Transmission analysis of a large tuberculosis outbreak in London: a mathematical modelling study using genomic data

• DOI: 10.1099/mgen.0.000450
• Publication Date: 2020-11-11T15:29:03Z
• Authors: Yuanwei Xu; Jessica E. Stockdale; Vijay Naidu; Hollie Hatherell; James Stimson; Helen R. Stagg; Ibrahim Abubakar; Caroline Colijn
• Keywords: Disease Transmission

Outbreaks of tuberculosis (TB) – such as the large isoniazid-resistant outbreak centred on London, UK, which originated in 1995 provide excellent opportunities to model transmission this devastating disease. Transmission chains for TB are notoriously difficult ascertain, but mathematical modelling approaches, combined with whole-genome sequencing data, have strong potential contribute analyses. Using we aimed reconstruct histories using a Bayesian approach, and use machine-learning techniques patient-level data identify key covariates associated transmission. By our reconstruction method that accounts phylogenetic uncertainty, able 21 events reasonable confidence, 9 zero SNP distance, maximum distance 3. Patient age, alcohol abuse history homelessness were found be most important predictors being credible transmitters.