Open Access Highly Accessed Research article

Inferring patient to patient transmission of Mycobacterium tuberculosis from whole genome sequencing data

Josephine M Bryant1, Anita C Schürch234, Henk van Deutekom5, Simon R Harris1, Jessica L de Beer2, Victor de Jager36, Kristin Kremer2, Sacha A F T van Hijum367, Roland J Siezen36, Martien Borgdorff58, Stephen D Bentley1, Julian Parkhill1* and Dick van Soolingen29

Author Affiliations

1 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK

2 RIVM, Tuberculosis Reference Laboratory, National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, (CIb/LIS, pb 22), P.O. Box 13720 BA, Bilthoven, The Netherlands

3 Radboud University Medical Centre/NCMLS, Centre for Molecular and Biomolecular Informatics, P.O. Box 91016500 HB, Nijmegen, The Netherlands

4 Department of Virology, Erasmus Medical Center, Rotterdam, The Netherlands

5 Department of tuberculosis control, Public Health Service, Amsterdam, The Netherlands

6 Netherlands Bioinformatics Centre (NBIC), P.O. Box 91016500HB, Nijmegen, The Netherlands

7 NIZO food research, P.O. Box 206710 BA, Ede, The Netherlands

8 Department of Clinical Epidemiology, Biostatistics, and Bioinformatics, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands

9 Department of Clinical Microbiology and department of Lung Disease, Radboud University Nijmegen Medical Centre, P.O. Box 9101, 6500 HB Nijmegen, The Netherlands

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BMC Infectious Diseases 2013, 13:110  doi:10.1186/1471-2334-13-110

Published: 27 February 2013

Additional files

Additional file 1:

Mutation analyses with PE and PPE genes completely removed.

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Additional file 2:

Histogram of RFLP cluster sizes.

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Additional file 3:

Excel spreadsheet providing details of 97 epipairs in this study.

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Additional file 4:

Figure providing details of homoplasic SNPs.

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Additional file 5:

File providing more detail into mutation rate estimation between epidemiologically linked pairs and the results obtained.

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Additional file 6:

Plot of age of cluster vs SNPs accumulated.

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