Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany

on behalf of the DZIF R-Net Study Group

doi:10.3390/antibiotics11101286

Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany

on behalf of the DZIF R-Net Study Group

Abstract

To analyse the epidemiology and population structure of third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant (CR) Klebsiella pneumoniae complex isolates, patients were screened for rectal colonisation with 3GCR/CR K. pneumoniae complex on admission to six German university hospitals (2016–2019). Also collected were 3GCR/CR and susceptible K. pneumoniae isolates from patients with bloodstream infections (2016–2018). Whole-genome sequencing was performed followed by multilocus sequencing typing (MLST), core-genome MLST, and resistome and virulome analysis. The admission prevalence of 3GCR K. pneumoniae complex isolates during the 4-year study period was 0.8%, and 1.0 bloodstream infection per 1000 patient admissions was caused by K. pneumoniae complex (3GCR prevalence, 15.1%). A total of seven K. pneumoniae complex bloodstream isolates were CR (0.8%). The majority of colonising and bloodstream 3GCR isolates were identified as K. pneumoniae, 96.7% and 98.8%, respectively; the remainder were K. variicola and K. quasipneumoniae. cgMLST showed a polyclonal population of colonising and bloodstream isolates, which was also reflected by MLST and virulome analysis. CTX-M-15 was the most prevalent extended-spectrum beta-lactamase, and 29.7% of the colonising and 48.8% of the bloodstream isolates were high-risk clones. The present study provides an insight into the polyclonal 3GCR K. pneumoniae population in German hospitals.

Original language	English
Article number	1286
Journal	Antibiotics
Volume	11
Issue number	10
ISSN	2079-6382
DOIs	https://doi.org/10.3390/antibiotics11101286
Publication status	Published - 10.2022

Funding

This work was supported by the German Centre for Infection Research (DZIF), project number TTU 08.811. We would like to thank Ahmad Saleh, Vivien Persy, Carina Müller, and Michael Sonnabend for excellent technical assistance. The results have been partially presented as poster presentation at the Joint Annual Meeting German Society of Infectious Diseases and German Centre for Infection Research (2019, Bad Nauheim, Germany and 2022, Stuttgart, Germany) and at the 31st and 32nd European Congress of Clinical Microbiology and Infectious Diseases (2021, online conference and 2022, Lisbon, Portugal). We thank the Institute Pasteur teams for the curation and maintenance of BIGSdb-Pasteur databases at http://bigsdb.pasteur.fr/ (accessed on 17 March 2022). In addition to the authors, the following members of the DZIF R-Net Study Group (in alphabetical order) contributed to the study: Lena Biehl, Cologne; Trinad Chakraborty, Giessen; Nadine Hoffmann, Tübingen; Florian Hölzl, Tübingen; Baris Bader, Tübingen; Michael Buhl, Tübingen; Frieder Fuchs, Cologne; Georg Häcker, Freiburg; Nathalie Jazmati, Cologne; Dana Lenke, Lübeck; Luis Alberto Peña Diaz, Berlin; Gabriele Peyerl-Hoffmann, Freiburg; Georg Pilarski, Berlin; Susanna Proske, Cologne; Sabine Schuster, Freiburg; Norbert Thoma, Berlin; Martina Vavra, Freiburg; Anna Weber, Berlin. We acknowledge support for the Article Processing Charge from the DFG (German Research Foundation, 491454339).

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

Research Areas and Centers

Academic Focus: Center for Infection and Inflammation Research (ZIEL)

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Cite this

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title = "Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany",

abstract = "To analyse the epidemiology and population structure of third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant (CR) Klebsiella pneumoniae complex isolates, patients were screened for rectal colonisation with 3GCR/CR K. pneumoniae complex on admission to six German university hospitals (2016–2019). Also collected were 3GCR/CR and susceptible K. pneumoniae isolates from patients with bloodstream infections (2016–2018). Whole-genome sequencing was performed followed by multilocus sequencing typing (MLST), core-genome MLST, and resistome and virulome analysis. The admission prevalence of 3GCR K. pneumoniae complex isolates during the 4-year study period was 0.8\%, and 1.0 bloodstream infection per 1000 patient admissions was caused by K. pneumoniae complex (3GCR prevalence, 15.1\%). A total of seven K. pneumoniae complex bloodstream isolates were CR (0.8\%). The majority of colonising and bloodstream 3GCR isolates were identified as K. pneumoniae, 96.7\% and 98.8\%, respectively; the remainder were K. variicola and K. quasipneumoniae. cgMLST showed a polyclonal population of colonising and bloodstream isolates, which was also reflected by MLST and virulome analysis. CTX-M-15 was the most prevalent extended-spectrum beta-lactamase, and 29.7\% of the colonising and 48.8\% of the bloodstream isolates were high-risk clones. The present study provides an insight into the polyclonal 3GCR K. pneumoniae population in German hospitals.",

