ALTAR: Uro-associated E. coli Long-Read Genome Analysis. ALTAR_SHRT_Ecoli

The Clinical trial ALTAR, aimed to determine that the non-antibiotic treatment methenamine hippurate in female recurrent UTI patients was not inferior to daily antibiotics. The outcome of ALTAR suggested that while the methenamine Hippurate group had a marginally higher rate of UTI episodes compared to a prophylactic antibiotic group (1.38 versus 0.89 UTI episodes) the absolute difference, 0.49 episodes per year, was of limited clinical consequence. The criteria used to choose 191 E. coli isolates from ALTAR for genome analysis included: i) date matched swab and urine associated isolates; ii) 2+ temporal urine associated isolates per patient; and/or 3) temporal perineal swab isolates that included a baseline E. coli isolate. This generated a data set that represented 145 colon-derived and 46 urine-associated E. coli isolates found in PRJEB85317. The 46 urine-associated isolates were further sequenced using long read technology alongside 46 trimethoprim resistant colon-derived isolates.