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Updated: Jul 27, 2025
07:13
A Two-interval Forced-choice Task for Multisensory Comparisons
Published on: November 9, 2018
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Comparing
Benjamin Sobkowiak1,2, Kamila Romanowski2,3, Inna Sekirov2,4
1Division of Respiratory Medicine, University of British Columbia, Vancouver, BC, Canada.
Epidemiology and Infection
|June 9, 2023
Summary
Genomic epidemiology tools for tracking tuberculosis (TB) transmission show variable accuracy. While specific, models like TransPhylo, Outbreaker2, and Phybreak identified true TB transmission links more effectively.
Area of Science:
- Genomic epidemiology
- Computational biology
- Infectious disease dynamics
Background:
- Genomic epidemiology tools are vital for understanding infectious disease transmission.
- Tuberculosis (TB) presents complex epidemiological challenges, including latency and within-host variation.
- The performance of genomic tools for TB transmission reconstruction remains unevaluated.
Purpose of the Study:
- To systematically compare the accuracy of six computational tools for reconstructing Mycobacterium tuberculosis transmission networks.
- To evaluate tool performance using simulated and real-world TB outbreak data.
- To inform the selection of appropriate tools for TB transmission analyses.
Main Methods:
- Systematic comparison of six publicly available transmission reconstruction models.
- Evaluation using simulated Mycobacterium tuberculosis outbreaks.
- Assessment against real-world TB cluster data, focusing on epidemiologically supported case-contact pairs.
Main Results:
- Observed significant variability in the number and accuracy of predicted transmission links across models.
- Simulated outbreaks showed low accuracy in predicting known transmission events.
- Real-world TB clusters revealed a low proportion of identified epidemiologically supported case-contact pairs.
- High specificity was noted for all models; TransPhylo, Outbreaker2, and Phybreak showed a higher proportion of true transmission links.
Conclusions:
- The performance of genomic epidemiology tools varies for tuberculosis transmission reconstruction.
- Models like TransPhylo, Outbreaker2, and Phybreak demonstrated better identification of true TB transmission links.
- Caution is advised when interpreting probabilistic transmission networks for TB due to performance limitations.
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