Identifying likely transmissions in Mycobacterium bovis infected populations of cattle and badgers using the Kolmogorov Forward Equations

Gianluigi Rossi, Joseph Crispell, Daniel Balaz, Samantha Lycett, Clare H. Benton, Richard J Delahay, Rowland Kao

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

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.
Original languageEnglish
JournalScientific Reports
Early online date15 Dec 2020
DOIs
Publication statusE-pub ahead of print - 15 Dec 2020

Keywords / Materials (for Non-textual outputs)

  • bovine tuberculosis
  • inter-species transmission
  • contact network
  • within-host evolution
  • Mycobacterium bovis
  • Woodchester Park

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