Declaring a tuberculosis outbreak over with genomic epidemiology

Microbial Genomics

Volumn 2, Issue 5, 2016, Pages

  Hatherell, Hollie Ann ^a   Didelot, Xavier ^b   Pollock, Sue L ^c   Tang, Patrick ^d   Crisan, Anamaria ^e   Johnston, James C ^f   Colijn, Caroline ^b   Gardy, Jennifer L ^e  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b IMPERIAL COLLEGE LONDON   (United Kingdom)

^c Interior Health Authority   (Canada)

^d SIDRA MEDICAL AND RESEARCH CENTER   (Qatar)

^e UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^f BRITISH COLUMBIA CENTRE FOR DISEASE CONTROL   (Canada)

Author keywords

Genomic epidemiology; Phylogenetics; Transmission; Tuberculosis

Indexed keywords

ARTICLE; DISEASE COURSE; DISEASE TRANSMISSION; FOLLOW UP; GENE SEQUENCE; HUMAN; METAGENOMICS; TUBERCULOSIS; EPIDEMIC; GENETICS; GENOMICS; INFECTION CONTROL; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM TUBERCULOSIS; PROCEDURES; TRANSMISSION;

DISEASE OUTBREAKS; GENOMICS; HUMANS; INFECTION CONTROL; MOLECULAR EPIDEMIOLOGY; MYCOBACTERIUM TUBERCULOSIS; TUBERCULOSIS;

EID: 85042694893     PISSN: None     EISSN: 20575858     Source Type: Journal    
DOI: 10.1099/mgen.0.000060     Document Type: Article

References (15)

1. Cheng, J. M., Hiscoe, L., Pollock, S. L., Hasselback, P., Gardy, J. L. & Parker, R. (2015). A clonal outbreak of tuberculosis in a homeless population in the interior of British Columbia, Canada, 2008-2015. Epidemiol Infect 143, 3220 –3226.
2. Croucher, N. J. & Didelot, X. (2015). The application of genomics to tracing bacterial pathogen transmission. Curr Opin Microbiol 23, 62–67.
3. Didelot, X., Gardy, J. & Colijn, C. (2014). Bayesian inference of infectious disease transmission from whole-genome sequence data. Mol Biol Evol 31, 869–1879.
4. Drummond, A. J. & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7, 214.
5. Interior Health Authority. (2015). Six year TB outbreak comes to an end. https://www.interiorhealth.ca/AboutUs/MediaCentre/NewsRe-leases/Documents/Six%20year%20TB%20outbreak%20comes%20to %20an%20end.pdf. last accessed January 14, 2016.
6. Kwong, J. C., McCallum, N., Sintchenko, V. & Howden, B. P. (2015). Whole genome sequencing in clinical and public health microbiology. Pathology 47, 199–210.
7. Li, H. & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1814.
8. Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., Marth, G., Abecasis, G, Durbin, R. & 1000 Genome Project Data Processing Subgroup. (2009). The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2087.
9. Poon, L.L., Song, T., Rosenfeld, R., Lin, X., Rogers, M. B., Zhou, B., Sebra, R., Halpin, R. A. & Guan, Y. (2016). Quantifying influenza virus diversity and transmission in humans. Nat Genet 48.
10. Worby, C. J., Chang, H. H., Hanage, W. P. & Lipsitch, M. (2014). The distribution of pairwise genetic distances: A tool for investigating disease transmission. Genetics 198, 1395–1404.
11. World Health Organization (2015). Guidelines on the management of latent tuberculosis infection. http://apps.who.int/iris/bit-stream/10665/136471/1/9789241548908_eng.pdf?ua=1&ua=1. Last accessed January 14, 2016.
12. Gardy, J. (2016). European Nucleotide Archive.http://www.ebi.ac.uk/ena/data/view/PRJEB12764
13. Gardy, J. (2016). FigShare. https://figshare.com/articles/Declaring_a_tuberculosis_outbreak_over_with_ genomic_epidemiology/3153280
14. Gardy, J. (2016). FigShare. https://figshare.com/articles/Declaring_a_tuberculosis_outbreak_over_with_ genomic_epidemiology/3153280
15. Didelot, X. (2015). GitHub. https://github.com/xavierdidelot/TransPhylo