%0 Journal Article %T Core/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain %+ Hospital de la Santa Creu i Sant Pau %+ University of Groningen [Groningen] %+ ESCMID [Basel] %+ Westfälische Wilhelms-Universität Münster = University of Münster (WWU) %+ Biodiversité et Epidémiologie des Bactéries pathogènes - Biodiversity and Epidemiology of Bacterial Pathogens %A Miro, Elisenda %A Rossen, John, W. A. %A Chlebowicz, Monika, A. %A Harmsen, Dag %A Brisse, Sylvain %A Passet, Virginie %A Navarro, Ferran %A Friedrich, Alex, W. %A García-Cobos, S. %Z This work was partly supported by Interreg IVa, EurSafety Health-net (III-1-02D73), and EurHealth-1Health projects, which are part of a Dutch-German cross-border network supported by the European Commission; the Dutch Ministry of Health, Welfare and Sport (VWS); the Ministry of Economy, Innovation, Digitalisation and Energy of the German Federal State of North Rhine-Westphalia; and the German Federal State of Lower Saxony. BIGSdb-Kp receives institutional funding from Institut Pasteur. %< avec comité de lecture %@ 1664-302X %J Frontiers in Microbiology %I Frontiers Media %V 10 %P 2961 %8 2020-01-31 %D 2020 %R 10.3389/fmicb.2019.02961 %M 32082262 %K K. pneumoniae %K OXA-48 %K WGS %K cgMLST %K molecular epidemiology %K wgMLST %Z Life Sciences [q-bio]/Biochemistry, Molecular Biology %Z Life Sciences [q-bio]/Biodiversity %Z Life Sciences [q-bio]/Santé publique et épidémiologieJournal articles %X Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48-producing Klebsiella pneumoniae isolates. We included isolates from the predominant sequence type ST405 (n = 31) OXA-48-producing K. pneumoniae clone and isolates from ST101 (n = 3), ST14 (n = 1), ST17 (n = 1), and ST1233 (n = 1), obtained from eight Catalan hospitals. Core-genome multilocus sequence typing (cgMLST) schemes from Institut Pasteur's BIGSdb-Kp (634 genes) and SeqSphere+ (2,365 genes), and a SeqSphere+ whole-genome MLST (wgMLST) scheme (4,891 genes) were used. Allele differences or allelic mismatches and the genetic distance, as the proportion of allele differences, were used to interpret the results from a gene-by-gene approach, whereas the number of SNPs was used for the cgSNP analysis. We observed between 0-10 and 0-14 allele differences among the predominant ST405 using cgMLST and wgMLST from SeqSphere+, respectively, and <2 allelic mismatches when using Institut Pasteur's BIGSdb-Kp cgMLST scheme. For ST101, we observed 14 and 54 allele differences when using cgMLST and wgMLST SeqSphere+, respectively, and 2-5 allelic mismatches for BIGSdb-Kp cgMLST. A low genetic distance (<0.0035, a previously established threshold for epidemiological link) was generally in concordance with a low number of allele differences (<8) when using the SeqSphere+ cgMLST scheme. The cgSNP analysis showed 6-29 SNPs in isolates with identical allelic SeqSphere+ cgMLST profiles and 16-61 cgSNPs among ST405 isolates. Furthermore, comparison of WGS-based typing results with previously obtained MLST and pulsed-field gel electrophoresis (PFGE) data showed some differences, demonstrating the different molecular principles underlying these techniques. In conclusion, the use of the different WGS-based typing methods that were used to elucidate the genetic relatedness of clonal OXA-48-producing K. pneumoniae all led to the same conclusions. Furthermore, threshold parameters in WGS-based typing methods should be applied with caution and should be used in combination with clinical epidemiological data and population and species characteristics. %G English %2 https://pasteur.hal.science/pasteur-03329667/document %2 https://pasteur.hal.science/pasteur-03329667/file/fmicb-10-02961.pdf %L pasteur-03329667 %U https://pasteur.hal.science/pasteur-03329667 %~ PASTEUR %~ SANTE_PUB_INSERM %~ GIP-BE