Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS. (10th March 2016)

• Record Type: Journal Article
• Authors: Sabirova, Julia S.; Xavier, Basil Britto; Coppens, Jasmine; Zarkotou, Olympia; Lammens, Christine; Janssens, Lore; Burggrave, Ronald; Wagner, Trevor; Goossens, Herman; Malhotra-Kumar, Surbhi
• Is Part Of: Journal of antimicrobial chemotherapy. Volume 71:Number 6(2016:Jun.)
• Page Start: 1501
• Page End: 1509
• Publication Date: 2016-03-10
• Subjects: Anti-infective agents -- Periodicals; Chemotherapy -- Periodicals; 615.58
• DOI: 10.1093/jac/dkw003
• Languages: English
• ISSNs: 0305-7453

Abstract

Abstract: Objectives: We utilized whole-genome mapping (WGM) and WGS to characterize 12 clinical carbapenem-resistant Klebsiella pneumoniae strains (TGH1–TGH12). Methods: All strains were screened for carbapenemase genes by PCR, and typed by MLST, PFGE (XbaI) and WGM (AflII ) (OpGen, USA). WGS (Illumina) was performed on TGH8 and TGH10. Reads were de novo assembled and annotated [SPAdes, Rapid Annotation Subsystem Technology (RAST)]. Contigs were aligned directly, and after in silico AflII restriction, with corresponding WGMs (MapSolver, OpGen; BioNumerics, Applied Maths). Results: All 12 strains were ST383. Of the 12 strains, 11 were carbapenem resistant, 7 harboured bla KPC-2 and 11 harboured bla VIM-19 . Varying the parameters for assigning WGM clusters showed that these were comparable to STs and to the eight PFGE types or subtypes (difference of three or more bands). A 95% similarity coefficient assigned all 12 WGMs to a single cluster, whereas a 99% similarity coefficient (or ≥10 unmatched-fragment difference) assigned the 12 WGMs to eight (sub)clusters. Based on a difference of three or more bands between PFGE profiles, the Simpson's diversity indices (SDIs) of WGM (0.94, Jackknife pseudo-values CI: 0.883–0.996) and PFGE (0.93, Jackknife pseudo-values CI: 0.828–1.000) were similar ( P = 0.649). However, the discriminatory power of WGM was significantly higher (SDI: 0.94, Jackknife pseudo-values CI: 0.883–0.996) than that of PFGE profiles typed on a difference of seven or more bands (SDI: 0.53, Jackknife pseudo-values CI: 0.212–0.849) ( P = 0.007). Conclusions: This study demonstrates the application of WGM to understanding the epidemiology of hospital-associated K. pneumoniae . Utilizing a combination of WGM and WGS, we also present here the first longitudinal genomic characterization of the highly dynamic carbapenem-resistant ST383 K. pneumoniae clone that is rapidly gaining importance in Europe.