Within-host evolution of Klebsiella spp. from intestinal carriage to bacteremia

Abstract

Gut colonization by the Gram-negative bacillus Klebsiella pneumoniae is a significant risk factor for extra-intestinal infections. However, the mechanisms by which this opportunistic pathogen causes disseminated infections remain poorly understood. To investigate this phenomenon, 22 strain pairs of Klebsiella spp. were sequentially isolated from rectal swabs and blood samples of ICU patients. All strains adhered to intestinal epithelial cells in vitro, but failed to invade or disrupt epithelial barrier integrity. Few phenotypic differences between strains of the same pair were observed regarding their biofilm-forming capacities and ampicillin resistance. Whole genome sequencing of five pairs showed diverse sequence types, the presence of numerous antibiotics resistance genes but few virulence genes. Pairwise comparison of genomic sequences of blood and fecal isolates evidenced a few single nucleotide polymorphisms and small insertions-deletions, mostly affecting genes involved in biosynthesis of surface structures (such as capsules, pili). Most genetic changes were driven by horizontal gene transfer events, with the notable acquisition of a plasmid that enhanced bacterial fitness by eliminating competitors. In addition, some blood isolates had reduced the number of antibiotic resistance genes, underscoring the high plasticity of the Klebsiella resistome. Finally, one bloodstream isolate carried a mutS mutation, conferring a hypermutator phenotype that could increase evolvability despite the fitness burden. Together, these findings indicate that within-host genetic adaptations, rather than the acquisition of virulence traits, can enhance the colonization, competitiveness and ultimately the ability of K. pneumoniae to cause invasive infections. ImportanceKlebsiella commonly colonizes the human gut, and this carriage can progress to infections, particularly in intensive care unit (ICU) patients. To better understand the in vivo evolution, genetically associated Klebsiella strains isolated from the feces and blood of ICU patients were analyzed. Although strains were able to adhere to intestinal cells, none could invade or damage the intestinal barrier. Genomic comparisons of pairs strains showed limited genetic differences, mostly mutations affecting surface structures. Frequent horizontal gene transfer events were observed, which could improve bacterial competitiveness and permits a remarkably flexible resistome. Overall, this study shows that within-host evolution, rather than the gain of virulence traits, can enhance the ability of Klebsiella to persist, outcompete other bacteria, and ultimately cause infections.