All 84 K. pneumoniae isolates were subjected to next-generation sequencing (NGS) using the Illumina HiSeq 2500 (BaseClear, Leiden, the Netherlands). The NGS data of the K. pneumoniae isolates were used for classical MLST and wgMLST analyses using the in-house wgMLST scheme in SeqSphere software version 6.0.2 (Ridom GmbH, Münster, Germany). The in-house K. pneumoniae wgMLST scheme was comprised of 4978 genes (3471 core-genome and 1507 accessory-genome targets) using K. pneumoniae MGH 78,578 (NC_009648.1) as a reference genome21 (link). For classical MLST, the existing scheme was used and cluster nomenclature were depicted in Table 134 (link). The resulting data was imported into Bionumerics version 7.6.3 for subsequent comparative analyses (Applied Maths, Sint-Martens-Latem, Belgium). The antibiotic resistance gene profile and plasmid replicon compositions in all of the isolates were determined by interrogating the online ResFinder (version 3.1.0) and PlasmidFinder (version 2.0.2) databases available at the Center for Genomic Epidemiology website (https://cge.cbs.dtu.dk/services/)35 (link),36 (link). For ResFinder, a 90% identity threshold and a minimum length of 60% were used as criteria, whereas for PlasmidFinder, an identity of 95% was utilized.
Hendrickx A.P., Landman F., de Haan A., Borst D., Witteveen S., van Santen-Verheuvel M.G., van der Heide H.G, & Schouls L.M. (2020). Plasmid diversity among genetically related Klebsiella pneumoniae blaKPC-2 and blaKPC-3 isolates collected in the Dutch national surveillance. Scientific Reports, 10, 16778.
Antibiotic resistance Gene profileGenes Genomic K pneumoniae Martens PlasmidReplicon
Corresponding Organization : National Institute for Public Health and the Environment
Other organizations :
University of Curaçao, Sint Maartenskliniek, Noordwest Ziekenhuisgroep, Meander Medisch Centrum, Amsterdam University Medical Centers, Academic Medical Center, OLVG, Public Health Service of Amsterdam, Gelre Hospitals, Amphia Ziekenhuis, IJsselland Ziekenhuis, Reinier de Graaf Hospital, Deventer Ziekenhuis, Slingeland Ziekenhuis, Admiraal De Ruyter Ziekenhuis, Groene Hart Ziekenhuis, Ziekenhuis Gelderse Vallei, Certe, University Medical Center Groningen, University of Groningen, Stichting Apotheek der Haarlemse Ziekenhuizen, Rijnstate Hospital, Zuyderland Medisch Centrum, Ziekenhuis Groep Twente, Tergooi, Maastricht University Medical Centre, St. Antonius Ziekenhuis, Canisius-Wilhelmina Ziekenhuis, Radboud University Nijmegen, Radboud University Medical Center, Laurentius Ziekenhuis, Bravis Ziekenhuis, Erasmus MC, Ikazia Ziekenhuis, Maasstad Ziekenhuis, Sint Franciscus Gasthuis, Alrijne Ziekenhuis, Haga Hospital, Jeroen Bosch Ziekenhuis, Elisabeth-TweeSteden Ziekenhuis, Diakonessenhuis hospital, University Medical Center Utrecht, PAMM, VieCuri Medisch Centrum, Isala, Franciscus Vlietland
Next-generation sequencing (NGS) using the Illumina HiSeq 2500
dependent variables
Classical MLST and wgMLST analyses
Antibiotic resistance gene profile
Plasmid replicon compositions
control variables
The in-house K. pneumoniae wgMLST scheme was comprised of 4978 genes (3471 core-genome and 1507 accessory-genome targets) using K. pneumoniae MGH 78,578 (NC_009648.1) as a reference genome
The existing MLST scheme was used for classical MLST analysis
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