causative agent of tuberculosis, Mycobacterium tuberculosis, is a bacterium with a complex cell wall and a complicated life cycle. The genome of M. tuberculosis contains well over 4000 genes thought to encode proteins. One of these codes for a putative enzyme referred to as Rv3404c, which has attracted research attention as a potential virulence factor for over 12 years. Here we demonstrate that Rv3404c functions as a sugar N-formyltransferase that converts dTDP-4-amino-4,6-dideoxyglucose into dTDP-4-formamido-4,6-dideoxyglucose using N10-formyltetrahydrofolate as the carbon source. Kinetic analyses demonstrate that Rv3404c displays a significant catalytic efficiency of 1.1 × 104 M-1 s-1. In addition, we report the X-ray structure of a ternary complex of Rv3404c solved in the presence of N5-formyltetrahydrofolate and dTDP-4-amino-4,6-dideoxyglucose. The final model of Rv3404c was refined to an overall R-factor of 16.8% at 1.6 Å resolution. The results described herein are especially intriguing given that there have been no published reports of N-formylated sugars associated with M. tuberculosis. The data thus provide a new avenue of research into this fascinating, yet deadly, organism that apparently has been associated with human infection since ancient times.
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Affiliation(s)
- Murray M Dunsirn
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - James B Thoden
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
| | - Michel Gilbert
- National Research Council Canada, Human Health Therapeutics, Ottawa, Ontario K1A 0R6, Canada
| | - Hazel M Holden
- Department of Biochemistry, University of Wisconsin , Madison, Wisconsin 53706, United States
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108
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Abstract
Paleopathology studies the traces of disease on human and animal remains from ancient times. Infectious diseases have been, for over a century, one of its main fields of interest. The applications of paleogenetics methods to microbial aDNA, that started in the 90s combined to the recent development of new sequencing techniques allowing 'paleogenomics' approaches, have completely renewed the issue of the infections in the past. These advances open up new challenges in the understanding of the evolution of human-pathogen relationships, integrated in "One Health" concept.In this perspective, an integrative multidisciplinary approach combining data from ancient texts and old bones to those of old molecules is of great interest for reconstructing the past of human infections. Despite some too optimistic prediction of their eradication in the late 20th century, some of these ancient human diseases, such as plague, leprosy or tuberculosis, are still present and continue their evolution at the beginning of this 21rst century. Better know the past to predict a part of the future of human diseases remains, more than ever, the motto of the paleopathological science.
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109
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Abstract
Tuberculosis is a significant global disease today, so understanding its origins and history is important. It is primarily a lung infection and is transmitted by infectious aerosols from person to person, so a high population density encourages its spread. The causative organism is Mycobacterium tuberculosis, an obligate pathogen in the M. tuberculosis complex that also contains closely related species, such as Mycobacterium bovis, that primarily infect animals. Typical bone lesions occur in about 5% of untreated infections. These can be recognized in historical and archaeological material, along with nonspecific paleopathology such as new bone formation (periostitis), especially on ribs. Based on such lesions, tuberculosis has been found in ancient Egypt, pre-Columbian America, and Neolithic Europe. The detection of M. tuberculosis ancient DNA (aDNA) by using PCR led to the development of the new field of paleomicrobiology. As a result, a large number of tuberculosis cases were recognized in mummified tissue and bones with nonspecific or no lesions. In parallel with these developments, M. tuberculosis cell wall lipid biomarkers have detected tuberculosis suggested by paleopathology and confirmed aDNA findings. In well-preserved cases, molecular typing has identified M. tuberculosis lineages and genotypes. The current interest in targeted enrichment, shotgun sequencing, and metagenomic analysis reveals ancient mixed infections with different M. tuberculosis strains and other pathogens. Identification of M. tuberculosis lineages from samples of known age enables the date of the emergence of strains and lineages to be calculated directly rather than by making assumptions on the rate of evolutionary change.
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110
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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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111
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Bouzid F, Brégeon F, Poncin I, Weber P, Drancourt M, Canaan S. Mycobacterium canettii Infection of Adipose Tissues. Front Cell Infect Microbiol 2017; 7:189. [PMID: 28567368 PMCID: PMC5434109 DOI: 10.3389/fcimb.2017.00189] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 05/02/2017] [Indexed: 01/17/2023] Open
Abstract
Adipose tissues were shown to host Mycobacterium tuberculosis which is persisting inside mature adipocytes. It remains unknown whether this holds true for Mycobacterium canettii, a rare representative of the M. tuberculosis complex responsible for lymphatic and pulmonary tuberculosis. Here, we infected primary murine white and brown pre-adipocytes and murine 3T3-L1 pre-adipocytes and mature adipocytes with M. canettii and M. tuberculosis as a positive control. Both mycobacteria were able to infect 18–22% of challenged primary murine pre-adipocytes; and to replicate within these cells during a 7-day experiment with the intracellular inoculums being significantly higher in brown than in white pre-adipocytes for M. canettii (p = 0.02) and M. tuberculosis (p = 0.03). Further in-vitro infection of 3T3-L1 mature adipocytes yielded 9% of infected cells by M. canettii and 17% of infected cells by M. tuberculosis (p = 0.001). Interestingly, M. canettii replicated and accumulated intra-cytosolic lipid inclusions within mature adipocytes over a 12-day experiment; while M. tuberculosis stopped replicating at day 3 post-infection. These results indicate that brown pre-adipocytes could be one of the potential targets for M. tuberculosis complex mycobacteria; and illustrate differential outcome of M. tuberculosis complex mycobacteria into adipose tissues. While white adipose tissue is an unlikely sanctuary for M. canettii, it is still an open question whether M. canettii and M. tuberculosis could persist in brown adipose tissues.
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Affiliation(s)
- Fériel Bouzid
- Aix-Marseille Université, CNRS, EIPL IMM FR3479Marseille, France.,Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée InfectionMarseille, France
| | - Fabienne Brégeon
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée InfectionMarseille, France.,Service des Explorations Fonctionnelles Respiratoires, Centre Hospitalo-Universitaire Nord, Pôle Cardio-Vasculaire et Thoracique, Assistance Publique Hôpitaux de MarseilleMarseille, France
| | - Isabelle Poncin
- Aix-Marseille Université, CNRS, EIPL IMM FR3479Marseille, France
| | - Pascal Weber
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée InfectionMarseille, France
| | - Michel Drancourt
- Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, IHU Méditerranée InfectionMarseille, France
| | - Stéphane Canaan
- Aix-Marseille Université, CNRS, EIPL IMM FR3479Marseille, France
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112
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Jankute M, Nataraj V, Lee OYC, Wu HHT, Ridell M, Garton NJ, Barer MR, Minnikin DE, Bhatt A, Besra GS. The role of hydrophobicity in tuberculosis evolution and pathogenicity. Sci Rep 2017; 7:1315. [PMID: 28465507 PMCID: PMC5431016 DOI: 10.1038/s41598-017-01501-0] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/29/2017] [Indexed: 12/24/2022] Open
Abstract
The evolution of tubercle bacilli parallels a route from environmental Mycobacterium kansasii, through intermediate "Mycobacterium canettii", to the modern Mycobacterium tuberculosis complex. Cell envelope outer membrane lipids change systematically from hydrophilic lipooligosaccharides and phenolic glycolipids to hydrophobic phthiocerol dimycocerosates, di- and pentaacyl trehaloses and sulfoglycolipids. Such lipid changes point to a hydrophobic phenotype for M. tuberculosis sensu stricto. Using Congo Red staining and hexadecane-aqueous buffer partitioning, the hydrophobicity of rough morphology M. tuberculosis and Mycobacterium bovis strains was greater than smooth "M. canettii" and M. kansasii. Killed mycobacteria maintained differential hydrophobicity but defatted cells were similar, indicating that outer membrane lipids govern overall hydrophobicity. A rough M. tuberculosis H37Rv ΔpapA1 sulfoglycolipid-deficient mutant had significantly diminished Congo Red uptake though hexadecane-aqueous buffer partitioning was similar to H37Rv. An M. kansasii, ΔMKAN27435 partially lipooligosaccharide-deficient mutant absorbed marginally more Congo Red dye than the parent strain but was comparable in partition experiments. In evolving from ancestral mycobacteria, related to "M. canettii" and M. kansasii, modern M. tuberculosis probably became more hydrophobic by increasing the proportion of less polar lipids in the outer membrane. Importantly, such a change would enhance the capability for aerosol transmission, affecting virulence and pathogenicity.
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Affiliation(s)
- Monika Jankute
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Vijayashankar Nataraj
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Oona Y-C Lee
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Houdini H T Wu
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Malin Ridell
- Department of Microbiology and Immunology, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Natalie J Garton
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - Michael R Barer
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, UK
| | - David E Minnikin
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Apoorva Bhatt
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK
| | - Gurdyal S Besra
- Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Edgbaston, Birmingham, UK.
