The Association between Resistance and Virulence of Klebsiella pneumoniae in High-Risk Clonal Lineages ST86 and ST101

Abstract

Klebsiella pneumoniae is an opportunistic pathogen known for two main pathotypes: classical K. pneumoniae (cKp), often multidrug-resistant and common in hospitals, and hypervirulent K. pneumoniae (hvKp), associated with severe community-acquired infections. The recent emergence of strains combining hypervirulence and resistance is alarming. This study investigates the distribution of sequence types (STs), resistance, and virulence factors in K. pneumoniae strains causing bloodstream and urinary tract infections in Croatia. In 2022, 200 consecutive K. pneumoniae isolates were collected from blood and urine samples across several Croatian hospitals. Whole genome sequencing was performed on 194 isolates. Within the analyzed K. pneumoniae population, the distribution of sequence types was determined with multi-locus sequence typing (MLST) and capsule loci, resistance, and virulence determinants were assessed with the bioinformatics tool Kleborate. The analysis identified 77 different STs, with ST101 (24.6%) being the most prevalent, predominantly linked to the K17 capsular type (CT), invasive device usage, high antimicrobial resistance, and low virulence scores. The highest virulence scores were recorded in ST86 isolates, which were predominantly linked to the K2 CT and included some strains with medium resistance scores. String tests were positive in 19 strains, but only four of those harbored hypermucoviscous genetic determinants. The most prevalent ST101 clone in Croatia demonstrated a diverging association between resistance and virulence. An alarming co-existence of resistance and virulence was recorded in the ST86 strains.

Keywords: Klebsiella pneumoniae; hypervirulence; resistance factors; virulence factors.

Figure 1

Neighbor-Joining tree based on a cgMLST distance matrix of 183 K. pneumoniae genomes, with annotations as shown in the figure legend. Resistance and virulence scores are represented by inner blue and outer red bar plots, respectively, with size and color indicating score variations. Sequence types are shown in the inner-colored strip, while the outer color strip displays capsular types. The presence of invasive devices and sample types are denoted by a binary box data frame. Yellow asterisk marks the ST290 strain, detected in two isolates.

Figure 2

The analysis of the 19 K. pneumoniae isolates that tested positive for the string test. Black squares indicate the presence of virulence and resistance determinants.