Are Escherichia coli causing recurrent cystitis just ordinary Uropathogenic E. coli (UPEC) strains?

Abstract Specific determinants associated with Uropathogenic Escherichia coli (UPEC) causing recurrent cystitis are still poorly characterized. The aims of this study were (i) to describe genomic and phenotypic traits associated with recurrence using a large collection of recurrent and paired sporadic UPEC isolates, and (ii) to explore within-host genomic adaptation associated with recurrence using series of 2 to 5 sequential UPEC isolates. Whole genome comparative analyses between 24 recurrent cystitis isolates (RCIs) and 24 phylogenetically paired sporadic cystitis isolates (SCIs) suggested a lower prevalence of putative mobile genetic elements (MGE) in RCIs, such as plasmids and prophages. The intra-patient evolution of the 24 RCI series over time was characterized by SNP occurrence in genes involved in metabolism or membrane transport, and by plasmid loss in 5 out of the 24 RCI series. Genomic evolution occurred early in the course of recurrence, suggesting rapid adaptation to strong selection pressure in the urinary tract. However, RCIs did not exhibit specific virulence factor determinants and could not be distinguished from SCIs by their fitness, biofilm formation, or ability to invade HTB-9 bladder epithelial cells. Taken together, these results suggest a rapid but not convergent adaptation of RCIs that involves both strain- and host-specific characteristics. Author summary The recurrence of cystitis is a frequent but poorly understood phenomenon. There are currently many hypotheses trying to explain recurrence, but data on large collections of well-characterized clinical isolates are lacking. In order to identify specific recurrence-associated markers, we conducted a large genomic and phenotypic study involving 48 well-characterized cystitis isolates: 24 recurrent cystitis isolates (RCIs) and 24 pairs of isolates causing sporadic cystitis (SCIs). Moreover, we were able to explore intra-host overtime RCI evolution, by analyzing up to 5 sequential UPEC isolates per RCI series. Our results suggest that RCI rapidly adapt to their host through mobile genetic elements loss and SNP accumulation in genes involved in metabolism and membrane transport. However, no convergent genomic nor phenotypic evolution was observed between isolates collected from distinct patients. Taken together, these results suggest a host-shaped evolution of RCIs, highlighting a need for future studies focused on the host-pathogen relationships.