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113
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Camassa S, Palucci I, Iantomasi R, Cubeddu T, Minerva M, De Maio F, Jouny S, Petruccioli E, Goletti D, Ria F, Sali M, Sanguinetti M, Manganelli R, Rocca S, Brodin P, Delogu G. Impact of pe_pgrs33 Gene Polymorphisms on Mycobacterium tuberculosis Infection and Pathogenesis. Front Cell Infect Microbiol 2017; 7:137. [PMID: 28484686 PMCID: PMC5399086 DOI: 10.3389/fcimb.2017.00137] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2017] [Accepted: 04/04/2017] [Indexed: 11/13/2022] Open
Abstract
PE_PGRS33 is a surface-exposed protein of Mycobacterium tuberculosis (Mtb) which exerts its role in macrophages entry and immunomodulation. In this study, we aimed to investigate the polymorphisms in the pe_pgrs33 gene of Mtb clinical isolates and evaluate their impact on protein functions. We sequenced pe_pgrs33 in a collection of 135 clinical strains, genotyped by 15-loci MIRU-VNTR and spoligotyping and belonging to the Mtb complex (MTBC). Overall, an association between pe_pgrs33 alleles and MTBC genotypes was observed and a dN/dS ratio of 0.64 was obtained, suggesting that a purifying selective pressure is acting on pe_pgrs33 against deleterious SNPs. Among a total of 19 pe_pgrs33 alleles identified in this study, 5 were cloned and used to complement the pe_pgrs33 knock-out mutant strain of Mtb H37Rv (MtbΔ33) to assess the functional impact of the respective polymorphisms in in vitro infections of primary macrophages. In human monocyte-derived macrophages (MDMs) infection, large in-frame and frameshift mutations were unable to restore the phenotype of Mtb H37Rv, impairing the cell entry capacity of Mtb, but neither its intracellular replication rate nor its immunomodulatory properties. In vivo studies performed in the murine model of tuberculosis (TB) demonstrated that the MtbΔ33 mutant strain was not impaired in the ability to infect and replicate in the lung tissue compared to the parental strain. Interestingly, MtbΔ33 showed an enhanced virulence during the chronic steps of infection compared to Mtb H37Rv. Similarly, the complementation of MtbΔ33 with a frameshift allele also resulted in a Mtb strain capable of causing a surprisingly enhanced tissue damage in murine lungs, during the chronic steps of infection. Together, these results further support the role of PE_PGRS33 in the pathogenesis and virulence of Mtb.
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Affiliation(s)
- Serena Camassa
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Ivana Palucci
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Raffaella Iantomasi
- Univ. Lille, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de LilleLille, France
| | - Tiziana Cubeddu
- Department of Veterinary Medicine, University of SassariSassari, Italy
| | - Mariachiara Minerva
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Flavio De Maio
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Samuel Jouny
- Univ. Lille, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de LilleLille, France
| | - Elisa Petruccioli
- Translational Research Unit, Department of Epidemiology and Preclinical Research, "Lazzaro Spallanzani" National Institute for Infectious DiseasesRome, Italy
| | - Delia Goletti
- Translational Research Unit, Department of Epidemiology and Preclinical Research, "Lazzaro Spallanzani" National Institute for Infectious DiseasesRome, Italy
| | - Francesco Ria
- Institute of General Pathology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Michela Sali
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | - Maurizio Sanguinetti
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
| | | | - Stefano Rocca
- Department of Veterinary Medicine, University of SassariSassari, Italy
| | - Priscille Brodin
- Univ. Lille, Centre National de la Recherche Scientifique, Institut National de la Santé et de la Recherche Médicale, CHU Lille, Institut Pasteur de Lille, U1019 - UMR 8204 - CIIL - Centre d'Infection et d'Immunité de LilleLille, France
| | - Giovanni Delogu
- Institute of Microbiology, Università Cattolica del Sacro Cuore - Fondazione Policlinico Universitario GemelliRome, Italy
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114
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Donoghue HD. Insights gained from ancient biomolecules into past and present tuberculosis—a personal perspective. Int J Infect Dis 2017; 56:176-180. [DOI: 10.1016/j.ijid.2016.11.413] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Revised: 11/17/2016] [Accepted: 11/20/2016] [Indexed: 01/24/2023] Open
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115
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Barberis I, Bragazzi N, Galluzzo L, Martini M. The history of tuberculosis: from the first historical records to the isolation of Koch's bacillus. JOURNAL OF PREVENTIVE MEDICINE AND HYGIENE 2017; 58:E9-E12. [PMID: 28515626 PMCID: PMC5432783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/30/2022]
Abstract
Tuberculosis (TB) is a contagious, infectious disease, due to Mycobacterium tuberculosis (MT) that has always been a permanent challenge over the course of human history, because of its severe social implications. It has been hypothesized that the genus Mycobacterium originated more than 150 million years ago. In the Middle Ages, scrofula, a disease affecting cervical lymph nodes, was described as a new clinical form of TB. The illness was known in England and France as "king's evil", and it was widely believed that persons affected could heal after a royal touch. In 1720, for the first time, the infectious origin of TB was conjectured by the English physician Benjamin Marten, while the first successful remedy against TB was the introduction of the sanatorium cure. The famous scientist Robert Koch was able to isolate the tubercle bacillus and presented this extraordinary result to the society of Physiology in Berlin on 24 March 1882. In the decades following this discovery, the Pirquet and Mantoux tuberculin skin tests, Albert Calmette and Camille Guérin BCG vaccine, Selman Waksman streptomycin and other anti-tuberculous drugs were developed.
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Affiliation(s)
- I. Barberis
- Department of Health Sciences, University of Genoa, Genoa, Italy;,Correspondence: Ilaria Barberis, Department of Health Sciences (DISSAL), University of Genoa, via A. Pastore 1, 16132 Genoa, Italy - Tel./ Fax +39 010 3538502 - E-mail:
| | - N.L. Bragazzi
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - L. Galluzzo
- Department of Cardiovascular, Dysmetabolic and Ageingassociated Diseases, Istituto Superiore di Sanità (Italian National Institute of Health), Rome, Italy
| | - M. Martini
- Department of Health Sciences, University of Genoa, Section of History of Medicine and Ethics, Genoa, Italy
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116
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Patané JS, Martins J, Castelão AB, Nishibe C, Montera L, Bigi F, Zumárraga MJ, Cataldi AA, Junior AF, Roxo E, Osório ALA, Jorge KS, Thacker TC, Almeida NF, Araújo FR, Setubal JC. Patterns and processes of Mycobacterium bovis evolution revealed by phylogenomic analyses. Genome Biol Evol 2017; 9:2992613. [PMID: 28201585 PMCID: PMC5381553 DOI: 10.1093/gbe/evx022] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 01/26/2017] [Accepted: 02/04/2017] [Indexed: 12/17/2022] Open
Abstract
Mycobacterium bovis is an important animal pathogen worldwide that parasitizes wild and domesticated vertebrate livestock as well as humans. A comparison of the five M. bovis complete genomes from the United Kingdom, South Korea, Brazil, and the United States revealed four novel large-scale structural variations of at least 2,000 bp. A comparative phylogenomic study including 2,483 core genes of 38 taxa from eight countries showed conflicting phylogenetic signal among sites. By minimizing this effect, we obtained a tree that better agrees with sampling locality. Results supported a relatively basal position of African strains (all isolated from Homo sapiens ), confirming that Africa was an important region for early diversification and that humans were one of the earliest hosts. Selection analyses revealed that functional categories such as “Lipid transport and metabolism,” “Cell cycle control, cell division, chromosome partitioning” and “Cell motility” were significant for the evolution of the group, besides other categories previously described, showing importance of genes associated with virulence and cholesterol metabolism in the evolution of M. bovis . PE/PPE genes, many of which are known to be associated with virulence, were major targets for large-scale polymorphisms, homologous recombination, and positive selection, evincing for the first time a plethora of evolutionary forces possibly contributing to differential adaptability in M. bovis . By assuming different priors, US strains originated and started to diversify around 150–5,210 ya. By further analyzing the largest set of US genomes to date (76 in total), obtained from 14 host species, we detected that hosts were not clustered in clades (except for a few cases), with some faster-evolving strains being detected, suggesting fast and ongoing reinfections across host species, and therefore, the possibility of new bovine tuberculosis outbreaks.
