Personalised genomic investigation reveals strain heterogeneity during chronic infection with E. coli ST131: The complete genome of E. coli ST131 Str. U15A

Recurrent urinary tract infections (rUTI) are extremely common, with ~25% of all women who suffer an initial UTI experiencing a recurrence within one year of the original infection. rUTI often occurs when bacteria from the initial infection persist after treatment. Escherichia coli ST131 is a major contributor to hospital and community acquired UTI and is strongly associated with limited treatment options and high rates of recurrence. Here, using a combination of both short and long read sequencing technologies we examined the dynamics of an E. coli ST131 population isolated over a 5-year period (2012-2016) from the urine and feces of a single individual. This longitudinal study provides the first comprehensive, in vivo, genomic analysis of a clonal lineage within a single individual and serves as a valuable resource for understanding how plasmid dynamics contribute to pathogen evolution in a chronic long-term infection.