Unlocking the Secrets of Urine Survival: an exploration of bacterial genetic adaptations

Abstract

Urinary tract infections (UTIs) are one of the most common bacterial infections and can be caused by a diverse range of bacterial species. Here we studied the relatedness and changes in gene presence and absence profiles of five species with uropathogenic potential, Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Enterococcus faecalis and Staphylococcus haemolyticus, in UTI and healthy states. Relatedness was analysed using k-mer-based, 16s and core genome phylogenies, showing no indication of relatedness between these species in the urinary tract. To analyse the potential functional changes in bacteria isolated from the urinary tract, we constructed a pan-genome for each species, revealing gene clusters unique to urine-derived strains. These unique gene clusters are involved in pathways known to increase bacterial virulence in the urinary tract as well as genes attributed to antibiotic resistance. In addition to individual genes and metabolic pathways, we analysed potential functional changes in gene clusters predicted to encode metabolites that are non essential for bacterial growth. While no clusters were found to be unique to urine-derived strains, several were enriched for their presence in urine-derived strains and were predicted to facilitate competition between bacteria in the urinary tract. Preliminary analysis of the presence and absence of metabolites before and after bacterial growth revealed a potential for nutrient competition for amino acids. Together, these findings show unique adaptations of bacteria living within the urinary tract, with functions influencing virulence and antibiotic resistance.