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Affiliation(s)
- José S.L. Patané
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | - Joaquim Martins
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
| | | | - Christiane Nishibe
- Faculdade de Computação Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Luciana Montera
- Faculdade de Computação Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Fabiana Bigi
- Instituto Nacional de Tecnologia Agropecuária, Córdoba, Argentina
| | | | - Angel A. Cataldi
- Instituto Nacional de Tecnologia Agropecuária, Córdoba, Argentina
| | - Antônio Fonseca Junior
- Rede de Laboratórios Agropecuários do Ministério da Agricultura, Pecuária e Abastecimento, Pedro Leopoldo, MG, Brazil
| | - Eliana Roxo
- Instituto Biológico de São Paulo, IB-USP, São Paulo, SP, Brazil
| | - Ana Luiza A.R. Osório
- Programa em Ciência Animal Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Klaudia S. Jorge
- Programa em Ciência Animal Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | - Tyler C. Thacker
- Agricultural Research Service, United States Department of Agriculture, Ames, Iowa
| | - Nalvo F. Almeida
- Faculdade de Computação Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | - João C. Setubal
- Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, SP, Brazil
- Biocomplexity Institute of Virginia Tech, Blacksburg, Virginia
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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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118
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The Evolution of Strain Typing in the Mycobacterium tuberculosis Complex. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2017; 1019:43-78. [PMID: 29116629 DOI: 10.1007/978-3-319-64371-7_3] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Tuberculosis (TB) is a contagious disease with a complex epidemiology. Therefore, molecular typing (genotyping) of Mycobacterium tuberculosis complex (MTBC) strains is of primary importance to effectively guide outbreak investigations, define transmission dynamics and assist global epidemiological surveillance of the disease. Large-scale genotyping is also needed to get better insights into the biological diversity and the evolution of the pathogen. Thanks to its shorter turnaround and simple numerical nomenclature system, mycobacterial interspersed repetitive unit-variable-number tandem repeat (MIRU-VNTR) typing, based on 24 standardized plus 4 hypervariable loci, optionally combined with spoligotyping, has replaced IS6110 DNA fingerprinting over the last decade as a gold standard among classical strain typing methods for many applications. With the continuous progress and decreasing costs of next-generation sequencing (NGS) technologies, typing based on whole genome sequencing (WGS) is now increasingly performed for near complete exploitation of the available genetic information. However, some important challenges remain such as the lack of standardization of WGS analysis pipelines, the need of databases for sharing WGS data at a global level, and a better understanding of the relevant genomic distances for defining clusters of recent TB transmission in different epidemiological contexts. This chapter provides an overview of the evolution of genotyping methods over the last three decades, which culminated with the development of WGS-based methods. It addresses the relative advantages and limitations of these techniques, indicates current challenges and potential directions for facilitating standardization of WGS-based typing, and provides suggestions on what method to use depending on the specific research question.
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Hartman TE, Wang Z, Jansen RS, Gardete S, Rhee KY. Metabolic Perspectives on Persistence. Microbiol Spectr 2017; 5:10.1128/microbiolspec.TBTB2-0026-2016. [PMID: 28155811 PMCID: PMC5302851 DOI: 10.1128/microbiolspec.tbtb2-0026-2016] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2016] [Indexed: 02/07/2023] Open
Abstract
Accumulating evidence has left little doubt about the importance of persistence or metabolism in the biology and chemotherapy of tuberculosis. However, knowledge of the intersection between these two factors has only recently begun to emerge. Here, we provide a focused review of metabolic characteristics associated with Mycobacterium tuberculosis persistence. We focus on metabolism because it is the biochemical foundation of all physiologic processes and a distinguishing hallmark of M. tuberculosis physiology and pathogenicity. In addition, it serves as the chemical interface between host and pathogen. Existing knowledge, however, derives largely from physiologic contexts in which replication is the primary biochemical objective. The goal of this review is to reframe current knowledge of M. tuberculosis metabolism in the context of persistence, where quiescence is often a key distinguishing characteristic. Such a perspective may help ongoing efforts to develop more efficient cures and inform on novel strategies to break the cycle of transmission sustaining the pandemic.
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Affiliation(s)
- Travis E. Hartman
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Zhe Wang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Robert S. Jansen
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Susana Gardete
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
| | - Kyu Y. Rhee
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
- Department of Microbiology & Immunology, Division of Infectious Diseases, Weill Cornell Medical College, New York, NY 10065
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121
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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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Abstract
Type VII secretion (T7S) systems of mycobacteria secrete substrates over the unusual diderm cell envelope. Furthermore, T7S gene clusters are present throughout the phylum Actinobacteria, and functional T7S-like systems have been identified in Firmicutes. Most of the T7S substrates can be divided into two families: the Esx proteins, which are found in both Firmicutes and Actinobacteria, and the PE and PPE proteins, which are more mycobacterium-specific. Members of both families have been shown to be secreted as folded heterodimers, suggesting that this is a conserved feature of T7S substrates. Most knowledge of the mechanism of T7S and the roles of T7S systems in virulence comes from studies of pathogenic mycobacteria. These bacteria can contain up to five T7S systems, called ESX-1 to ESX-5, each having its own role in bacterial physiology and virulence. In this article, we discuss the general composition of T7S systems and the role of the individual components in secretion. These conserved components include two membrane proteins with (predicted) enzymatic activities: a predicted ATPase (EccC), likely to be required for energy provision of T7S, and a subtilisin-like protease (MycP) involved in processing of specific substrates. Additionally, we describe the role of a conserved intracellular chaperone in T7S substrate recognition, based on recently published crystal structures and molecular analysis. Finally, we discuss system-specific features of the different T7S systems in mycobacteria and their role in pathogenesis and provide an overview of the role of T7S in virulence of other pathogenic bacteria.
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123
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Charlier P, Augias A, Jacqueline S, Benmoussa N, Huynh-Charlier I. Une histoire biologique du cancer. ACTA ACUST UNITED AC 2016; 44:726-727. [DOI: 10.1016/j.gyobfe.2016.10.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2016] [Accepted: 10/11/2016] [Indexed: 10/20/2022]
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Transposition mechanism, molecular characterization and evolution of IS6110, the specific evolutionary marker of Mycobacterium tuberculosis complex. Mol Biol Rep 2016; 44:25-34. [DOI: 10.1007/s11033-016-4084-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 09/16/2016] [Indexed: 10/20/2022]
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125
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Refrégier G, Abadia E, Matsumoto T, Ano H, Takashima T, Tsuyuguchi I, Aktas E, Cömert F, Gomgnimbou MK, Panaiotov S, Phelan J, Coll F, McNerney R, Pain A, Clark TG, Sola C. Turkish and Japanese Mycobacterium tuberculosis sublineages share a remote common ancestor. INFECTION GENETICS AND EVOLUTION 2016; 45:461-473. [PMID: 27746295 DOI: 10.1016/j.meegid.2016.10.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 09/23/2016] [Accepted: 10/12/2016] [Indexed: 12/19/2022]
Abstract
Two geographically distant M. tuberculosis sublineages, Tur from Turkey and T3-Osaka from Japan, exhibit partially identical genotypic signatures (identical 12-loci MIRU-VNTR profiles, distinct spoligotyping patterns). We investigated T3-Osaka and Tur sublineages characteristics and potential genetic relatedness, first using MIRU-VNTR locus analysis on 21 and 25 samples of each sublineage respectively, and second comparing Whole Genome Sequences of 8 new samples to public data from 45 samples uncovering human tuberculosis diversity. We then tried to date their Most Recent Common Ancestor (MRCA) using three calibrations of SNP accumulation rate (long-term=0.03SNP/genome/year, derived from a tuberculosis ancestor of around 70,000years old; intermediate=0.2SNP/genome/year derived from a Peruvian mummy; short-term=0.5SNP/genome/year). To disentangle between these scenarios, we confronted the corresponding divergence times with major human history events and knowledge on human genetic divergence. We identified relatively high intrasublineage diversity for both T3-Osaka and Tur. We definitively proved their monophyly; the corresponding super-sublineage (referred to as "T3-Osa-Tur") shares a common ancestor with T3-Ethiopia and Ural sublineages but is only remotely related to other Euro-American sublineages such as X, LAM, Haarlem and S. The evolutionary scenario based on long-term evolution rate being valid until T3-Osa-Tur MRCA was not supported by Japanese fossil data. The evolutionary scenario relying on short-term evolution rate since T3-Osa-Tur MRCA was contradicted by human history and potential traces of past epidemics. T3-Osaka and Tur sublineages were found likely to have diverged between 800y and 2000years ago, potentially at the time of Mongol Empire. Altogether, this study definitively proves a strong genetic link between Turkish and Japanese tuberculosis. It provides a first hypothesis for calibrating TB Euro-American lineage molecular clock; additional studies are needed to reliably date events corresponding to intermediate depths in tuberculosis phylogeny.
