These are important figures for the distinction between outbreak and non-outbreak isolates when interpreting WGS results. We also showed that epidemiological linked isolates showed less than 26 SNPs or 13 allele differences. aeruginosa wgMLST scheme in BioNumerics TM is as discriminatory as the core-SNP calling approach and apparently useful for outbreak investigations. In one dataset, a putative homologous recombination of a large DNA fragment (202 loci) was identified among these isolates, affecting its phylogeny, but with no impact on the epidemiological analysis of outbreak isolates. When compared to core-SNP calling, a higher coefficient of correlation was obtained with cgMLST ( R 2 of 0.92–0.99) than with wgMLST (0.78–0.99). The number of SNPs and allele difference between isolates with close epidemiological linkage varies between 0–26 and 0–13, respectively. Correlation between SNP calling and wg- or cg-MLST results were evaluated by calculating linear regressions and their coefficient of correlations ( R 2) between the number of SNPs and the number of allele differences in pairwise comparison of isolates. In this study, wg- and cg-MLST were performed in BioNumerics TM using a scheme developed by Applied-Maths. All isolates were previously analyzed by a core SNP approach. The fourth dataset consisted of 10 isolates from an investigation of P. aeruginosa collected in our ICUs over a 5-year period. Three datasets included 155 isolates from three different sequence types (ST) of P. 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. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. 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 genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. Service of Hospital Preventive Medicine, Lausanne University Hospital, University of Lausanne, Lausanne, Switzerland.Blanc *, Bárbara Magalhães, Isabelle Koenig, Laurence Senn and Bruno Grandbastien
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