Complete Genome Sequences of Seven Uropathogenic Escherichia coli Strains Isolated from Postmenopausal Women with Recurrent Urinary Tract Infection

Uropathogenic Escherichia coli (UPEC) is the most common cause of urinary tract infection (UTI). This disease disproportionately affects women and frequently develops into recurrent UTI (rUTI) in postmenopausal women. Here, we report the complete genome sequences of seven UPEC isolates obtained from the urine of postmenopausal women with rUTI.

UPEC strains from postmenopausal women with rUTI are understudied. The availability of complete genomes enables analysis of the mobile genetic elements and resistance genes that complicate the management of rUTI and may inform new treatment strategies. We report the complete genomes of seven UPEC strains (Table 1) isolated from the urine of consenting postmenopausal women meeting criteria for uncomplicated rUTI as part of an institutional review board (IRB)-approved study (STU 032016-006, MR 17-120) (7).
Clean-catch midstream urine was collected from seven subjects and plated onto CHROMagar Orientation (BD) and blood agar media. After overnight incubation at 37°C, well-isolated single colonies were picked for species identification by Sanger sequencing of the 16S rRNA gene and a nonredundant/nucleotide (nr/nt) database query using MegaBLAST (BLAST v2.10.0) (7,8). Identified UPEC isolates were grown in brain heart infusion broth overnight at 37°C, and genomic DNA was extracted using a DNeasy blood and tissue kit (Qiagen).
The genomic DNA, assessed by the 260/280-nm absorbance ratio and agarose gel electrophoresis, was sequenced using Illumina and Oxford Nanopore (ONT) technologies. Illumina library preparation and sequencing were performed using the Nextera DNA Flex library prep kit and the NextSeq 500 system (300 cycles) to generate 2 ϫ 150-bp paired-end reads. ONT libraries were prepared using the ligation sequencing kit (SQK-LSK109) and barcode expansion kit 1-12 (EXP-NBD104); then, they were sequenced on the MinION instrument using R9 FLO-MIN106 flow cells. Live fast base calling, demultiplexing, and barcode trimming were performed using ONT MinKNOW software.
Hybrid assembly enabled the complete resolution of chromosome and plasmid sequences. These data provide insight into the plasmids harbored by diverse rUTI UPEC strains isolated from postmenopausal women.
Data availability. The complete sequences were deposited in GenBank under BioProject accession number PRJNA636382. The BioSample and SRA accession numbers for each isolate can be found in Table 1.