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Affiliation(s)
- Guislaine Refrégier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France.
| | - Edgar Abadia
- Instituto Venezolano de Investigaciones Científicas (IVIC), Caracas, Venezuela
| | - Tomoshige Matsumoto
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Hiromi Ano
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Tetsuya Takashima
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Izuo Tsuyuguchi
- Department of Clinical Research and Development, Osaka Prefectural Hospital Organization, Osaka Prefectural Medical Center for Respiratory and Allergic Diseases, Habikino-city, Japan
| | - Elif Aktas
- Şişli Etfal Research and Training Hopital, Istanbul, Turkey
| | - Füsun Cömert
- Faculty of Medicine, Bülent Ecevit University, Zonguldak, Turkey
| | - Michel Kireopori Gomgnimbou
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
| | - Stefan Panaiotov
- National Center of Parasitic and Infectious Diseases, Sofia, Bulgaria
| | - Jody Phelan
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Francesc Coll
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Ruth McNerney
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Infection and Immunity Unit, UCT Lung Institute, University of Cape Town, Old Main Building, Groote Schuur Hospital, Cape Town,South Africa
| | - Arnab Pain
- Pathogen Genomics Group, Biological, Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Christophe Sola
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, 91198, Gif-sur-Yvette cedex, France
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126
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Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria. Proc Natl Acad Sci U S A 2016; 113:9876-81. [PMID: 27528665 DOI: 10.1073/pnas.1604921113] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Horizontal gene transfer (HGT) is a major driving force of bacterial diversification and evolution. For tuberculosis-causing mycobacteria, the impact of HGT in the emergence and distribution of dominant lineages remains a matter of debate. Here, by using fluorescence-assisted mating assays and whole genome sequencing, we present unique experimental evidence of chromosomal DNA transfer between tubercle bacilli of the early-branching Mycobacterium canettii clade. We found that the obtained recombinants had received multiple donor-derived DNA fragments in the size range of 100 bp to 118 kbp, fragments large enough to contain whole operons. Although the transfer frequency between M. canettii strains was low and no transfer could be observed among classical Mycobacterium tuberculosis complex (MTBC) strains, our study provides the proof of concept for genetic exchange in tubercle bacilli. This outstanding, now experimentally validated phenomenon presumably played a key role in the early evolution of the MTBC toward pathogenicity. Moreover, our findings also provide important information for the risk evaluation of potential transfer of drug resistance and fitness mutations among clinically relevant mycobacterial strains.
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127
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Abstract
ABSTRACT
With the advent of next-generation sequencing technology, the genotyping of clinical
Mycobacterium tuberculosis
strains went through a major breakup that dramatically improved the field of molecular epidemiology but also revolutionized our deep understanding of the
M. tuberculosis
complex evolutionary history. The intricate paths of the pathogen and its human host are reflected by a common geographical origin in Africa and strong biogeographical associations that largely reflect the past migration waves out of Africa. This long coevolutionary history is cardinal for our understanding of the host-pathogen dynamic, including past and ongoing demographic components, strains’ genetic background, as well as the immune system genetic architecture of the host. Coalescent- and Bayesian-based analyses allowed us to reconstruct population size changes of
M. tuberculosis
through time, to date the most recent common ancestor and the several phylogenetic lineages. This information will ultimately help us to understand the spread of the Beijing lineage, the rise of multidrug-resistant sublineages, or the fall of others in the light of socioeconomic events, antibiotic programs, or host population densities. If we leave the present and go through the looking glass, thanks to our ability to handle small degraded molecules combined with targeted capture, paleomicrobiology covering the Pleistocene era will possibly unravel lineage replacements, dig out extinct ones, and eventually ask for major revisions of the current model.
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128
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Controlled fire use in early humans might have triggered the evolutionary emergence of tuberculosis. Proc Natl Acad Sci U S A 2016; 113:9051-6. [PMID: 27457933 DOI: 10.1073/pnas.1603224113] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Tuberculosis (TB) is caused by the Mycobacterium tuberculosis complex (MTBC), a wildly successful group of organisms and the leading cause of death resulting from a single bacterial pathogen worldwide. It is generally accepted that MTBC established itself in human populations in Africa and that animal-infecting strains diverged from human strains. However, the precise causal factors of TB emergence remain unknown. Here, we propose that the advent of controlled fire use in early humans created the ideal conditions for the emergence of TB as a transmissible disease. This hypothesis is supported by mathematical modeling together with a synthesis of evidence from epidemiology, evolutionary genetics, and paleoanthropology.
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129
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Cannas A, Mazzarelli A, Di Caro A, Delogu G, Girardi E. Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination. Infect Dis Rep 2016; 8:6567. [PMID: 27403266 PMCID: PMC4927935 DOI: 10.4081/idr.2016.6567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 04/29/2016] [Indexed: 11/23/2022] Open
Abstract
Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.
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Affiliation(s)
- Angela Cannas
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | | | - Antonino Di Caro
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
| | - Giovanni Delogu
- National Institute for Infectious Diseases L. Spallanzani, Rome, Italy; Institute of Microbiology, Sacro Cuore Catholic University, Rome, Italy
| | - Enrico Girardi
- National Institute for Infectious Diseases L. Spallanzani , Rome, Italy
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130
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Darling MI, Donoghue HD. Insights from paleomicrobiology into the indigenous peoples of pre-colonial America - a review. Mem Inst Oswaldo Cruz 2016; 109:131-9. [PMID: 24714964 PMCID: PMC4015261 DOI: 10.1590/0074-0276140589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Indexed: 02/06/2023] Open
Abstract
This review investigates ancient infectious diseases in the Americas dated to the
pre-colonial period and considers what these findings can tell us about the history
of the indigenous peoples of the Americas. It gives an overview, but focuses on four
microbial pathogens from this period: Helicobacter pylori,
Mycobacterium tuberculosis, Trypanosoma cruzi
and Coccidioides immitis, which cause stomach ulceration and gastric
cancer, tuberculosis, Chagas disease and valley fever, respectively. These pathogens
were selected as H. pylori can give insight into ancient human
migrations into the Americas, M. tuberculosis is associated with
population density and urban development, T. cruzi can elucidate
human living conditions and C. immitis can indicate agricultural
development. A range of methods are used to diagnose infectious disease in ancient
human remains, with DNA analysis by polymerase chain reaction one of the most
reliable, provided strict precautions are taken against cross contamination. The
review concludes with a brief summary of the changes that took place after European
exploration and colonisation.
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Affiliation(s)
- Millie I Darling
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
| | - Helen D Donoghue
- Division of Biosciences, Centre for Clinical Microbiology, University College London, London, UK
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131
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Clarke C, Van Helden P, Miller M, Parsons S. Animal-adapted members of the Mycobacterium tuberculosis complex endemic to the southern African subregion. J S Afr Vet Assoc 2016; 87:1322. [PMID: 27246904 PMCID: PMC6138107 DOI: 10.4102/jsava.v87i1.1322] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2015] [Revised: 10/30/2015] [Accepted: 12/02/2015] [Indexed: 11/15/2022] Open
Abstract
Members of the Mycobacterium tuberculosis complex (MTC) cause tuberculosis (TB) in both animals and humans. In this article, three animal-adapted MTC strains that are endemic to the southern African subregion – that is, Mycobacterium suricattae, Mycobacterium mungi, and the dassie bacillus – are reviewed with a focus on clinical and pathological presentations, geographic distribution, genotyping methods, diagnostic tools and evolution. Moreover, factors influencing the transmission and establishment of TB pathogens in novel host populations, including ecological, immunological and genetic factors of both the host and pathogen, are discussed. The risks associated with these infections are currently unknown and further studies will be required for greater understanding of this disease in the context of the southern African ecosystem.
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Affiliation(s)
| | | | | | - Sven Parsons
- SAMRC Centre for TB Research, DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University.
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132
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Antimicrobial Resistance in Mycobacterium tuberculosis: The Odd One Out. Trends Microbiol 2016; 24:637-648. [PMID: 27068531 DOI: 10.1016/j.tim.2016.03.007] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 02/13/2016] [Accepted: 03/15/2016] [Indexed: 01/29/2023]
Abstract
Antimicrobial resistance (AMR) threats are typically represented by bacteria capable of extensive horizontal gene transfer (HGT). One clear exception is Mycobacterium tuberculosis (Mtb). It is an obligate human pathogen with limited genetic diversity and a low mutation rate which lacks any evidence for HGT. Such features should, in principle, reduce its ability to rapidly evolve AMR. We identify key features in its biology and epidemiology that allow it to overcome its low adaptive potential. We focus in particular on its innate resistance to drugs, its unusual life cycle, including an often extensive latent phase, and its ability to shelter from exposure to antimicrobial drugs within cavities it induces in the lungs.
