Applied phyloepidemiology: Detecting drivers of pathogen transmission from genomic signatures using density measures.

ABSTRACT: Understanding the driving forces of an epidemic is key to inform intervention strategies against it. Correlating measures of the epidemic success of a pathogen with ancillary parameters such as its drug resistance profile provides a flexible tool to identify such driving forces. The recently described time-scaled haplotypic density (THD) method facilitates the inference of a pathogen's epidemic success from genetic data. Contrary to demogenetic approaches that define success in an aggregated fashion, the THD computes an independent index of success for each isolate in a collection. Modeling this index using multivariate regression, thus, allows us to control for various sources of bias and to identify independent predictors of success. We illustrate the use of THD to address key questions

SUBMITTER: Wirth T 

PROVIDER: S-EPMC7359849 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature