Declaring a tuberculosis outbreak over with genomic epidemiology

Hollie-Ann Hatherell; Xavier Didelot; Sue L. Pollock; Patrick Tang; Anamaria Crisan; James C. Johnston; Caroline Colijn; Jennifer L. Gardy

doi:10.1099/mgen.0.000060

Volume 2, Issue 5

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Open Access

Declaring a tuberculosis outbreak over with genomic epidemiology

Hollie-Ann Hatherell¹, Xavier Didelot², Sue L. Pollock³, Patrick Tang⁴, Anamaria Crisan⁵, James C. Johnston⁶, Caroline Colijn⁷ and Jennifer L. Gardy⁵
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Affiliations: ¹ 1CoMPLEX, University College London Research Department of Infection and Population Health, University College London, London, UK ² 2Department of Infectious Disease Epidemiology, Imperial College London, London, UK ³ 3Interior Health Authority, British Columbia, Canada ⁴ 4British Columbia Centre for Disease Control Public Health Laboratory Department of Pathology, and Sidra Medical and Research Center, British Columbia, Canada ⁵ 5Communicable Disease Prevention and Control Services, British Columbia Centre for Disease Control, and School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada ⁶ 6Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada ⁷ 7Department of Mathematics, Imperial College London, London, UK
Correspondence [email protected]
Published: 31 May 2016 https://doi.org/10.1099/mgen.0.000060

Abstract

We report an updated method for inferring the time at which an infectious disease was transmitted between persons from a time-labelled pathogen genome phylogeny. We applied the method to 48 Mycobacterium tuberculosis genomes as part of a real-time public health outbreak investigation, demonstrating that although active tuberculosis (TB) cases were diagnosed through 2013, no transmission events took place beyond mid-2012. Subsequent cases were the result of progression from latent TB infection to active disease, and not recent transmission. This evolutionary genomic approach was used to declare the outbreak over in January 2015.

Received: 16/02/2016
Accepted: 12/04/2016
Revised: 01/04/2016
Published Online: 31/05/2016

Keyword(s): genomic epidemiology , phylogenetics , transmission and Tuberculosis

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.

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References

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 [View Article][PubMed]
[Google Scholar]
Croucher N. J., Didelot X. 2015; The application of genomics to tracing bacterial pathogen transmission. Curr Opin Microbiol 23:62–67 [View Article][PubMed]
[Google Scholar]
Didelot X., Gardy J., Colijn C. 2014; Bayesian inference of infectious disease transmission from whole-genome sequence data. Mol Biol Evol 31: 869–1879 [View Article][PubMed]
[Google Scholar]
Drummond A. J., Rambaut A. 2007; BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol 7:214 [View Article][PubMed]
[Google Scholar]
Interior Health Authority 2015; Six year TB outbreak comes to an end. https://www.interiorhealth.ca/AboutUs/MediaCentre/NewsReleases/Documents/Six%20year%20TB%20outbreak%20comes%20to%20an%20end.pdf last accessed January 14, 2016
Kwong J. C., McCallum N., Sintchenko V., Howden B. P. 2015; Whole genome sequencing in clinical and public health microbiology. Pathology 47:199–210 [View Article][PubMed]
[Google Scholar]
Li H., Durbin R. 2009; Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25:1754–1814 [View Article][PubMed]
[Google Scholar]
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 [View Article][PubMed]
[Google Scholar]
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:
[Google Scholar]
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 [View Article][PubMed]
[Google Scholar]
World Health Organization 2015; Guidelines on the management of latent tuberculosis infection. http://apps.who.int/iris/bitstream/10665/136471/1/9789241548908_eng.pdf?ua=1&ua=1 Last accessed January 14, 2016
Gardy, J. (2016). European Nucleotide Archive. http://www.ebi.ac.uk/ena/data/view/PRJEB12764
Gardy, J. (2016). FigShare. https://figshare.com/articles/Declaring_a_tuberculosis_outbreak_over_with_genomic_epidemiology/3153280
Gardy, J. (2016). FigShare. https://figshare.com/articles/Declaring_a_tuberculosis_outbreak_over_with_genomic_epidemiology/3153280
Didelot, X. (2015). GitHub. https://github.com/xavierdidelot/TransPhylo

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Declaring a tuberculosis outbreak over with genomic epidemiology

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Volume 2, Issue 5

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Declaring a tuberculosis outbreak over with genomic epidemiology

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