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133
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Kim BJ, Kim BR, Lee SY, Kim GN, Kook YH, Kim BJ. Molecular Taxonomic Evidence for Two Distinct Genotypes of Mycobacterium yongonense via Genome-Based Phylogenetic Analysis. PLoS One 2016; 11:e0152703. [PMID: 27031100 PMCID: PMC4816341 DOI: 10.1371/journal.pone.0152703] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 03/17/2016] [Indexed: 12/30/2022] Open
Abstract
Recently, we introduced a distinct Mycobacterium intracellulare INT-5 genotype, distantly related to other genotypes of M. intracellulare (INT-1 to -4). The aim of this study is to determine the exact taxonomic status of the M. intracellulare INT-5 genotype via genome-based phylogenetic analysis. To this end, genome sequences of the two INT-5 strains, MOTT-H4Y and MOTT-36Y were compared with M. intracellulare ATCC 13950T and Mycobacterium yongonense DSM 45126T. Our phylogenetic analysis based on complete genome sequences, multi-locus sequence typing (MLST) of 35 target genes, and single nucleotide polymorphism (SNP) analysis indicated that the two INT-5 strains were more closely related to M. yongonense DSM 45126T than the M. intracellulare strains. These results suggest their taxonomic transfer from M. intracellulare into M. yongonense. Finally, we selected 5 target genes (argH, dnaA, deaD, hsp65, and recF) and used SNPs for the identification of M. yongonese strains from other M. avium complex (MAC) strains. The application of the SNP analysis to 14 MAC clinical isolates enabled the selective identification of 4 M. yongonense clinical isolates from the other MACs. In conclusion, our genome-based phylogenetic analysis showed that the taxonomic status of two INT-5 strains, MOTT-H4Y and MOTT-36Y should be revised into M. yongonense. Our results also suggest that M. yongonense could be divided into 2 distinct genotypes (the Type I genotype with the M. parascrofulaceum rpoB gene and the Type II genotype with the M. intracellulare rpoB gene) depending on the presence of the lateral gene transfer of rpoB from M. parascrofulaceum.
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Affiliation(s)
- Byoung-Jun Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bo-Ram Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - So-Young Lee
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Ga-Na Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Yoon-Hoh Kook
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Bum-Joon Kim
- Department of Biomedical Sciences, Microbiology and Immunology, Cancer Research Institute, Institute of Endemic Diseases, and Seoul National University Medical Research Center (SNUMRC), Seoul National University College of Medicine, Seoul, Republic of Korea
- * E-mail:
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134
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Wee WY, Tan TK, Jakubovics NS, Choo SW. Whole-Genome Sequencing and Comparative Analysis of Mycobacterium brisbanense Reveals a Possible Soil Origin and Capability in Fertiliser Synthesis. PLoS One 2016; 11:e0152682. [PMID: 27031249 PMCID: PMC4816395 DOI: 10.1371/journal.pone.0152682] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 03/17/2016] [Indexed: 11/18/2022] Open
Abstract
Mycobacterium brisbanense is a member of Mycobacterium fortuitum third biovariant complex, which includes rapidly growing Mycobacterium spp. that normally inhabit soil, dust and water, and can sometimes cause respiratory tract infections in humans. We present the first whole-genome analysis of M. brisbanense UM_WWY which was isolated from a 70-year-old Malaysian patient. Molecular phylogenetic analyses confirmed the identification of this strain as M. brisbanense and showed that it has an unusually large genome compared with related mycobacteria. The large genome size of M. brisbanense UM_WWY (~7.7Mbp) is consistent with further findings that this strain has a highly variable genome structure that contains many putative horizontally transferred genomic islands and prophage. Comparative analysis showed that M. brisbanense UM_WWY is the only Mycobacterium species that possesses a complete set of genes encoding enzymes involved in the urea cycle, suggesting that this soil bacterium is able to synthesize urea for use as plant fertilizers. It is likely that M. brisbanense UM_WWY is adapted to live in soil as its primary habitat since the genome contains many genes associated with nitrogen metabolism. Nevertheless, a large number of predicted virulence genes were identified in M. brisbanense UM_WWY that are mostly shared with well-studied mycobacterial pathogens such as Mycobacterium tuberculosis and Mycobacterium abscessus. These findings are consistent with the role of M. brisbanense as an opportunistic pathogen of humans. The whole-genome study of UM_WWY has provided the basis for future work of M. brisbanense.
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Affiliation(s)
- Wei Yee Wee
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Tze King Tan
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
| | - Nicholas S. Jakubovics
- Center for Oral Health Research, School of Dental Sciences, Newcastle University, Framlington Place, Newcastle upon Tyne, United Kingdom
- Genome Solutions Sdn Bhd, Suite 8, Innovation Incubator UM, Level 5, Research Management & Innovation Complex, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Siew Woh Choo
- Genome Informatics Research Laboratory, High Impact Research Building (HIR) Building, University of Malaya, Kuala Lumpur, 50603, Malaysia
- Department of Oral Biology and Biomedical Sciences, Faculty of Dentistry, University of Malaya, Kuala Lumpur, 50603, Malaysia
- * E-mail:
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Sapriel G, Konjek J, Orgeur M, Bouri L, Frézal L, Roux AL, Dumas E, Brosch R, Bouchier C, Brisse S, Vandenbogaert M, Thiberge JM, Caro V, Ngeow YF, Tan JL, Herrmann JL, Gaillard JL, Heym B, Wirth T. Genome-wide mosaicism within Mycobacterium abscessus: evolutionary and epidemiological implications. BMC Genomics 2016; 17:118. [PMID: 26884275 PMCID: PMC4756508 DOI: 10.1186/s12864-016-2448-1] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 02/08/2016] [Indexed: 11/16/2022] Open
Abstract
Background In mycobacteria, conjugation differs from the canonical Hfr model, but is still poorly understood. Here, we quantified this evolutionary processe in a natural mycobacterial population, taking advantage of a large clinical strain collection of the emerging pathogen Mycobacterium abscessus (MAB). Results Multilocus sequence typing confirmed the existence of three M. abscessus subspecies, and unravelled extensive allelic exchange between them. Furthermore, an asymmetrical gene flow occurring between these main lineages was detected, resulting in highly admixed strains. Intriguingly, these mosaic strains were significantly associated with cystic fibrosis patients with lung infections or chronic colonization. Genome sequencing of those hybrid strains confirmed that half of their genomic content was remodelled in large genomic blocks, leading to original tri-modal ‘patchwork’ architecture. One of these hybrid strains acquired a locus conferring inducible macrolide resistance, and a large genomic insertion from a slowly growing pathogenic mycobacteria, suggesting an adaptive gene transfer. This atypical genomic architecture of the highly recombinogenic strains is consistent with the distributive conjugal transfer (DCT) observed in M. smegmatis. Intriguingly, no known DCT function was found in M. abscessus chromosome, however, a p-RAW-like genetic element was detected in one of the highly admixed strains. Conclusion Taken together, our results strongly suggest that MAB evolution is sporadically punctuated by dramatic genome wide remodelling events. These findings might have far reaching epidemiological consequences for emerging mycobacterial pathogens survey in the context of increasing numbers of rapidly growing mycobacteria and M. tuberculosis co-infections. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2448-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Guillaume Sapriel
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,Laboratoire des Sciences du Climat et de l'Environnement, LSCE, UMR8212, Université de Versailles St. Quentin - CEA - CNRS, Saint-Aubin, France. .,Atelier de Bioinformatique, ISYEB, UMR 7205, Paris, France.
| | - Julie Konjek
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Mickael Orgeur
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | - Laurent Bouri
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Lise Frézal
- Institut of Biology of the Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris, Cedex 05, France.
| | | | - Emilie Dumas
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France.
| | - Roland Brosch
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France.
| | | | - Sylvain Brisse
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | | | | | - Valérie Caro
- Institut Pasteur, Genotyping of Pathogens and Public Health, Paris, France.
| | - Yun Fong Ngeow
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Joon Liang Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.
| | - Jean-Louis Herrmann
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Raymond Poincaré, Service de Microbiologie et Hygiène, Garches, France.
| | - Jean-Louis Gaillard
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Beate Heym
- EA3647-EPIM, UFR des Sciences de La Santé, Université de Versailles St. Quentin, Montigny le Bretonneux, France. .,AP-HP, Hôpital Ambroise Paré, Service de Microbiologie et Hygiène, Boulogne-Billancourt, France.
| | - Thierry Wirth
- Laboratoire de Biologie intégrative des populations, Evolution moléculaire, Ecole Pratique des Hautes Etudes, Paris, France. .,Institut de Systématique, Evolution, Biodiversité, ISYEB, UMR 7205, CNRS, MNHN, UPMC, EPHE, Muséum national d'Histoire naturelle, Sorbonne Universités, 16 rue Buffon, F-75231, Paris, Cedex 05, France.
