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An updated phylogenetic method reveals transmission times for infectious diseases. For a tuberculosis outbreak, no new transmissions occurred after mid-2012, with later cases stemming from latent infections.

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Area of Science:

  • Epidemiology
  • Evolutionary Biology
  • Genomics

Background:

  • Understanding infectious disease transmission dynamics is crucial for public health interventions.
  • Distinguishing between recent transmission and progression of latent infections is a key challenge in outbreak investigations.

Purpose of the Study:

  • To present an updated computational method for inferring transmission times using pathogen genome phylogenies.
  • To apply this method to a real-time investigation of a Mycobacterium tuberculosis outbreak.

Main Methods:

  • Phylogenetic analysis of time-labelled pathogen genomes.
  • Application of an updated inference method to 48 Mycobacterium tuberculosis genomes.

Main Results:

  • The study identified that no new Mycobacterium tuberculosis transmissions occurred after mid-2012.
  • Diagnosed tuberculosis cases after mid-2012 were attributed to the progression of latent infections, not recent transmission events.

Conclusions:

  • The developed evolutionary genomic approach accurately differentiates transmission events from disease progression.
  • This method enabled the declaration of the tuberculosis outbreak as over in January 2015.