Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS

Julia S Sabirova; Basil Britto Xavier; Jasmine Coppens; Olympia Zarkotou; Christine Lammens; Lore Janssens; Ronald Burggrave; Trevor Wagner; Herman Goossens; Surbhi Malhotra-Kumar

doi:10.1093/jac/dkw003

Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS

Julia S Sabirova, Basil Britto Xavier, Jasmine Coppens, Olympia Zarkotou, Christine Lammens, Lore Janssens, Ronald Burggrave, Trevor Wagner, Herman Goossens, Surbhi Malhotra-Kumar

Clinical Reference Laboratory

Research output: Contribution to journal › A1: Web of Science-article › peer-review

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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 blaKPC-2 and 11 harboured blaVIM-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.

Original language	English
Journal	Journal of Antimicrobial Chemotherapy
Volume	71
Issue number	6
Pages (from-to)	1501-1509
Number of pages	9
ISSN	0305-7453
DOIs	https://doi.org/10.1093/jac/dkw003
Publication status	Published - 2016

Keywords

Bacterial Proteins/genetics
Chromosome Mapping/methods
Electrophoresis, Gel, Pulsed-Field
Europe/epidemiology
Genotype
Humans
Klebsiella Infections/epidemiology
Klebsiella pneumoniae/classification
Longitudinal Studies
Molecular Epidemiology/methods
Multilocus Sequence Typing/methods
beta-Lactamases/genetics

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10.1093/jac/dkw003

2016jach1501Final published version, 1.53 MBLicence: Unspecified

Cite this

Sabirova, J. S., Xavier, B. B., Coppens, J., Zarkotou, O., Lammens, C., Janssens, L., Burggrave, R., Wagner, T., Goossens, H., & Malhotra-Kumar, S. (2016). Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS. Journal of Antimicrobial Chemotherapy, 71(6), 1501-1509. https://doi.org/10.1093/jac/dkw003

@article{68b201b6b18b4a2aa83bcb79c33d680d,

title = "Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS",

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 blaKPC-2 and 11 harboured blaVIM-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.",

keywords = "Bacterial Proteins/genetics, Chromosome Mapping/methods, Electrophoresis, Gel, Pulsed-Field, Europe/epidemiology, Genotype, Humans, Klebsiella Infections/epidemiology, Klebsiella pneumoniae/classification, Longitudinal Studies, Molecular Epidemiology/methods, Multilocus Sequence Typing/methods, beta-Lactamases/genetics",

author = "Sabirova, {Julia S} and Xavier, {Basil Britto} and Jasmine Coppens and Olympia Zarkotou and Christine Lammens and Lore Janssens and Ronald Burggrave and Trevor Wagner and Herman Goossens and Surbhi Malhotra-Kumar",

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year = "2016",

doi = "10.1093/jac/dkw003",

language = "English",

volume = "71",

pages = "1501--1509",

journal = "Journal of Antimicrobial Chemotherapy",

issn = "0305-7453",

publisher = "Oxford University Press",

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Sabirova, JS, Xavier, BB, Coppens, J, Zarkotou, O, Lammens, C, Janssens, L, Burggrave, R, Wagner, T, Goossens, H & Malhotra-Kumar, S 2016, 'Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS', Journal of Antimicrobial Chemotherapy, vol. 71, no. 6, pp. 1501-1509. https://doi.org/10.1093/jac/dkw003

TY - JOUR

T1 - Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS

AU - Sabirova, Julia S

AU - Xavier, Basil Britto

AU - Coppens, Jasmine

AU - Zarkotou, Olympia

AU - Lammens, Christine

AU - Janssens, Lore

AU - Burggrave, Ronald

AU - Wagner, Trevor

AU - Goossens, Herman

AU - Malhotra-Kumar, Surbhi

N1 - FTX;

PY - 2016

Y1 - 2016

N2 - 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 blaKPC-2 and 11 harboured blaVIM-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.

AB - 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 blaKPC-2 and 11 harboured blaVIM-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.

KW - Bacterial Proteins/genetics

KW - Chromosome Mapping/methods

KW - Electrophoresis, Gel, Pulsed-Field

KW - Europe/epidemiology

KW - Genotype

KW - Humans

KW - Klebsiella Infections/epidemiology

KW - Klebsiella pneumoniae/classification

KW - Longitudinal Studies

KW - Molecular Epidemiology/methods

KW - Multilocus Sequence Typing/methods

KW - beta-Lactamases/genetics

U2 - 10.1093/jac/dkw003

DO - 10.1093/jac/dkw003

M3 - A1: Web of Science-article

C2 - 26968884

SN - 0305-7453

VL - 71

SP - 1501

EP - 1509

JO - Journal of Antimicrobial Chemotherapy

JF - Journal of Antimicrobial Chemotherapy

IS - 6

ER -

Whole-genome typing and characterization of blaVIM19-harbouring ST383 Klebsiella pneumoniae by PFGE, whole-genome mapping and WGS

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