Characterization of a carbapenemase-producing Klebsiella pneumoniae isolate of a patient in an intensive care unit in Greece: A study of resistome, virulome, and mobilome

Klebsiella pneumoniae is a major pathogen associated with hospital-acquired infections, particularly those involving multidrug-resistant strains. Carbapenem resistance, often driven by carbapenemases such as KPC, VIM, OXA-48, and NDM, poses a significant challenge in clinical settings. This study reports on K. pneumoniae strain A165, isolated from a blood culture of a 51-year-old female patient hospitalized for respiratory distress post-SARS-CoV-2 infection. This K. pneumoniae strain exhibited resistance to several antibiotics, including carbapenems, cephalosporins, aminoglycosides, and fluoroquinolones, but remained susceptible to gentamicin, colistin, and trimethoprim-sulfamethoxazole. Next-generation sequencing was performed on Ion torrent platform, that revealed a genome size of 5,676,404 bp, including a chromosome and six plasmids. The strain was classified as sequence type 11 (ST11), a high-risk lineage associated with carbapenem resistance. The resistome of A165 included multiple beta-lactamase genes, such as blaNDM-1 and blaOXA-48, as well as genes conferring resistance to other antibiotic classes. The virulome analysis identified genes involved in iron acquisition (yersiniabactin operon genes: ybtE, ybtT, irp1, irp2; aerobactin receptor: iutA), adhesion (mrkA-J, fimA-K), capsule and biofilm formation (rcsA, rcsB, ompA) and resistance to complement (traT) contributing to its pathogenic potential. The mobilome analysis revealed nine insertion sequences, including ISKpn1, ISKpn18, ISKpn43, ISKpn28, ISKpn14, ISEcp1, and IS6100. The strain also harbored six replicons: Col440II, ColRNAI, IncFIA(HI1), IncFIB(K), IncFII(K), and IncR, which are associated with the horizontal transfer of resistance and virulence genes. Comparative analysis with global isolates demonstrated the widespread dissemination of carbapenemase-producing K. pneumoniae, with notable occurrences in Europe, Asia, and the Americas. This study highlights the growing concern of multidrug-resistant K. pneumoniae in hospital settings and emphasizes the need for robust surveillance and infection control measures.