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Updated: Sep 8, 2025
08:03
Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations
Published on: December 7, 2021
2.3K
Characterizing the informativeness of pathogen genome sequence datasets about transmission between population groups
Cécile Tran-Kiem1, Amanda C Perofsky2, Justin Lessler3,4
1Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
Medrxiv : the Preprint Server for Health Sciences
|August 20, 2025
Summary
Pathogen genome analysis reveals transmission patterns. Faster mutation rates in pathogens allow for more detailed tracking of transmission routes and population mixing, but sample size also limits this resolution.
Area of Science:
- Microbiology
- Genomics
- Epidemiology
Background:
- Pathogen genome analysis is crucial for understanding transmission dynamics between populations.
- The accumulation of mutations in pathogen genomes provides information about transmission history.
- The rate of mutation accumulation influences the resolution of phylogeographic studies.
Purpose of the Study:
- To investigate how mutation rate, transmission dynamics, population mixing, and sampling affect phylogeographic analyses.
- To develop a framework for quantifying the power of pathogen sequences in characterizing migration history.
- To identify limits on the scale of population mixing that can be characterized by sequence data.
Main Methods:
- Development of a conceptual probabilistic framework to assess sequence data's ability to capture migration history.
- Exploration of the interplay between mutation accumulation rate and migration event rate.
- Simulation studies to evaluate the impact of sequencing intensity (sample size) on phylogeographic resolution.
Main Results:
- Identified a pathogen-intrinsic limit on the scale of population mixing that can be resolved, with faster-mutating pathogens enabling finer spatial characterization.
- Demonstrated that sample size imposes an additional limit on the characterization of mixing processes.
- Highlighted inherent horizons of observability for population mixing dependent on pathogen evolution, transmission, mixing, and sampling.
Conclusions:
- Phylogeographic study design must consider the inherent limitations imposed by pathogen evolution and sampling strategies.
- The granularity of transmission characterization is fundamentally linked to the pathogen's mutation rate and the scale of population mixing.
- Understanding these limits is essential for accurately interpreting pathogen sequence data in epidemiological contexts.
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