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Microb Genom. 2016 May 31;2(5):e000060. doi: 10.1099/mgen.0.000060. eCollection 2016 May.

Declaring a tuberculosis outbreak over with genomic epidemiology.

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CoMPLEX, University College London Research Department of Infection and Population Health, University College London , London , UK.
Department of Infectious Disease Epidemiology, Imperial College London , London , UK.
Interior Health Authority , British Columbia, Canada.
British Columbia Centre for Disease Control Public Health Laboratory Department of Pathology, and Sidra Medical and Research Center , British Columbia , Canada.
Communicable 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.
Clinical Prevention Services, British Columbia Centre for Disease Control , Vancouver, BC , Canada.
Department of Mathematics, Imperial College London , London , UK.


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.


Tuberculosis; genomic epidemiology; phylogenetics; transmission

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