title: Declaring a tuberculosis outbreak over with genomic epidemiology.
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 48Mycobacterium tuberculosisgenomes 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.
authors.affiliation: 1​CoMPLEX, University College London Research Department of Infection and Population Health, University College London, London, UK.
authors.forename: Hollie-Ann
authors.initials: HA
authors.lastname: Hatherell
authors.affiliation: 2​Department of Infectious Disease Epidemiology, Imperial College London, London, UK.
authors.forename: Xavier
authors.initials: X
authors.lastname: Didelot
authors.affiliation: 3​Interior Health Authority, British Columbia, Canada.
authors.forename: Sue L
authors.initials: SL
authors.lastname: Pollock
authors.affiliation: 4​British Columbia Centre for Disease Control Public Health Laboratory Department of Pathology, and Sidra Medical and Research Center, British Columbia, Canada.
authors.forename: Patrick
authors.initials: P
authors.lastname: Tang
authors.affiliation: 5​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.
authors.forename: Anamaria
authors.initials: A
authors.lastname: Crisan
authors.affiliation: 6​Clinical Prevention Services, British Columbia Centre for Disease Control, Vancouver, BC, Canada.
authors.forename: James C
authors.initials: JC
authors.lastname: Johnston
authors.affiliation: 7​Department of Mathematics, Imperial College London, London, UK.
authors.forename: Caroline
authors.initials: C
authors.lastname: Colijn
authors.affiliation: 5​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.
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Gardy
mesh_terms: D004196:Disease Outbreaks; D023281:Genomics; D006801:Humans; D017053:Infection Control; D017720:Molecular Epidemiology / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics*; D014376:Tuberculosis / Q000453:epidemiology* / Q000517:prevention & control / Q000635:transmission
keywords: Tuberculosis; genomic epidemiology; phylogenetics; transmission