Genomic analysis of the initial dissemination of carbapenem-resistant Klebsiella pneumoniae clones in a tertiary hospital

Abstract

Carbapenem-resistant Klebsiella pneumoniae is a major cause of hospital-acquired infections and the fastest-growing pathogen in Europe. Carbapenem resistance was detected at the Consorcio Hospital General Universitario de Valencia (CHGUV) in early 2015, and there has been a significant increase in carbapenem-resistant isolates since then. In this study, we collected carbapenem-resistant isolates from this hospital during the period of increase (from 2015 to 2019) and studied how K. pneumoniae carbapenem-resistant isolates emerged and spread in the hospital. A total of 225 isolates were subjected to whole-genome sequencing with Illumina NextSeq. We characterized the isolates by identifying lineages and antimicrobial resistance genes and plasmids, especially those related to reduced carbapenem susceptibility. Our findings show that the initial carbapenem resistance emergence and dissemination at the CHGUV occurred during a short period of 1 year. Furthermore, it was complex, involving six different lineages of types ST307, ST11, ST101 and ST437, different resistance-determinant factors, including OXA-48, NDM-1, NDM-23 and DHA-1, and different plasmids.

Keywords: Klebsiella pneumoniae; carbapenem resistance; plasmids; surveillance.

Fig. 1.

(a) Isolate distribution in Carba-R groups and STs. Dots in the central plot and bars in the upper barplot are coloured by ST, while bars in the right barplot are coloured by Carba-R group. (b) Distribution of the different Carba-R genes found in group 1. Bars are coloured by ST.

Fig. 2.

Maximum-likelihood phylogenetic tree of the K. pneumoniae isolates collected at the CHGUV from 2015 to 2018. The tree was constructed from the core genome (90%) alignment (3 570 188 bp) of the 224 isolates. STs, capsular loci, Carba-R groups and the presence of bla _OXA-48 and bla _NDM genes are shown.

Fig. 3.

The proportion of isolates in each Carba-R group and sublineage that (a) showed phenotypic resistance to each antimicrobial tested, (b) carried the antimicrobial resistance genes identified and (c) harboured any of the plasmid incompatibility groups detected.

Fig. 4.

Maximum-likelihood phylogenetic trees (and length of the alignments used) for the (a) ST11 (4 081 060 bp), (b) ST307 (4 461 655 bp), (c) ST101 (4 278 965 bp) and (d) ST437 (4 346 386 bp) isolates from the CHGUV and downloaded from GenBank with Spanish origin.

Fig. 5.

Maximum-likelihood phylogenetic trees for plasmids carrying carbapenemase genes (a) bla _OXA-48 (61 881 bp) and (b) bla _NDM-like (97 784 bp).

Fig. 6.

Distribution of Carba-R groups in each lineage throughout the sample collection period.