word count: 395 20 Text word count: 5300 21 22 2 Abstract 23Most urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC), 24 which depend on an extracellular organelle (Type 1 pili) for adherence to bladder cells during 25 infection. Type 1 pilus expression is partially regulated by inversion of a piece of DNA referred 26 to as fimS, which contains the promoter for the fim operon encoding Type 1 pili. fimS inversion is 27 regulated by up to five recombinases collectively known as Fim recombinases. These Fim 28 recombinases are currently known to regulate two other switches: the ipuS and hyxS switches. A 29 long-standing question has been whether the Fim recombinases regulate the inversion of other 30 switches, perhaps to coordinate expression for adhesion or virulence. We answered this question 31 using whole genome sequencing with a newly developed algorithm (Structural Variation 32 detection using Relative Entropy, SVRE) for calling structural variations using paired-end short 33 read sequencing. SVRE identified all of the previously known switches, refining the specificity 34 of which recombinases act at which switches. Strikingly, we found no new inversions that were 35 mediated by the Fim recombinases. We conclude that the Fim recombinases are each highly 36 specific for a small number of switches. We hypothesize that the unlinked Fim recombinases 37 have been recruited to regulate fimS, and fimS only, as a secondary locus; this further implies that 38 regulation of Type 1 pilus expression (and its role in gastrointestinal and/or genitourinary 39 colonization) is important enough, on its own, to influence the evolution and maintenance of 40 multiple additional genes within the accessory genome of E. coli. 41 42 Importance 43UTIs are a common ailment that affects more than half of all women during their lifetime. The 44 leading cause of UTIs is UPEC, which rely on Type 1 pili to colonize and persist within the 45 3 bladder during infection. The regulation of Type 1 pili is remarkable for an epigenetic 46 mechanism in which a section of DNA containing a promoter is inverted. The inversion 47 mechanism relies on what are thought to be dedicated recombinase genes; however, the full 48 repertoire for these recombinases is not known. We show here that there are no additional targets 49 beyond those already identified for the recombinases in the entire genome of two UPEC strains, 50 arguing that Type 1 pilus expression itself is the driving evolutionary force for the presence of 51 these recombinase genes. This further suggests that targeting the Type 1 pilus is a rational 52 alternative non-antibiotic strategy for the treatment of UTI. 53 54 Introduction 55Uropathogenic Escherichia coli (UPEC) are the primary cause of urinary tract infections 56 (UTIs) (1, 2), which are estimated to affect more than half of all women during their lifetime (3).
57The total annual cost of community-acquired and nosocomial UTIs in the United States was 58 estimated to be $2 billion in 1995 (3). Altho...