Deconvoluting the diversity of within-host pathogen strains in a multi-locus sequence typing framework.

ABSTRACT:

Background

Bacterial pathogens exhibit an impressive amount of genomic diversity. This diversity can be informative of evolutionary adaptations, host-pathogen interactions, and disease transmission patterns. However, capturing this diversity directly from biological samples is challenging.

Results

We introduce a framework for understanding the within-host diversity of a pathogen using multi-locus sequence types (MLST) from whole-genome sequencing (WGS) data. Our approach consists of two stages. First we process each sample individually by assigning it, for each locus in the MLST scheme, a set of alleles and a proportion for each allele. Next, we associate to each sample a set of strain types using the alleles and the strain proportions obtained in the first step. We achieve

SUBMITTER: Gan GL 

PROVIDER: S-EPMC6915855 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature