Evaluation of Klebsiella pneumoniae pathogenicity through holistic gene content analysis

<i>Klebsiella pneumoniae</i> is a Gram-negative bacterium that causes both community- and healthcare-associated infections. Although various virulence factors and highly pathogenic phenotypes have been reported, the pathogenicity of <i>K. pneumoniae</i> is still not fully understood. In this study, we utilized whole-genome sequencing data of 168 clinical <i>K. pneumoniae</i> strains to assess pathogenicity. This work was based on the concept that the genetic composition of individual genomes (referred to as holistic gene content) of the strains may contribute to their pathogenicity. Holistic gene content analysis revealed two distinct groups of <i>K. pneumoniae</i> strains ('major group' and 'minor group'). The minor group included strains with known highly pathogenic clones (ST23, ST375, ST65 and ST86). The minor group had higher rates of capsular genotype K1 and presence of nine specific virulence genes (<i>rmpA</i>, <i>iucA</i>, <i>iutA</i>, <i>irp2</i>, <i>fyuA</i>, <i>ybtS</i>, <i>iroN</i>, <i>allS</i> and <i>clbA</i>) compared to the major group. Pathogenicity was assessed using <i>Galleria mellonella</i> larvae. Infection experiments revealed lower survival rates of larvae infected with strains from the minor group, indicating higher virulence. In addition, the minor group had a higher string test positivity rate than the major group. Holistic gene content analysis predicted possession of virulence genes, string test positivity and pathogenicity as observed in the <i>G. mellonella</i> infection model. Moreover, the findings suggested the presence of as yet unrecognized genomic elements that are either involved in the acquisition of virulence genes or associated with pathogenicity.