Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile.

ABSTRACT: Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in Clostridium difficile, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six

SUBMITTER: Eyre DW 

PROVIDER: S-EPMC6935933 | biostudies-literature | 2019 Dec

REPOSITORIES: biostudies-literature