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Nat Microbiol. 2019 Jul 29. doi: 10.1038/s41564-019-0492-8. [Epub ahead of print]

Epidemic of carbapenem-resistant Klebsiella pneumoniae in Europe is driven by nosocomial spread.

Author information

1
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, UK.
2
Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany.
3
Pathogen Genomics, Wellcome Sanger Institute, Cambridge, UK.
4
Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
5
Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy.
6
Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
7
Natural Sciences, University of Bath, Bath, UK.
8
Pathogen Informatics, Wellcome Sanger Institute, Cambridge, UK.
9
Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath, UK.
10
Clinical Microbiology and Virology Unit, Florence Careggi University Hospital, Florence, Italy.
11
Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Cambridge, UK. david.aanensen@sanger.ac.uk.
12
Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, Nuffield Department of Medicine, University of Oxford, Oxford, UK. david.aanensen@sanger.ac.uk.
13
Institute for Infection Prevention and Hospital Epidemiology, Faculty of Medicine, University of Freiburg, Freiburg, Germany. hajo.grundmann@uniklinik-freiburg.de.
14
Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. hajo.grundmann@uniklinik-freiburg.de.

Abstract

Public health interventions to control the current epidemic of carbapenem-resistant Klebsiella pneumoniae rely on a comprehensive understanding of its emergence and spread over a wide range of geographical scales. We analysed the genome sequences and epidemiological data of >1,700 K. pneumoniae samples isolated from patients in 244 hospitals in 32 countries during the European Survey of Carbapenemase-Producing Enterobacteriaceae. We demonstrate that carbapenemase acquisition is the main cause of carbapenem resistance and that it occurred across diverse phylogenetic backgrounds. However, 477 of 682 (69.9%) carbapenemase-positive isolates are concentrated in four clonal lineages, sequence types 11, 15, 101, 258/512 and their derivatives. Combined analysis of the genetic and geographic distances between isolates with different β-lactam resistance determinants suggests that the propensity of K. pneumoniae to spread in hospital environments correlates with the degree of resistance and that carbapenemase-positive isolates have the highest transmissibility. Indeed, we found that over half of the hospitals that contributed carbapenemase-positive isolates probably experienced within-hospital transmission, and interhospital spread is far more frequent within, rather than between, countries. Finally, we propose a value of 21 for the number of single nucleotide polymorphisms that optimizes the discrimination of hospital clusters and detail the international spread of the successful epidemic lineage, ST258/512.

PMID:
31358985
DOI:
10.1038/s41564-019-0492-8

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