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pks5-recombination-mediated surface remodelling in Mycobacterium tuberculosis emergence. Nat Microbiol 2016; 1:15019. [PMID: 27571976 DOI: 10.1038/nmicrobiol.2015.19] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 11/19/2015] [Indexed: 01/09/2023]
Abstract
Mycobacterium tuberculosis is a major, globally spread, aerosol-transmitted human pathogen, thought to have evolved by clonal expansion from a Mycobacterium canettii-like progenitor. In contrast, extant M. canettii strains are rare, genetically diverse, and geographically restricted mycobacteria of only marginal epidemiological importance. Here, we show that the contrasting evolutionary success of these two groups is linked to loss of lipooligosaccharide biosynthesis and subsequent morphotype changes. Spontaneous smooth-to-rough M. canettii variants were found to be mutated in the polyketide-synthase-encoding pks5 locus and deficient in lipooligosaccharide synthesis, a phenotype restored by complementation. Importantly, these rough variants showed an altered host-pathogen interaction and increased virulence in cellular- and animal-infection models. In one variant, lipooligosaccharide deficiency occurred via homologous recombination between two pks5 genes and removal of the intervening acyltransferase-encoding gene. The resulting single pks5 configuration is similar to that fixed in M. tuberculosis, which is known to lack lipooligosaccharides. Our results suggest that pks5-recombination-mediated bacterial surface remodelling increased virulence, driving evolution from putative generalist mycobacteria towards professional pathogens of mammalian hosts.
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138
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Aboubaker Osman D, Bouzid F, Canaan S, Drancourt M. Smooth Tubercle Bacilli: Neglected Opportunistic Tropical Pathogens. Front Public Health 2016; 3:283. [PMID: 26793699 PMCID: PMC4707939 DOI: 10.3389/fpubh.2015.00283] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 12/18/2015] [Indexed: 11/23/2022] Open
Abstract
Smooth tubercle bacilli (STB) including “Mycobacterium canettii” are members of the Mycobacterium tuberculosis complex (MTBC), which cause non-contagious tuberculosis in human. This group comprises <100 isolates characterized by smooth colonies and cordless organisms. Most STB isolates have been obtained from patients exposed to the Republic of Djibouti but seven isolates, including the three seminal ones obtained by Georges Canetti between 1968 and 1970, were recovered from patients in France, Madagascar, Sub-Sahara East Africa, and French Polynesia. STB form a genetically heterogeneous group of MTBC organisms with large 4.48 ± 0.05 Mb genomes, which may link Mycobacterium kansasii to MTBC organisms. Lack of inter-human transmission suggested a yet unknown environmental reservoir. Clinical data indicate a respiratory tract route of contamination and the digestive tract as an alternative route of contamination. Further epidemiological and clinical studies are warranted to elucidate areas of uncertainty regarding these unusual mycobacteria and the tuberculosis they cause.
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Affiliation(s)
- Djaltou Aboubaker Osman
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Centre d'Études et de Recherche de Djibouti (CERD), Institut de Recherche Médicinale (IRM), Djibouti, Republic of Djibouti
| | - Feriel Bouzid
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Marseille, France; Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université, Marseille, France
| | - Stéphane Canaan
- Enzymologie Interfaciale et Physiologie de la Lipolyse UMR7282, Centre National de la Recherche Scientifique (CNRS), Aix-Marseille Université , Marseille , France
| | - Michel Drancourt
- Aix-Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095 , Marseille , France
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139
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Abstract
Most mycobacterial species are harmless saprophytes, often found in aquatic environments. A few species seem to have evolved from this pool of environmental mycobacteria into major human pathogens, such as Mycobacterium tuberculosis, the agent of tuberculosis, Mycobacterium leprae, the leprosy bacillus, and Mycobacterium ulcerans, the agent of Buruli ulcer. While the pathogenicity of M. ulcerans relates to the acquisition of a large plasmid encoding a polyketide-derived toxin, the molecular mechanisms by which M. leprae or M. tuberculosis have evolved to cause disease are complex and involve the interaction between the pathogen and the host. Here we focus on M. tuberculosis and closely related mycobacteria and discuss insights gained from recent genomic and functional studies. Comparison of M. tuberculosis genome data with sequences from nontuberculous mycobacteria, such as Mycobacterium marinum or Mycobacterium kansasii, provides a perception of the more distant evolution of M. tuberculosis, while the recently accomplished genome sequences of multiple tubercle bacilli with smooth colony morphology, named Mycobacterium canettii, have allowed the ancestral gene pool of tubercle bacilli to be estimated. The resulting findings are instrumental for our understanding of the pathogenomic evolution of tuberculosis-causing mycobacteria. Comparison of virulent and attenuated members of the M. tuberculosis complex has further contributed to identification of a specific secretion pathway, named ESX or Type VII secretion. The molecular machines involved are key elements for mycobacterial pathogenicity, strongly influencing the ability of M. tuberculosis to cope with the immune defense mounted by the host.
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140
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Abstract
The causative agent of human tuberculosis (TB), Mycobacterium tuberculosis, is an obligate pathogen that evolved to exclusively persist in human populations. For M. tuberculosis to transmit from person to person, it has to cause pulmonary disease. Therefore, M. tuberculosis virulence has likely been a significant determinant of the association between M. tuberculosis and humans. Indeed, the evolutionary success of some M. tuberculosis genotypes seems at least partially attributable to their increased virulence. The latter possibly evolved as a consequence of human demographic expansions. If co-evolution occurred, humans would have counteracted to minimize the deleterious effects of M. tuberculosis virulence. The fact that human resistance to infection has a strong genetic basis is a likely consequence of such a counter-response. The genetic architecture underlying human resistance to M. tuberculosis remains largely elusive. However, interactions between human genetic polymorphisms and M. tuberculosis genotypes have been reported. Such interactions are consistent with local adaptation and allow for a better understanding of protective immunity in TB. Future 'genome-to-genome' studies, in which locally associated human and M. tuberculosis genotypes are interrogated in conjunction, will help identify new protective antigens for the development of better TB vaccines.
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Affiliation(s)
- Daniela Brites
- Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute and University of Basel, Basel, Switzerland
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Biadglegne F, Merker M, Sack U, Rodloff AC, Niemann S. Tuberculous Lymphadenitis in Ethiopia Predominantly Caused by Strains Belonging to the Delhi/CAS Lineage and Newly Identified Ethiopian Clades of the Mycobacterium tuberculosis Complex. PLoS One 2015; 10:e0137865. [PMID: 26376441 PMCID: PMC4573740 DOI: 10.1371/journal.pone.0137865] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Accepted: 08/23/2015] [Indexed: 11/18/2022] Open
Abstract
Background Recently, newly defined clades of Mycobacterium tuberculosis complex (MTBC) strains, namely Ethiopia 1–3 and Ethiopia H37Rv-like strains, and other clades associated with pulmonary TB (PTB) were identified in Ethiopia. In this study, we investigated whether these new strain types exhibit an increased ability to cause TB lymphadenitis (TBLN) and raised the question, if particular MTBC strains derived from TBLN patients in northern Ethiopia are genetically adapted to their local hosts and/or to the TBLN. Methods Genotyping of 196 MTBC strains isolated from TBLN patients was performed by spoligotyping and 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR) typing. A statistical analysis was carried out to see possible associations between patient characteristics and phylogenetic MTBC strain classification. Results Among 196 isolates, the majority of strains belonged to the Delhi/CAS (38.8%) lineage, followed by Ethiopia 1 (9.7%), Ethiopia 3 (8.7%), Ethiopia H37RV-like (8.2%), Ethiopia 2 and Haarlem (7.7% each), URAL (3.6%), Uganda l and LAM (2% each), S-type (1.5%), X-type (1%), and 0.5% isolates of TUR, EAI, and Beijing genotype, respectively. Overall, 15 strains (7.7%) could not be allocated to a previously described phylogenetic lineage. The distribution of MTBC lineages is similar to that found in studies of PTB samples. The cluster rate (35%) in this study is significantly lower (P = 0.035) compared to 45% in the study of PTB in northwestern Ethiopia. Conclusion In the studied area, lymph node samples are dominated by Dehli/CAS genotype strains and strains of largely not yet defined clades based on MIRU-VNTR 24-loci nomenclature. We found no indication that strains of particular genotypes are specifically associated with TBLN. However, a detailed analysis of specific genetic variants of the locally contained Ethiopian clades by whole genome sequencing may reveal new insights into the host-pathogen co-evolution and specific features that are related to the local host immune system.
