Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions.

ABSTRACT: Whole-genome sequencing (WGS) is increasingly used to aid the understanding of pathogen transmission. A first step in analyzing WGS data is usually to define "transmission clusters," sets of cases that are potentially linked by direct transmission. This is often done by including two cases in the same cluster if they are separated by fewer single-nucleotide polymorphisms (SNPs) than a specified threshold. However, there is little agreement as to what an appropriate threshold should be. We propose a probabilistic alternative, suggesting that the key inferential target for transmission clusters is the number of transmissions separating cases. We characterize this by combining the number of SNP differences and the length of time over which those differences have accumulated, using information

SUBMITTER: Stimson J 

PROVIDER: S-EPMC6389316 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature