Genomic analysis of antibiotic resistance and virulence factors in the uropathogen Citrobacter koseri

Citrobacter koseri is a significant bacterial cause of community-acquired urinary tract infections in female college students. Given limited previous attention to genomic analysis and molecular epidemiology of this species, whole-genome sequencing was carried out for eight uropathogenic C. koseri clinical isolates. Six complete and two draft assemblies are presented. Genome organization was largely conserved between isolates, and comparative analysis with archived genomes suggests that more than 90% of C. koseri genes are conserved across the species. These isolates contained relatively few mobile genetic elements (plasmids, prophage, transposons and insertion elements) and extensive antiphage defence systems. Other than a single conserved chromosomal β-lactamase gene, little or no acquired antibiotic resistance was observed. Clues to urovirulence were sought among genes conserved in C. koseri but not found in other Citrobacter genomes, suggesting roles for iron acquisition, motility and adhesion.