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Affiliation(s)
- Fantahun Biadglegne
- College of Medicine and Health Sciences, Bahir Dar University, Bahir Dar, Ethiopia; Institute of Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany; Institute of Clinical Immunology, University Hospital, University of Leipzig, Leipzig, Germany; Translational Centre for Regenerative Medicine (TRM)-Leipzig, University of Leipzig, Leipzig, Germany
| | - Matthias Merker
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany
| | - Ulrich Sack
- Institute of Clinical Immunology, University Hospital, University of Leipzig, Leipzig, Germany; Translational Centre for Regenerative Medicine (TRM)-Leipzig, University of Leipzig, Leipzig, Germany
| | - Arne C Rodloff
- Institute of Medical Microbiology and Epidemiology of Infectious Diseases, University Hospital, University of Leipzig, Leipzig, Germany
| | - Stefan Niemann
- Molecular Mycobacteriology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Borstel, Borstel, Germany
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Meng C, Wan T, Xu Z, Liu Y, Shan F, Sun L, Yin Y, Chen X, Jiao X. Screening putative antigens as stimulators in the Mycobacterium bovis interferon-gamma release assay for cattle. Vet Immunol Immunopathol 2015; 168:111-7. [PMID: 26375813 DOI: 10.1016/j.vetimm.2015.09.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Revised: 09/02/2015] [Accepted: 09/03/2015] [Indexed: 01/12/2023]
Abstract
Bovine tuberculosis (BTB) represents not only a significant economic concern, but also an important public health problem. Currently, interferon-gamma (IFN-γ) release assays (IGRAs) are widely used as an adjunct to the tuberculin test (TST) for the diagnosis of BTB. A great number of international studies have demonstrated that the sensitivity of the IFN-γ assay, which uses purified protein derivatives (PPDs) as diagnostic reagents, is superior to that of the TST. However, there are concerns about its specificity, largely because of the cross reactivity of common antigens shared by pathogenic and non-pathogenic mycobacterial species. The use of pathogen-specific antigens theoretically offers the most effective way to improve the specificity of IGRAs. In this study, we evaluated the potential utility of 13 purified recombinant putative antigens, which are highly specific to the Mycobacterium tuberculosis complex, as diagnostic reagents in IGRAs. A CFP-10-ESAT-6 fusion protein (abbreviated CE) displayed the greatest potential, whereas four region of difference 2 (RD2) antigens, especially Rv1985c were identified as potential candidate antigens, and can be included in an IGRA cocktail, together with CE as stimulators in the IFN-γ release assay for the diagnosis of BTB.
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Affiliation(s)
- Chuang Meng
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Ting Wan
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Zhengzhong Xu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yan Liu
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Fa Shan
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Lin Sun
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yuelan Yin
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Xiang Chen
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
| | - Xinan Jiao
- Jiangsu Key Laboratory of Zoonosis/Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China.
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Le Chevalier F, Cascioferro A, Majlessi L, Herrmann JL, Brosch R. Mycobacterium tuberculosis evolutionary pathogenesis and its putative impact on drug development. Future Microbiol 2015; 9:969-85. [PMID: 25302954 DOI: 10.2217/fmb.14.70] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Mycobacterium tuberculosis, the etiological agent of human TB, is the most important mycobacterial pathogen in terms of global patient numbers and gravity of disease. The molecular mechanisms by which M. tuberculosis causes disease are complex and the result of host-pathogen coevolution that might have started already in the time of its Mycobacterium canettii-like progenitors. Despite research progress, M. tuberculosis still holds many secrets of its successful strategy for circumventing host defences, persisting in the host and developing resistance, which makes anti-TB treatment regimens extremely long and often inefficient. Here, we discuss what we have learned from recent studies on the evolution of the pathogen and its putative new drug targets that are essential for mycobacterial growth under in vitro or in vivo conditions.
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Affiliation(s)
- Fabien Le Chevalier
- Institut Pasteur, Unit for Integrated Mycobacterial Pathogenomics, Paris, France
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Thabet S, Namouchi A, Mardassi H. Evolutionary Trends of the Transposase-Encoding Open Reading Frames A and B (orfA and orfB) of the Mycobacterial IS6110 Insertion Sequence. PLoS One 2015; 10:e0130161. [PMID: 26087177 PMCID: PMC4473070 DOI: 10.1371/journal.pone.0130161] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2015] [Accepted: 05/17/2015] [Indexed: 12/25/2022] Open
Abstract
Background The IS6110 insertion sequence, a member of the IS3 family of insertion sequences, was found to be specific to the Mycobacterium tuberculosis complex (MTBC). Although IS6110 has been extensively characterized as a transposable genetic marker, the evolutionary history of its own transposase-encoding sequence has not, to the best of our knowledge, been investigated. Methodology/Principal Findings Here we explored the evolution of the IS6110 sequence by analysing the genetic variability and the selective forces acting on its transposase-encoding open reading frames (ORFs) A and B (orfA and orfB). For this purpose, we used a strain collection consisting of smooth tubercle bacilli (STB), an early branching lineage of the MTBC, and present-day M. tuberculosis strains representing the full breadth of genetic diversity in Tunisia. In each ORF, we found a major haplotype that dominated over a flat distribution of rare descendent haplotypes, consisting mainly of single- and double-nucleotide variant singletons. The predominant haplotypes consisted of both ancestral and present-day strains, suggesting that IS6110 acquisition predated the emergence of the MTBC. There was no evidence of recombination and both ORFs were subjected to strict purifying selection, as demonstrated by their dN/dS ratios (0.29 and 0.51, respectively), as well as their significantly negative Tajima’s D statistics. Strikingly, the purifying selection acting on orfA proved much more stringent, suggesting its critical role in regulating the transpositional process. Maximum likelihood analyses further excluded any possibility of positive selection acting on single amino acid residues. Conclusions/Significance Taken together our data fit with an evolutionary scenario according to which the observed variability pattern of the IS6110 transposase-encoding ORFs is generated mainly through random point mutations that accrued on a functionally optimal IS6110 copy, whose acquisition predated the emergence of the MTBC complex. Background selection acting against deleterious mutations led to an excess of low-frequency variants.
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Affiliation(s)
- Sara Thabet
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development; Institut Pasteur de Tunis, Tunis, Tunisia
| | - Amine Namouchi
- Unit of Typing and Genetics of Mycobacteria, Laboratory of Molecular Microbiology, Vaccinology, and Biotechnology Development; Institut Pasteur de Tunis, Tunis, Tunisia
| | - 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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Wang J, McIntosh F, Radomski N, Dewar K, Simeone R, Enninga J, Brosch R, Rocha EP, Veyrier FJ, Behr MA. Insights on the emergence of Mycobacterium tuberculosis from the analysis of Mycobacterium kansasii. Genome Biol Evol 2015; 7:856-70. [PMID: 25716827 PMCID: PMC5322544 DOI: 10.1093/gbe/evv035] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
By phylogenetic analysis, Mycobacterium kansasii is closely related to Mycobacterium tuberculosis. Yet, although both organisms cause pulmonary disease, M. tuberculosis is a global health menace, whereas M. kansasii is an opportunistic pathogen. To illuminate the differences between these organisms, we have sequenced the genome of M. kansasii ATCC 12478 and its plasmid (pMK12478) and conducted side-by-side in vitro and in vivo investigations of these two organisms. The M. kansasii genome is 6,432,277 bp, more than 2 Mb longer than that of M. tuberculosis H37Rv, and the plasmid contains 144,951 bp. Pairwise comparisons reveal conserved and discordant genes and genomic regions. A notable example of genomic conservation is the virulence locus ESX-1, which is intact and functional in the low-virulence M. kansasii, potentially mediating phagosomal disruption. Differences between these organisms include a decreased predicted metabolic capacity, an increased proportion of toxin–antitoxin genes, and the acquisition of M. tuberculosis-specific genes in the pathogen since their common ancestor. Consistent with their distinct epidemiologic profiles, following infection of C57BL/6 mice, M. kansasii counts increased by less than 10-fold over 6 weeks, whereas M. tuberculosis counts increased by over 10,000-fold in just 3 weeks. Together, these data suggest that M. kansasii can serve as an image of the environmental ancestor of M. tuberculosis before its emergence as a professional pathogen, and can be used as a model organism to study the switch from an environmental opportunistic pathogen to a professional host-restricted pathogen.
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Affiliation(s)
- Joyce Wang
- Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada McGill International TB Centre, Montreal, Québec, Canada
| | - Fiona McIntosh
- McGill International TB Centre, Montreal, Québec, Canada Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - Nicolas Radomski
- McGill International TB Centre, Montreal, Québec, Canada Research Institute of the McGill University Health Centre, Montreal, Québec, Canada
| | - Ken Dewar
- McGill University and Génome Québec Innovation Center, Montreal, Québec, Canada
| | - Roxane Simeone
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France
| | - Jost Enninga
- Dynamics of Host-Pathogen Interactions Unit, Institut Pasteur, Paris, France
| | - Roland Brosch
- Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur, Paris, France
| | - Eduardo P Rocha
- Microbial Evolutionary Genomics Unit, Institut Pasteur, Paris, France
| | - Frédéric J Veyrier
- McGill International TB Centre, Montreal, Québec, Canada INRS-Institut Armand-Frappier, Laval, Québec, Canada
| | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, Montreal, Québec, Canada McGill International TB Centre, Montreal, Québec, Canada Department of Medicine, McGill University, Montreal, Québec, Canada
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146
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Genome-wide transposon mutagenesis indicates that Mycobacterium marinum customizes its virulence mechanisms for survival and replication in different hosts. Infect Immun 2015; 83:1778-88. [PMID: 25690095 DOI: 10.1128/iai.03050-14] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Accepted: 02/05/2015] [Indexed: 11/20/2022] Open
Abstract
The interaction of environmental bacteria with unicellular eukaryotes is generally considered a major driving force for the evolution of intracellular pathogens, allowing them to survive and replicate in phagocytic cells of vertebrate hosts. To test this hypothesis on a genome-wide level, we determined for the intracellular pathogen Mycobacterium marinum whether it uses conserved strategies to exploit host cells from both protozoan and vertebrate origin. Using transposon-directed insertion site sequencing (TraDIS), we determined differences in genetic requirements for survival and replication in phagocytic cells of organisms from different kingdoms. In line with the general hypothesis, we identified a number of general virulence mechanisms, including the type VII protein secretion system ESX-1, biosynthesis of polyketide lipids, and utilization of sterols. However, we were also able to show that M. marinum contains an even larger set of host-specific virulence determinants, including proteins involved in the modification of surface glycolipids and, surprisingly, the auxiliary proteins of the ESX-1 system. Several of these factors were in fact counterproductive in other hosts. Therefore, M. marinum contains different sets of virulence factors that are tailored for specific hosts. Our data imply that although amoebae could function as a training ground for intracellular pathogens, they do not fully prepare pathogens for crossing species barriers.
