Reconstructing transmission trees for communicable diseases using densely sampled genetic data
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Abstract: Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of control measures. We considered disease outbreaks in a setting with dense genomic sampling, and formulated stochastic epidemic models to investigate person-to-person transmission, based on observed genomic and epidemiological data. We constructed models in which the genetic distance between sampled genotypes depends on the epidemiological relationship between the hosts. A data augmented Markov chain Monte Carlo algorithm was used to sample over the transmission trees, providing a posterior probability for any given transmission route. We investigated the predictive performance of our methodology using simulated data, demonstrating high sensitivity and specificity, particularly for rapidly mutating pathogens with low transmissibility. We then analyzed data collected during an outbreak of methicillin-resistant Staphylococcus aureus in a hospital, identifying probable transmission routes and estimating epidemiological parameters. Our approach overcomes limitations of previous methods, providing a framework with the flexibility to allow for unobserved infection times, multiple independent introductions of the pathogen, and within-host genetic diversity, as well as allowing forward simulation.
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Cites work
Cited in
(13)- Design and analysis of infectious disease studies. Abstracts from the workshop held February 18--24, 2018
- Multi-type branching processes modeling of nosocomial epidemics
- Bayesian inference for multistrain epidemics with application to \textit{Escherichia coli} O157:H7 in feedlot cattle
- Integrating genealogy and epidemiology: The ancestral infection and selection graph as a model for reconstructing host virus histories
- Reconstructing transmission trees for communicable diseases using densely sampled genetic data
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- Tajima's D and Site-Specific Nucleotide Frequency in a Population during an Infectious Disease Outbreak
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- Modelling, Bayesian inference, and model assessment for nosocomial pathogens using whole-genome-sequence data
- Evidence synthesis for stochastic epidemic models
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- Bayesian estimation of transmission networks for infectious diseases
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