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      Genomic characterization of Mycobacterium tuberculosis lineage 7 and a proposed name: ‘Aethiops vetus’

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          Abstract

          Lineage 7 of the Mycobacterium tuberculosis complex has recently been identified among strains originating from Ethiopia. Using different DNA typing techniques, this study provides additional information on the genetic heterogeneity of five lineage 7 strains collected in the Amhara Region of Ethiopia. It also confirms the phylogenetic positioning of these strains between the ancient lineage 1 and TbD1-deleted, modern lineages 2, 3 and 4 of Mycobacterium tuberculosis. Four newly identified large sequence polymorphisms characteristic of the Amhara Region lineage 7 strains are described. While lineage 7 strains have been previously identified in the Woldiya area, we show that lineage 7 strains circulate in other parts of the Amhara Region and also among foreign-born individuals from Eritrea and Somalia in The Netherlands. For ease of documenting future identification of these strains in other geographical locations and recognizing the place of origin, we propose to assign lineage 7 strains the lineage name Aethiops vetus .

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          Most cited references 18

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          Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

          Motivation: Artemis and Artemis Comparison Tool (ACT) have become mainstream tools for viewing and annotating sequence data, particularly for microbial genomes. Since its first release, Artemis has been continuously developed and supported with additional functionality for editing and analysing sequences based on feedback from an active user community of laboratory biologists and professional annotators. Nevertheless, its utility has been somewhat restricted by its limitation to reading and writing from flat files. Therefore, a new version of Artemis has been developed, which reads from and writes to a relational database schema, and allows users to annotate more complex, often large and fragmented, genome sequences. Results: Artemis and ACT have now been extended to read and write directly to the Generic Model Organism Database (GMOD, http://www.gmod.org) Chado relational database schema. In addition, a Gene Builder tool has been developed to provide structured forms and tables to edit coordinates of gene models and edit functional annotation, based on standard ontologies, controlled vocabularies and free text. Availability: Artemis and ACT are freely available (under a GPL licence) for download (for MacOSX, UNIX and Windows) at the Wellcome Trust Sanger Institute web sites: http://www.sanger.ac.uk/Software/Artemis/ http://www.sanger.ac.uk/Software/ACT/ Contact: artemis@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
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            Restricted structural gene polymorphism in the Mycobacterium tuberculosis complex indicates evolutionarily recent global dissemination.

            One-third of humans are infected with Mycobacterium tuberculosis, the causative agent of tuberculosis. Sequence analysis of two megabases in 26 structural genes or loci in strains recovered globally discovered a striking reduction of silent nucleotide substitutions compared with other human bacterial pathogens. The lack of neutral mutations in structural genes indicates that M. tuberculosis is evolutionarily young and has recently spread globally. Species diversity is largely caused by rapidly evolving insertion sequences, which means that mobile element movement is a fundamental process generating genomic variation in this pathogen. Three genetic groups of M. tuberculosis were identified based on two polymorphisms that occur at high frequency in the genes encoding catalase-peroxidase and the A subunit of gyrase. Group 1 organisms are evolutionarily old and allied with M. bovis, the cause of bovine tuberculosis. A subset of several distinct insertion sequence IS6110 subtypes of this genetic group have IS6110 integrated at the identical chromosomal insertion site, located between dnaA and dnaN in the region containing the origin of replication. Remarkably, study of approximately 6,000 isolates from patients in Houston and the New York City area discovered that 47 of 48 relatively large case clusters were caused by genotypic group 1 and 2 but not group 3 organisms. The observation that the newly emergent group 3 organisms are associated with sporadic rather than clustered cases suggests that the pathogen is evolving toward a state of reduced transmissability or virulence.
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              Differentiation of Mycobacterium tuberculosis complex by PCR amplification of genomic regions of difference.

              Differentiation of members of the Mycobacterium tuberculosis complex by conventional mycobacteriological methods is time consuming, making surveillance of species-specific disease difficult. A two-step, multiplex polymerase chain reaction (PCR) method based on genomic regions of difference (RD1, RD1(mic), RD2(seal), RD4, RD9 and RD12) was developed for the differentiation of M. canettii, M. tuberculosis, M. africanum, M. microti, M. pinnipedii, M. caprae, M. bovis and M. bovis BCG. The size of the respective multiplex PCR amplification products corresponded to the presence of the different M. tuberculosis complex members. This method allows for rapid differentiation, making it suitable for routine laboratories and surveillance purposes.
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                Author and article information

                Journal
                Microb Genom
                Microb Genom
                MGen
                Microbial Genomics
                Microbiology Society
                2057-5858
                June 2016
                24 June 2016
                : 2
                : 6
                Affiliations
                [ 1]Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
                [ 2]Department of Microbiology, Genome Dynamics and Microbial Pathogenesis Group, Oslo University Hospital, Oslo, Norway
                [ 3]Infection Control and Environmental Health, Norwegian Institute of Public Health , Oslo, Norway
                [ 4]Unit for Integrated Mycobacterial Pathogenomics, Institut Pasteur , Paris, France
                [ 5]Department of Medical Microbiology, Radboud University Medical Centre, Nijmegen, The Netherlands
                Author notes
                Correspondence Hanna Nebenzahl-Guimaraes ( hanna.guimaraes@ 123456gmail.com )
                [†]

                These authors contributed equally to this work.

                All supporting data, code and protocols have been provided within the article or through supplementary data files.

                Article
                mgen000063
                10.1099/mgen.0.000063
                5320646
                © 2016 The Authors

                This is an open access article under the terms of the Creative Commons Attribution 4.0 International License, which permits unrestricted use, distribution and reproduction in any medium, provided the original author and source are credited.

                Product
                Funding
                Funded by: Fundação para a Ciência e a Tecnologia
                Award ID: SFRH/BD/33902/2009
                Funded by: Fondation pour la Recherche Médicale
                Award ID: DEQ20130326471
                Funded by: Norges Forskningsråd
                Award ID: 192468/S50
                Categories
                Research Paper
                Microbial evolution and epidemiology: Phylogeography
                Custom metadata
                0

                tuberculosis, phylogenetic lineage, ethiopia

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