Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences.

ABSTRACT: Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions. Yet, there is no current consensus on how to measure genomic variation. To test the effect of the variant-identification approach on transmission inferences for Mycobacterium tuberculosis, we conducted an experiment in which five genomic epidemiology groups applied variant-identification pipelines to the same outbreak sequence data. We compared the variants identified by each group in addition to transmission and phylogenetic inferences made with each variant set. To measure the performance of commonly used variant-identification tools, we simulated an outbreak. We compared the performance of three mapping algorith

SUBMITTER: Walter KS 

PROVIDER: S-EPMC7641424 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature