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Inference of infectious disease transmission through a relaxed bottleneck using multiple genomes per host
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Carson, Jake, Keeling, Matthew James, Wyllie, David, Ribeca, Paolo, Didelot, Xavier and Hepp, Crystal (2024) Inference of infectious disease transmission through a relaxed bottleneck using multiple genomes per host. Molecular Biology and Evolution, 41 (1). msad288. doi:10.1093/molbev/msad288 ISSN 0737-4038.
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Official URL: http://doi.org/10.1093/molbev/msad288
Abstract
In recent times, pathogen genome sequencing has become increasingly used to investigate infectious disease outbreaks. When genomic data is sampled densely enough amongst infected individuals, it can help resolve who infected whom. However, transmission analysis cannot rely solely on a phylogeny of the genomes but must account for the within-host evolution of the pathogen, which blurs the relationship between phylogenetic and transmission trees. When only a single genome is sampled for each host, the uncertainty about who infected whom can be quite high. Consequently, transmission analysis based on multiple genomes of the same pathogen per host has a clear potential for delivering more precise results, even though it is more laborious to achieve. Here we present a new methodology that can use any number of genomes sampled from a set of individuals to reconstruct their transmission network. Furthermore, we remove the need for the assumption of a complete transmission bottleneck. We use simulated data to show that our method becomes more accurate as more genomes per host are provided, and that it can infer key infectious disease parameters such as the size of the transmission bottleneck, within-host growth rate, basic reproduction number and sampling fraction. We demonstrate the usefulness of our method in applications to real datasets from an outbreak of Pseudomonas aeruginosa amongst cystic fibrosis patients and a nosocomial outbreak of Klebsiella pneumoniae.
Item Type: | Journal Article | ||||||
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Subjects: | Q Science > QH Natural history Q Science > QR Microbiology R Medicine > RB Pathology R Medicine > RC Internal medicine |
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Divisions: | Faculty of Science, Engineering and Medicine > Science > Life Sciences (2010- ) Faculty of Science, Engineering and Medicine > Science > Mathematics Faculty of Science, Engineering and Medicine > Science > Statistics |
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Library of Congress Subject Headings (LCSH): | Bacterial diseases -- Epidemiology, Bacterial genomes, Communicable diseases, Communicable diseases -- Transmission, Host-virus relationships, Human gene mapping | ||||||
Journal or Publication Title: | Molecular Biology and Evolution | ||||||
Publisher: | Oxford University Press | ||||||
ISSN: | 0737-4038 | ||||||
Official Date: | 3 January 2024 | ||||||
Dates: |
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Volume: | 41 | ||||||
Number: | 1 | ||||||
Article Number: | msad288 | ||||||
DOI: | 10.1093/molbev/msad288 | ||||||
Status: | Peer Reviewed | ||||||
Publication Status: | Published | ||||||
Access rights to Published version: | Open Access (Creative Commons) | ||||||
Date of first compliant deposit: | 8 January 2024 | ||||||
Date of first compliant Open Access: | 10 January 2024 | ||||||
RIOXX Funder/Project Grant: |
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