[bioRxiv, 15 July 2024]

We introduce and apply Bayesian Reconstruction and Evolutionary Analysis of Transmission Histories (BREATH), a method to simultaneously construct phylogenetic trees and transmission trees using sequence data for a person-to-person outbreak. BREATH’s transmission process that accounts for a flexible natural history of infection (including a latent period if desired) and a separate process for sampling. It allows for unsampled individuals and for individuals to have diverse within-host infections. BREATH also accounts for the fact that an outbreak may still be ongoing at the time of analysis, using a recurrent events approach to account for right truncation. We perform a simulation study to verify our implementation, and apply BREATH to a previously-described 13-year outbreak of tuber-culosis. We find that using a transmission process to inform the phylogenetic reconstruction results in better resolution of the phylogeny (in topology, branch length and tree height) and a more precise estimate of the time of origin of the outbreak. Considerable uncertainty remains about transmission events in the outbreak, but our reconstructed transmission network resolves two major waves of transmission consistent with the previously-described epidemiology, estimates the numbers of unsampled individuals, and describes some highprobability transmission pairs.

An open source implementation of BREATH is available from:

https://github.com/rbo...

…as the BREATH package to BEAST 2.

[The Lancet Microbe, 28 November 2024]

Background: Mycobacterium tuberculosis complex (MTBC) species evolve slowly, so isolates from individuals linked in transmission often have identical or nearly identical genomes, making it difficult to reconstruct transmission chains. Finding additional sources of shared MTBC variation could help overcome this problem. Previous studies have reported MTBC diversity within infected individuals; however, whether within-host variation improves transmission inferences remains unclear. Here, we aimed to quantify within-host MTBC variation and assess whether such information improves transmission inferences.

Methods: We conducted a retrospective genomic epidemiology study in which we reanalysed publicly available sequence data from household transmission studies published in PubMed from database inception until Jan 31, 2024, for which both genomic and epidemiological contact data were available, using household membership as a proxy for transmission linkage. We quantified minority variants (ie, positions with two or more alleles each supported by at least five-fold coverage and with a minor allele frequency of 1% or more) outside of PE and PPE genes, within individual samples and shared across samples. We used receiver operator characteristic (ROC) curves to compare the performance of a general linear model for household membership that included shared minority variants and one that included only fixed genetic differences.

Findings: We identified three MTBC household transmission studies with publicly available whole-genome sequencing data and epidemiological linkages: a household transmission study in Vitória, Brazil (Colangeli et al), a retrospective population-based study of paediatric tuberculosis in British Columbia, Canada (Guthrie et al), and a retrospective population-based study in Oxfordshire, England (Walker et al). We found moderate levels of minority variation present in MTBC sequence data from cultured isolates that varied significantly across studies: mean 168·6 minority variants (95% CI 151·4–185·9) for the Colangeli et al dataset, 5·8 (1·5–10·2) for Guthrie et al (p<0·0001, Wilcoxon rank sum test, vs Colangeli et al), and 7·1 (2·4–11·9) for Walker et al (p<0·0001, Wilcoxon rank sum test, vs Colangeli et al). Isolates from household pairs shared more minority variants than did randomly selected pairs of isolates: mean 97·7 shared minority variants (79·1–116·3) versus 9·8 (8·6–11·0) in Colangeli et al, 0·8 (0·1–1·5) versus 0·2 (0·1–0·2) in Guthrie et al, and 0·7 (0·1–1·3) versus 0·2 (0·2–0·2) in Walker et al (all p<0·0001, Wilcoxon rank sum test). Shared within-host variation was significantly associated with household membership (odds ratio 1·51 [95% CI 1·30–1·71], p<0·0001), for one standard deviation increase in shared minority variants. Models that included shared within-host variation versus models without within-host variation improved the accuracy of predicting household membership in all three studies: area under the ROC curve 0·95 versus 0·92 for the Colangeli et al study, 0·99 versus 0·95 for the Guthrie et al study, and 0·93 versus 0·91 for the Walker et al study.

Interpretation: Within-host MTBC variation persists through culture of sputum and could enhance the resolution of transmission inferences. The substantial differences in minority variation recovered across studies highlight the need to optimise approaches to recover and incorporate within-host variation into automated phylogenetic and transmission inference.