Tuberculosis outbreak investigation using phylodynamic analysis.
Denise Kühnert,Mireia Coscolla,Daniela Brites,David Stucki,John Z. Metcalfe,Lukas Fenner,Sebastien Gagneux,Tanja Stadler +7 more
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TLDR
Phylodynamic analysis gives insight into mycobacterium tuberculosis outbreaks and robust estimation of epidemiological parameters in Bern thanks to high sampling rate.About:
This article is published in Epidemics.The article was published on 2018-12-01 and is currently open access. It has received 19 citations till now. The article focuses on the topics: Outbreak.read more
Citations
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Whole genome sequencing of Mycobacterium tuberculosis: current standards and open issues.
Conor J. Meehan,Galo A. Goig,Thomas Kohl,Lennert Verboven,Anzaan Dippenaar,Matthew Ezewudo,Maha R. Farhat,Jennifer L. Guthrie,Kris Laukens,Paolo Miotto,Boatema Ofori-Anyinam,Viola Dreyer,Philip Supply,Anita Suresh,Christian Utpatel,Dick van Soolingen,Yang Zhou,Philip Ashton,Daniela Brites,Daniela Brites,Andrea M. Cabibbe,Bouke C. de Jong,Margaretha de Vos,Fabrizio Menardo,Fabrizio Menardo,Sebastien Gagneux,Sebastien Gagneux,Qian Gao,Tim H. Heupink,Qingyun Liu,Chloé Loiseau,Chloé Loiseau,Leen Rigouts,Timothy C. Rodwell,Elisa Tagliani,Timothy M Walker,Robin M. Warren,Yanlin Zhao,Matteo Zignol,Marco Schito,Jennifer L. Gardy,Daniela Maria Cirillo,Stefan Niemann,Iñaki Comas,Annelies Van Rie +44 more
TL;DR: The current landscape of WGS pipelines and applications, and best practices for M.tuberculosis WGS, are outlined, including standards for bioinformatics pipelines, curated repositories of resistance-causing variants, phylogenetic analyses, quality control and standardized reporting.
Journal ArticleDOI
The molecular clock of Mycobacterium tuberculosis.
Fabrizio Menardo,Fabrizio Menardo,Sebastián Duchêne,Daniela Brites,Daniela Brites,Sebastien Gagneux,Sebastien Gagneux +6 more
TL;DR: It is found that sampling times below 15–20 years were often insufficient to calibrate the clock of MTB, and a clock rate between 1x10-8 and 5x 10-7 nucleotide changes per-site-per-year was obtained, with substantial differences between clades.
Posted ContentDOI
The molecular clock of Mycobacterium tuberculosis
Fabrizio Menardo,Fabrizio Menardo,Sebastián Duchêne,Daniela Brites,Daniela Brites,Sebastien Gagneux,Sebastien Gagneux +6 more
TL;DR: A systematic study of the MTB molecular clock on a large genomic data set covering most of the global MTB diversity and representing different epidemiological settings found wide variation in the degree of clocklike structure among data sets, indicating that sampling times are sometimes insufficient to calibrate the clock of MTB.
Journal ArticleDOI
A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
Susanna Sabin,Alexander Herbig,Åshild J. Vågene,Åshild J. Vågene,Torbjörn Ahlström,Gracijela Bozovic,Caroline Arcini,Denise Kühnert,Kirsten I. Bos +8 more
TL;DR: A most recent common ancestor date is estimated for the Mycobacterium tuberculosis complex of between 2190 and 4501 before present and for Lineage 4 of between 929 and 2084 before present using multiple models, confirming a Neolithic emergence for the MTBC.
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Fundamental identifiability limits in molecular epidemiology
Stilianos Louca,Angela McLaughlin,Ailene MacPherson,Ailene MacPherson,Jeffrey B. Joy,Matthew W. Pennell +5 more
TL;DR: In this article, the authors show that for any candidate epidemiological scenario, there exists a myriad of alternative, markedly different, and yet plausible "congruent" scenarios that cannot be distinguished using phylogenetic data alone, no matter how large the data set.
References
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The Sequence Alignment/Map format and SAMtools
Heng Li,Bob Handsaker,Alec Wysoker,T. J. Fennell,Jue Ruan,Nils Homer,Gabor T. Marth,Gonçalo R. Abecasis,Richard Durbin +8 more
TL;DR: SAMtools as discussed by the authors implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.
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Heng Li,Richard Durbin +1 more
TL;DR: Burrows-Wheeler Alignment tool (BWA) is implemented, a new read alignment package that is based on backward search with Burrows–Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps.
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Relaxed Phylogenetics and Dating with Confidence
TL;DR: In this paper, the authors introduce a new approach to perform relaxed phylogenetic analysis, which can be used to estimate phylogenies and divergence times in the face of uncertainty in evolutionary rates and calibration times.
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BEAST 2: A Software Platform for Bayesian Evolutionary Analysis
Remco R. Bouckaert,Joseph Heled,Denise Kühnert,Timothy G. Vaughan,Chieh-Hsi Wu,Dong Xie,Marc A. Suchard,Andrew Rambaut,Alexei J. Drummond +8 more
TL;DR: BEAST 2 now has a fully developed package management system that allows third party developers to write additional functionality that can be directly installed to the BEAST 2 analysis platform via a package manager without requiring a new software release of the platform.
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Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen)
TL;DR: The cross-platform software tool, TempEst (formerly known as Path-O-Gen), is introduced, for the visualization and analysis of temporally sampled sequence data and can be used to assess whether there is sufficient temporal signal in the data to proceed with phylogenetic molecular clock analysis, and identify sequences whose genetic divergence and sampling date are incongruent.