Genotyping genetically heterogeneous <i>Cyclospora cayetanensis</i> infections to complement epidemiological case linkage.

ABSTRACT: Sexually reproducing pathogens such as Cyclospora cayetanensis often produce genetically heterogeneous infections where the number of unique sequence types detected at any given locus varies depending on which locus is sequenced. The genotypes assigned to these infections quickly become complex when additional loci are analysed. This genetic heterogeneity confounds the utility of traditional sequence-typing and phylogenetic approaches for aiding epidemiological trace-back, and requires new methods to address this complexity. Here, we describe an ensemble of two similarity-based classification algorithms, including a Bayesian and heuristic component that infer the relatedness of C. cayetanensis infections. The ensemble requires a set of haplotypes as input and assigns arbitrary distances to

SUBMITTER: Barratt JLN 

PROVIDER: S-EPMC6699905 | biostudies-literature | 2019 Sep

REPOSITORIES: biostudies-literature