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

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.

Figure 1. Geographical distribution of carbapenem resistance mechanisms amongst isolates submitted during the EuSCAPE survey.

a, Total number of isolates submitted by participating countries that were analysed in this study. Isolates are partitioned into those that possess one or more of four major carbapenemase genes (bla_KPC-like, bla_OXA-48-like, bla_NDM-like and bla_VIM-like) regardless of whether they were submitted as carbapenem-non-susceptible or -susceptible, those which lack any of the four genes that were submitted as carbapenem-non-susceptible (“Other mechanism”), and those submitted as carbapenem-susceptible. b, Pie charts representing the proportion of isolates submitted as carbapenem-non-susceptible from participating hospitals with different resistance mechanisms as in a.

Figure 2. Carbapenemase-positive isolates are concentrated in major clonal lineages of K. pneumoniae.

a, Phylogenetic tree of 1717 EuSCAPE isolates analysed in this study, constructed using 2539 core genes, demonstrates division into four species. b, Phylogenetic tree of 1649 isolates belonging to K. pneumoniae sensu stricto with STs containing more than 20 isolates shown in the inner ring and labelled. The outer ring colours isolates by resistance mechanism as in Figure 1a. The scale in both trees represents the number of SNPs per variable site. Similar visualisations are available at: https://microreact.org/project/EuSCAPE_Kp/bc81fffe (a) and https://microreact.org/project/EuSCAPE_Kp/2585de34 (b)

Figure 3. Carbapenemase-positive isolates show strong geographical clustering.

a, Barplots show the distribution of minimum inhibitory concentration (MIC) values amongst 1518 re-tested K. pneumoniae sensu stricto isolates with different beta-lactam resistance determinants. b, Barplots show the proportion of genetically nearest neighbours (gNNs) for K. pneumoniae sensu stricto isolates with different beta-lactam resistance determinants that are from different geographic contexts (the same hospital, a different hospital in the same country, or a hospital in a different country). The black error bars represent 95% confidence intervals (CI) of these proportions. The proportions of gNNs in the absence of geographic structure were calculated from 100 repeat analyses in which the hospital codes were randomly permutated, and the mean and 95% CI of these results are shown in red.

Figure 4. Determination of a SNP cut-off to aid outbreak investigations of ST258/512.

a-c, Number of core chromosomal SNPs between each of 236 ST258/512 isolates submitted during EuSCAPE and the most closely related isolate submitted by the same hospital (a), a different hospital in the same country (b), and a hospital in a different country (c). d-e, Number of SNPs between each ST258/512 isolate and the most closely related isolate submitted by the same hospital, when isolates are predicted to have been involved in intra-hospital (d) or inter-hospital (e) transmission. The dotted lines are drawn at the number of SNPs whereby the combined false positive and negative rates for correctly identifying intra-hospital transmission, calculated using the predictions as the reference, are at a minimum. f, False positive and negatives rates when different SNP cut-offs are used.

Figure 5. International spread of the epidemic ST258/512 clone.

a, Phylogenetic tree of 651 isolates of ST258 and 512 (and a derivative of ST512, ST868), comprising 236 isolates submitted during the EuSCAPE survey and 415 isolates with publicly available sequence data. The tree was rooted using an ST11 isolate that was later removed. The isolate tips are coloured by the country of isolation, and metadata columns show the bla_KPC-like variant and capsule (K-) type. b, An unrooted version of the same tree as in A. Similar visualisations are available at: https://microreact.org/project/EuSCAPE_ST258/bbafcc1c (a) and https://microreact.org/project/EuSCAPE_ST258/dd960284 (b).