Projects per year
Abstract
Established methods for whole-genome-sequencing (WGS) technology allow for the detection of single-nucleotide polymorphisms (SNPs) in the pathogen genomes sourced from host samples. The information obtained can be used to track the pathogen’s evolution in time and potentially identify ‘who-infected-whom’ with unprecedented accuracy. Successful methods include ‘phylodynamic approaches’ that integrate evolutionary and epidemiological data. However, they are typically computationally intensive, require extensive data, and are best applied when there is a strong molecular clock signal and substantial pathogen diversity.
To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemic Mycobacterium bovis (the causative agent of bovine/zoonotic tuberculosis, bTB) infection.
Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks, but can be sensitive to assumptions about within-host evolution.
To determine how much transmission information can be inferred when pathogen genetic diversity is low and metadata limited, we propose an analytical approach that combines pathogen WGS data and sampling times from infected hosts. It accounts for ‘between-scale’ processes, in particular within-host pathogen evolution and between-host transmission. We applied this to a well-characterised population with an endemic Mycobacterium bovis (the causative agent of bovine/zoonotic tuberculosis, bTB) infection.
Our results show that, even with such limited data and low diversity, the computation of the transmission probability between host pairs can help discriminate between likely and unlikely infection pathways and therefore help to identify potential transmission networks, but can be sensitive to assumptions about within-host evolution.
Original language | English |
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Journal | Scientific Reports |
Early online date | 15 Dec 2020 |
DOIs | |
Publication status | E-pub ahead of print - 15 Dec 2020 |
Keywords
- bovine tuberculosis
- inter-species transmission
- contact network
- within-host evolution
- Mycobacterium bovis
- Woodchester Park
Fingerprint
Dive into the research topics of 'Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations'. Together they form a unique fingerprint.Projects
- 2 Finished
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Joint estimation of epidemiological and genetic processes for Mycobacterium bovis transmission dynamics in cattle and badgers
15/09/17 → 30/06/18
Project: Research
Profiles
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Rowland Kao
- Royal (Dick) School of Veterinary Studies - Chair of Veterinary Epidemiology and Data Science
- School of Physics and Astronomy - Personal Chair
Person: Academic: Research Active