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147
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Sola C. Clustured regularly interspersed short palindromic repeats (CRISPR) genetic diversity studies as a mean to reconstruct the evolution of the Mycobacterium tuberculosis complex. Tuberculosis (Edinb) 2015; 95 Suppl 1:S159-66. [PMID: 25748060 DOI: 10.1016/j.tube.2015.02.029] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The natural history of tuberculosis may be tackled by various means, among which the record of molecular scars that have been registered by the Mycobacterium tuberculosis complex (MTBC) genomes transmitted from patient to patient for tens of thousands years and possibly more. Recently discovered polymorphic loci, the CRISPR sequences, are indirect witnesses of the historical phage-bacteria struggle, and may be related to the time when the ancestor of today's tubercle bacilli were environmental bacteria, i.e. before becoming intracellular parasites. In this article, we present what are CRISPRs and try to summarize almost 20 years of research results obtained using the genetic diversity of the CRISPR loci in MTBC as a perspective for studying new models. We show that the study of the diversity of CRISPR sequences, thanks to «spoligotyping», has played a great role in our global understanding of the population structure of MTBC.
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Affiliation(s)
- Christophe Sola
- Institut de Biologie Intégrative de la Cellule (I2BC), CEA, CNRS, Université Paris-Saclay, Orsay, France.
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148
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Abstract
This paper follows the dramatic changes in scientific research during the last 20 years regarding the relationship between the Mycobacterium tuberculosis complex and its hosts - bovids and/or humans. Once the M. tuberculosis and Mycobacterium bovis genomes were sequenced, it became obvious that the old story of M. bovis evolving into the human pathogen should be reversed, as M. tuberculosis is more ancestral than M. bovis. Nevertheless, the timescale and geographical origin remained an enigma. In the current study human and cattle bone samples were examined for evidence of tuberculosis from the site of Atlit-Yam in the Eastern Mediterranean, dating from 9250 to 8160 (calibrated) years ago. Strict precautions were used to prevent contamination in the DNA analysis, and independent centers used to confirm authenticity of findings. DNA from five M. tuberculosis genetic loci was detected and had characteristics consistent with extant genetic lineages. High performance liquid chromatography was used as an independent method of verification and it directly detected mycolic acid lipid biomarkers, specific for the M. tuberculosis complex. These, together with pathological changes detected in some of the bones, confirm the presence of the disease in the Levantine populations during the Pre-pottery Neolithic C period, more than 8000 years ago.
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149
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Pósa A, Maixner F, Mende BG, Köhler K, Osztás A, Sola C, Dutour O, Masson M, Molnár E, Pálfi G, Zink A. Tuberculosis in Late Neolithic-Early Copper Age human skeletal remains from Hungary. Tuberculosis (Edinb) 2015; 95 Suppl 1:S18-22. [PMID: 25857937 DOI: 10.1016/j.tube.2015.02.011] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Alsónyék-Bátaszék in Southern Hungary is one of the largest late Neolithic settlements and cemeteries excavated in Central Europe. In total, 2359 burials from the Late Neolithic - Early Copper Age Lengyel culture were found between 2006 and 2009 [1]. Anthropological investigations previously carried out on individuals from this site revealed an interesting paleopathological case of tuberculosis in the form of Pott's disease dated to the early 5(th) millennium BC. In this study, selected specimens from this osteoarcheological series were subjected to paleomicrobiological analysis to establish the presence of MTBC bacteria. As all individuals showing clear osteological signs of TB infection belonged to a single grave group, 38 individuals from this grave group were analysed. The sample included the case of Pott's disease as well as individuals both with and without osseous TB manifestations. The detection of TB DNA in the individual with Pott's disease provided further evidence for the occurrence of TB in Neolithic populations of Europe. Moreover, our molecular analysis indicated that several other individuals of the same grave group were also infected with TB, opening the possibility for further analyses of this unique Neolithic skeletal series.
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Affiliation(s)
- Annamária Pósa
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary; Department of Genetics, University of Szeged, Szeged, Hungary.
| | - Frank Maixner
- Institute for Mummies and the Iceman, EURAC Research, Bolzano, Italy
| | - Balázs Gusztáv Mende
- Research Centre for the Humanities, Institute of Archaeology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Kitti Köhler
- Research Centre for the Humanities, Institute of Archaeology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anett Osztás
- Research Centre for the Humanities, Institute of Archaeology, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christophe Sola
- Institut de Biologie Intégrative de la Cellule I2BC CEA-CNRS-Université Paris-Saclay, UMR9198, Bât. 400 F-91405 ORSAY-Cedex, France
| | - Olivier Dutour
- Laboratoire d'Anthropologie biologique Paul Broca, Ecole Pratique des Hautes Etudes, UMR 5199 PACEA, Université de Bordeaux, Pessac, France; Department of Anthropology, University of Western Ontario, Canada
| | - Muriel Masson
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC Research, Bolzano, Italy
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150
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Spigelman M, Donoghue HD, Abdeen Z, Ereqat S, Sarie I, Greenblatt CL, Pap I, Szikossy I, Hershkovitz I, Bar-Gal GK, Matheson C. Evolutionary changes in the genome of Mycobacterium tuberculosis and the human genome from 9000 years BP until modern times. Tuberculosis (Edinb) 2015; 95 Suppl 1:S145-9. [PMID: 25771203 DOI: 10.1016/j.tube.2015.02.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The demonstration of Mycobacterium tuberculosis DNA in ancient skeletons gives researchers an insight into its evolution. Findings of the last two decades sketched the biological relationships between the various species of tubercle bacilli, the time scale involved, their possible origin and dispersal. This paper includes the available evidence and on-going research. In the submerged Eastern Mediterranean Neolithic village of Atlit Yam (9000 BP), a human lineage of M. tuberculosis, defined by the TbD1 deletion in its genome, was demonstrated. An infected infant at the site provides an example of active tuberculosis in a human with a naïve immune system. Over 4000 years later tuberculosis was found in Jericho. Urbanization increases population density encouraging M. tuberculosis/human co-evolution. As susceptible humans die of tuberculosis, survivors develop genetic resistance to disease. Thus in 18th century Hungarian mummies from Vác, 65% were positive for tuberculosis yet a 95-year-old woman had clearly survived a childhood Ghon lesion. Whole genome studies are in progress, to detect changes over the millennia both in bacterial virulence and also host susceptibility/resistance genes that determine the NRAMP protein and Killer Cell Immunoglobulin-like Receptors (KIRs). This paper surveys present evidence and includes initial findings.
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Affiliation(s)
- Mark Spigelman
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel.
| | - Helen D Donoghue
- Centre for Clinical Microbiology, Division of Infection & Immunity, University College London, London, UK; Centre for the History of Medicine, Division of Biosciences, University College London, London, UK.
| | - Ziad Abdeen
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Suheir Ereqat
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Issa Sarie
- Al-Quds Nutrition and Health Research Institute, Faculty of Medicine, Al-Quds University, Abu-Deis, P.O. Box 201760, West Bank, Palestine.
| | - Charles L Greenblatt
- Kuvin Center for the Study of Infectious & Tropical Diseases and Ancient DNA, Hadassah Medical School, The Hebrew University, Jerusalem, Israel.
| | - Ildikó Pap
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary.
| | - Ildikó Szikossy
- Department of Anthropology, Hungarian Natural History Museum, Budapest, Hungary
| | - Israel Hershkovitz
- Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Gila Kahila Bar-Gal
- Koret School of Veterinary Medicine, The Hebrew University of Jerusalem, Rehovot, Israel.
| | - Carney Matheson
- Paleo-DNA Laboratory, Departments of Anthropology and Biology, Lakehead University, Thunder Bay, Ontario, Canada.
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