author = "\{on behalf of the DZIF R-Net Study Group\} and Kyriaki Xanthopoulou and Can Imirzalioglu and Walker, \{Sarah V.\} and Michael Behnke and Dinkelacker, \{Ariane G.\} and Simone Eisenbeis and Petra Gastmeier and Hanna G{\"o}lz and Nadja K{\"a}ding and Kern, \{Winfried V.\} and Axel Kola and Evelyn Kramme and Kai Lucassen and Alexander Mischnik and Silke Peter and Rohde, \{Anna M.\} and Jan Rupp and Evelina Tacconelli and David Tobys and Vehreschild, \{Maria J.G.T.\} and Julia Wille and Harald Seifert and Higgins, \{Paul G.\}",

note = "Publisher Copyright: {\textcopyright} 2022 by the authors.",

year = "2022",

month = oct,

doi = "10.3390/antibiotics11101286",

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volume = "11",

journal = "Antibiotics",

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T1 - Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany

AU - on behalf of the DZIF R-Net Study Group

AU - Xanthopoulou, Kyriaki

AU - Imirzalioglu, Can

AU - Walker, Sarah V.

AU - Behnke, Michael

AU - Dinkelacker, Ariane G.

AU - Eisenbeis, Simone

AU - Gastmeier, Petra

AU - Gölz, Hanna

AU - Käding, Nadja

AU - Kern, Winfried V.

AU - Kola, Axel

AU - Kramme, Evelyn

AU - Lucassen, Kai

AU - Mischnik, Alexander

AU - Peter, Silke

AU - Rohde, Anna M.

AU - Rupp, Jan

AU - Tacconelli, Evelina

AU - Tobys, David

AU - Vehreschild, Maria J.G.T.

AU - Wille, Julia

AU - Seifert, Harald

AU - Higgins, Paul G.

PY - 2022/10

Y1 - 2022/10

N2 - To analyse the epidemiology and population structure of third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant (CR) Klebsiella pneumoniae complex isolates, patients were screened for rectal colonisation with 3GCR/CR K. pneumoniae complex on admission to six German university hospitals (2016–2019). Also collected were 3GCR/CR and susceptible K. pneumoniae isolates from patients with bloodstream infections (2016–2018). Whole-genome sequencing was performed followed by multilocus sequencing typing (MLST), core-genome MLST, and resistome and virulome analysis. The admission prevalence of 3GCR K. pneumoniae complex isolates during the 4-year study period was 0.8%, and 1.0 bloodstream infection per 1000 patient admissions was caused by K. pneumoniae complex (3GCR prevalence, 15.1%). A total of seven K. pneumoniae complex bloodstream isolates were CR (0.8%). The majority of colonising and bloodstream 3GCR isolates were identified as K. pneumoniae, 96.7% and 98.8%, respectively; the remainder were K. variicola and K. quasipneumoniae. cgMLST showed a polyclonal population of colonising and bloodstream isolates, which was also reflected by MLST and virulome analysis. CTX-M-15 was the most prevalent extended-spectrum beta-lactamase, and 29.7% of the colonising and 48.8% of the bloodstream isolates were high-risk clones. The present study provides an insight into the polyclonal 3GCR K. pneumoniae population in German hospitals.

AB - To analyse the epidemiology and population structure of third-generation cephalosporin-resistant (3GCR) and carbapenem-resistant (CR) Klebsiella pneumoniae complex isolates, patients were screened for rectal colonisation with 3GCR/CR K. pneumoniae complex on admission to six German university hospitals (2016–2019). Also collected were 3GCR/CR and susceptible K. pneumoniae isolates from patients with bloodstream infections (2016–2018). Whole-genome sequencing was performed followed by multilocus sequencing typing (MLST), core-genome MLST, and resistome and virulome analysis. The admission prevalence of 3GCR K. pneumoniae complex isolates during the 4-year study period was 0.8%, and 1.0 bloodstream infection per 1000 patient admissions was caused by K. pneumoniae complex (3GCR prevalence, 15.1%). A total of seven K. pneumoniae complex bloodstream isolates were CR (0.8%). The majority of colonising and bloodstream 3GCR isolates were identified as K. pneumoniae, 96.7% and 98.8%, respectively; the remainder were K. variicola and K. quasipneumoniae. cgMLST showed a polyclonal population of colonising and bloodstream isolates, which was also reflected by MLST and virulome analysis. CTX-M-15 was the most prevalent extended-spectrum beta-lactamase, and 29.7% of the colonising and 48.8% of the bloodstream isolates were high-risk clones. The present study provides an insight into the polyclonal 3GCR K. pneumoniae population in German hospitals.

UR - https://www.scopus.com/pages/publications/85140783817

U2 - 10.3390/antibiotics11101286

DO - 10.3390/antibiotics11101286

M3 - Journal articles

AN - SCOPUS:85140783817

SN - 2079-6382

VL - 11

JO - Antibiotics

JF - Antibiotics

IS - 10

M1 - 1286

ER -

Surveillance and Genomic Analysis of Third-Generation Cephalosporin-Resistant and Carbapenem-Resistant Klebsiella pneumoniae Complex in Germany

Abstract

Funding

UN SDGs

Research Areas and Centers

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