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      Population genomics of post-vaccine changes in pneumococcal epidemiology

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          Abstract

          Whole genome sequencing of 616 asymptomatically carried pneumococci was used to study the impact of the 7-valent pneumococcal conjugate vaccine. Comparison of closely related isolates revealed the role of transformation in facilitating capsule switching to non-vaccine serotypes and the emergence of drug resistance. However, such recombination was found to occur at significantly different rates across the species, and the evolution of the population was primarily driven by changes in the frequency of distinct genotypes extant pre-vaccine. These alterations resulted in little overall effect on accessory genome composition at the population level, contrasting with the fall in pneumococcal disease rates after the vaccine’s introduction.

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          Most cited references43

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          The Bioperl toolkit: Perl modules for the life sciences.

          Jason E Stajich, David Block, Kris Boulez … (2002)
          The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
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            R: A Language and Environment for Statistical Computing

            R Core Team, R Development Core Team R, R Development Core Team … (2011)
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              Is Open Access

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

              Tim Carver, Matthew Berriman, Adrian Tivey … (2008)
              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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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 9216904
                Journal ID (pubmed-jr-id): 2419
                Journal ID (nlm-ta): Nat Genet
                Journal ID (iso-abbrev): Nat. Genet.
                Title: Nature genetics
                ISSN (Print): 1061-4036
                ISSN (Electronic): 1546-1718
                Publication date Nihms-submitted: 21 May 2013
                Publication date (Electronic): 05 May 2013
                Publication date (Print): June 2013
                Publication date PMC-release: 05 November 2013
                Volume: 45
                Issue: 6
                Electronic Location Identifier: 10.1038/ng.2625
                Affiliations
                [1 ]Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard School of Public Health, Boston, MA 02115, USA
                [2 ]Pathogen Genomics, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.
                [3 ]Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
                [4 ]Division of General Pediatrics, Boston Children’s Hospital, Boston, MA 02115, USA
                [5 ]Maxwell Finland Laboratory for Infectious Diseases, Boston University Medical Center, MA 02118, USA
                [6 ]Department of Laboratory Medicine and Division of Infectious Diseases, Department of Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
                [7 ]Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, CB2 0QQ, UK
                [8 ]Department of Immunology and Infectious Diseases, Harvard School of Public Health, Boston, MA 02115, USA
                Author notes
                [+ ]To whom correspondence should be addressed: whanage@ 123456hsph.harvard.edu
                [*]

                These authors contributed equally

                Article
                Manuscript ID: EMS53147
                DOI: 10.1038/ng.2625
                PMC ID: 3725542
                PubMed ID: 23644493
                SO-VID: dcc921be-e8fb-4db0-9f8e-2f6bdabf355d
                License:

                Users may view, print, copy, download and text and data- mine the content in such documents, for the purposes of academic research, subject always to the full Conditions of use: http://www.nature.com/authors/editorial_policies/license.html#terms

                History
                Funding
                Funded by: Wellcome Trust :
                Award ID: 098051 || WT
                Categories
                Subject: Article

                ScienceOpen disciplines: Genetics
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                ScienceOpen disciplines: Genetics

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