High frequency of acquired virulence factors in carbapenemase-producing Klebsiella pneumoniae isolates from a large German university hospital, 2013-2021

Abstract

Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) isolates are a public health concern as they can cause severe hospital-acquired infections that are difficult to treat. It has recently been shown that CP-Kp can take up virulence factors from hypervirulent K. pneumoniae lineages. In this study, 109 clinical CP-Kp isolates from the University Hospital Cologne were examined for the presence of acquired virulence factors using whole-genome sequencing and phenotypic tests, and results were linked to clinical data. The virulence factor iuc was present in 18/109 of the CP-Kp isolates. Other acquired virulence factors, such as ybt, cbt, iro, rmpA/rmpA2, peg-344, and hypervirulence-associated capsule types were detected in various combinations among these isolates. The iuc-positive isolates produced OXA-232 (n = 7), OXA-48 (n = 6), OXA-48+NDM (n = 3), NDM, and KPC (each n = 1), and 7/18 isolates were resistant to ceftazidime-avibactam, colistin, and/or cefiderocol. Four isolates carried hybrid plasmids that harbored acquired virulence factors alongside the carbapenemase genes bla_NDM-1/5 or bla_OXA-48. In 15/18 patients, iuc-positive CP-Kp were isolated from a clinically manifest infection site. Among these, four patients had osteomyelitis, and four patients died from pneumonia with OXA-232-producing ST231 isolates, three of them as part of an outbreak. In conclusion, acquired virulence factors are frequently detected in various combinations in carbapenemase-producing K. pneumoniae isolates in Germany, warranting continuous monitoring of infections caused by these strains.

Keywords: Klebsiella pneumoniae; aerobactin; carbapenem resistance; carbapenemase; convergence; hypervirulent Klebsiella pneumoniae; multidrug resistance; surveillance; virulence factors.

FIG 1

Minimal inhibitory concentrations (MICs) for last-resort antibiotics of iuc-positive carbapenemase-producing K. pneumoniae isolates from clinical samples at the University Hospital Cologne, Germany, 2013–2021. Interpretation of MICs according to EUCAST breakpoints is colour encoded; red = resistant; yellow = susceptible, increased exposure; green = susceptible, standard dosing regimen. For aztreonam-avibactam, breakpoints for aztreonam were applied. AZA, aztreonam-avibactam; CID, cefiderocol; COL, colistin; CTA, ceftazidime-avibactam; ERT, ertapenem; IMI, imipenem; IMR, imipenem-relebactam; MER, meropenem.

FIG 2

Whole-genome SNP phylogeny, sequence type (ST), presence of carbapenemase genes and genetic hypervirulence markers of iuc-positive carbapenemase-producing K. pneumoniae isolates from clinical samples at the University Hospital Cologne, Germany, 2013–2021. Isolate names are colour-encoded according to their ST type. The presence of a complete hypervirulence gene is indicated by a filled box. The presence of a truncated hypervirulence gene is indicated by an empty box. The tree scale indicates SNPs per aligned genome (80% of the reference genome) in per cent.

FIG 3

Genetic composition of the carbapenemase/hypervirulence hybrid plasmids pKLPN-IUC-12_OXA-48 (a) and pKLPN-IUC-NDM-1 (b). Blue regions show strong sequence homology between the hypervirulence plasmid pK2044 and the hybrid plasmids. Red regions carry the carbapenemase genes. White regions are neither related to a hypervirulence nor a carbapenemase gene environment. Red arrows = genes associated with antibiotic resistance, black arrows = insertion sequences, grey arrows = other genes or open reading frames.