Comparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumerics^TM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa.

ABSTRACT: Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. While SNP variant calling is currently considered as the most suitable method, the choice of a representative reference genome and the isolate dependency of results limit standardization and affect resolution in an unknown manner. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. Here, we assess the accuracy of wg- and cg-MLST by comparing results of four Pseudomonas aeruginosa datasets for which epidemiological and genomic data were previously described. Three datasets included 155 isolates from three different sequence types (ST) of P. aeruginosa collected in our ICUs over a 5-year period. The fourth dataset consisted of 10

SUBMITTER: Blanc DS 

PROVIDER: S-EPMC7387498 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature