The Potential Roles of Prophages in the Pathogenicity of Klebsiella pneumoniae Strains from Kenya

<b>Background/Objectives:</b> Antimicrobial resistance (AMR) in <i>Klebsiella pneumoniae</i> poses a serious threat to healthcare, especially in sub-Saharan Africa (SSA). To complement AMR infection control in Kenya, here, clinical and environmental genomes were investigated to determine the potential roles prophages play in <i>K. pneumoniae</i> pathogenicity. <b>Methods:</b> Prophages were extracted from 89 Kenyan <i>K. pneumoniae</i> genomes. The intact prophages were examined for virulence genes carriage, and their phylogenetic relationships were established. <b>Results:</b> Eighty-eight (~99%) of the genomes encode at least a single prophage, and there is an average of four prophages and 2.8% contributory genomes per bacterial strain. From the 364 prophages identified, 250 (68.7%) were intact, while 58 (15.9%) and 57 (15.7%) were questionable and incomplete, respectively. Approximately, 30% of the intact prophages encode 38 virulence genes that are linked to iron uptake (8), regulation (6), adherence (5), secretion system (4), antiphagocytosis (4), autotransporter (4), immune modulation (3), invasion (2), toxin (1) and cell surface/capsule (1). Phylogenetic analyses revealed three distinct clades of the intact prophages irrespective of their hosts, sources and locations, which support the plasticity of the genomes and potential to mediate horizontal gene transfer. <b>Conclusions:</b> This study provides first evidence showing the diverse prophages that are encoded in <i>K. pneumoniae</i> from SSA with particular focus on Kenyan strains. This also shows the potential roles these prophages play in the pathogenicity and success of <i>K. pneumoniae</i> and could improve knowledge and complement control strategies in the region and across the globe. Further work is needed to show the expression of these genes through lysogenisation.