Genomic insights into virulence and antimicrobial resistance of Klebsiella pneumoniae ST25

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Abstract
Here, we described the resistome and virulome of worldwide K. pneumoniae ST25 (Kp-ST25) genomes and established their phylogenetic relationship. Out of a collection of 32 KPC-2-producing Kp-ST25 recovered in Argentina during 2015–2017, eight isolates were selected for whole-genome sequencing (WGS). Additionally, 256 Kp-ST25 genomes were downloaded from NCBI. Bioinformatic analysis was carried out using Unicycler, PROKKA, and Quast. Resistome and virulome were inspected using Kleborate, AMRFinderPlus, BACMET, and VFDB. Phylogenetic estimation included a core genome SNP-based analysis carried out using Roary and IQ-TREE. The tree was visualized using Microrreact. The capsular type K2 was detected in 98% of Kp-ST25 genomes. LPS O1 ab was the most prevalent, followed by O2 afg and O3/O3 a . Most isolates carried the yersiniabactin coding gene, while aerobactin, salmochelin, and RmpADC coding genes were less common. Resistome includes multiple genes for aminoglycosides and quinolones resistance, while 23% of Kp-ST25 harbored carbapenemase-encoding genes ( bla KPC-2,-3 ; bla NDM-1,-4,-7 ; bla OXA-48,-181,-232 ). In 37% of Kp-ST25, ESBL-encoding genes ( bla CTX-M-2,-15 , bla SHV-12 ) were detected as the only acquired bla marker. Phylogeny revealed two clades. Clade A is smaller and more virulent, and Clade B is larger and more diverse in virulence and resistance features. Argentinian isolates fall within clade B, showing high resistance and moderate virulence, except one isolate, which displays higher virulence. Furthermore, the Kp-ST25 lineage exhibited intermediate virulence and resistance levels in the genomic analysis. IMPORTANCE: Hypervirulent K. pneumoniae (hv Kp ) strains cause invasive infections in both healthy and immunocompromised individuals, displaying a more virulent phenotype than classical strains. Apart from lipopolysaccharides (LPSs) and fimbriae, hv Kp can present a hypermucoid phenotype due to K1, K2, or K5 polysaccharide capsule and acquired virulence factors encoding the siderophores yersiniabactin (Ybt), aerobactin (Iuc), and salmochelin (Iro), as well as the genotoxin colibactin (Clb). Furthermore, hv Kp is becoming increasingly resistant to antibiotics, rendering infection by these strains very challenging to treat. Most of the hv Kp isolates belong to sequence types ST23, ST25, ST65, and ST86. Among these, K. pneumoniae ST25 was first detected in Argentina in a surveillance study during 2015–2017. These isolates displayed resistance to carbapenems, one of the last-resort antibiotics for Gram-negative complicated hospital infections. The present study contributes to the knowledge of the virulence, resistance, and phylogeny of K. pneumoniae ST25 isolated in Argentina, along with others recovered worldwide.
Funding Information
  • Universidad de Buenos Aires (UBACyT 20020190100031BA)
  • Universidad de Buenos Aires (UBACyT 20020170100473BA)
  • Consejo Nacional de Investigaciones Científicas y Técnicas (PIP 11220200102425CO)
  • Consejo Nacional de Investigaciones Científicas y Técnicas (PIBAA 28720210100671CO)
  • Agencia Nacional de Promoción Científica y Tecnológica (PICT 2021-GRF-TII-00309)
  • Universidad de Buenos Aires (PIDAE 2025 RESCS-2024-1909 No 5184)

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