Comparative genomics of hypervirulent Klebsiella pneumoniae isolates from Brazil

Klebsiella pneumoniae represents a major public health threat at the convergence of antimicrobial resistance and hypervirulence. While classical K. pneumoniae (cKp) is a leading cause of healthcare-associated infections, hypervirulent K. pneumoniae (hvKp) causes severe invasive disease in otherwise healthy individuals. We performed a comparative genomic analysis of hvKp (n = 8) and cKp (n = 17) isolates recovered in Salvador, Brazil. The eight Brazilian hvKp isolates displayed the canonical hypervirulence genotype, encoding the five major biomarkers (iroB, iucA, peg-344, rmpA, and rmpA2) while carrying only a limited repertoire of intrinsic antimicrobial resistance genes. These isolates belonged to sequence types ST23, ST65, ST86, ST3690, and ST5750 and were associated with K1 or K2 capsular types and the O1 antigen. In three isolates, iroB was detected in both chromosomal and plasmid-associated regions, a dual localization reported at low frequency among hvKp. The predominant plasmid replicons were IncHI1B (pNDM-MAR) and repB_KLEB, with IncFIB (K) in two isolates. Screening for mobile genetic elements recovered an F-type conjugative transfer locus in these two isolates only. Chromosomes and plasmids showed high similarity with well-characterized reference hvKp strains, including SGH10 and NTUH-K2044, as well as the pLVPK virulence plasmid. Comparative proteomics analysis identified 53 protein clusters conserved across hvKp strains examined. Among these were four hypothetical proteins previously associated with invasive liver infection, containing DUF1471, DUF417, and carboxymuconolactone decarboxylase-related domains, suggesting potential roles in pathogenicity. Collectively, these findings expand current knowledge of hvKp genetic diversity in Salvador, Brazil and highlight genomic features that may contribute to the emergence and maintenance of the hypervirulent phenotype.