Complete Genome Sequence of a CTX-M-15-Producing Escherichia coli Strain from the H30Rx Subclone of Sequence Type 131 from a Patient with Recurrent Urinary Tract Infections, Closely Related to a Lethal Urosepsis Isolate from the Patient’s Sister

We report here the complete genome sequence, including five plasmid sequences, of Escherichia coli sequence type 131 (ST131) strain JJ1887. The strain was isolated in 2007 in the United States from a patient with recurrent cystitis, whose caregiver sister died from urosepsis caused by a nearly identical strain.

prevalent extraintestinal E. coli lineage (1). Its ST131-H30 sublineage accounts for most E. coli isolates that are fluoroquinolone resistant and produce extended-spectrum ␤-lactamases (ESBLs) (2). Carriage of bla CTX-M-15 is associated with the ST131-H30Rx sublineage within ST131-H30 (3). ST131-H30 is associated with recurrent urinary tract infections, pyelonephritis, and urosepsis (1,(4)(5)(6)(7). We sequenced two E. coli clinical isolates from two adult sisters, one with recurrent E. coli cystitis, and the other with fatal E. coli urosepsis that developed after caring for her sister. We previously reported the complete genome sequence of the deceased sister's fatal E. coli strain (JJ1886), from the ST131-H30Rx sublineage (8). Here, we present the complete genome sequence of the surviving sister's E. coli strain (JJ1887), which is also from ST131-H30Rx and nearly identical to JJ1886. Whether the sisters' distinct clinical outcomes are attributable to host response differences, strain-specific features, or other factors, the JJ1887 genome represents a valuable added resource for understanding the pathogenicity of the ST131-H30Rx lineage.
JJ1887 was sequenced on the PacBio platform (P5-C3 chemistry), which generated 66,442 raw PacBio reads (mean read length, 10,942 bp; total nucleotides, 764,654,567). The PacBio sequence reads were manually error corrected using Illumina short reads (125ϫ coverage, TruSeq chemistry) using CLC Genomics Workbench version 7. The resultant data were assembled using the Hierarchical Genome Assembly Process (HGAP) version 3 in the PacBio single-molecule real-time (SMRT) Portal, which produced a circular chromosome and five closed plasmids, with a mean coverage of 118ϫ. The short-read mapping was further analyzed with Delly (9) and the Northern Arizona SNP Pipeline (NASP) (http://TGenNorth.github.io/NASP). The verified sequences were annotated using Prokka 1.10 (10) and the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Antimicrobial resistance genes were identified using ResFinder 2.1 (11), and phage regions were identified using PHAST (12).
Patricia Stogsdill, Lonny Yarmus, Rob Owens, John Quinn, and Karen Lolans facilitated the provision of E. coli JJ1887 and associated clinical data. Computational resources for PacBio assembly were provided through the Minnesota Supercomputing Institute.
The opinions presented here are those of the authors and do not represent the official policy or position of the U.S. Government or any of its agencies.

FUNDING INFORMATION
This work, including the efforts of James R. Johnson, was funded by Office of Research and Development, Medical Research Service, Department of Veterans Affairs (1I01CX000192). This work, including the efforts of Maliha Aziz and Lance B. Price, was funded by TGEN Foundation. This work, including the efforts of Lance B. Price, was funded by USAMRMC. This work, including the efforts of Paal Skytt Andersen, was funded by Statens Serum Institut. This work, including the efforts of Lance B. Price, was funded by USAMRMC (W81XWH-10-1-0753). This work, including the efforts of Evgeni Sokurenko and James R. Johnson, was funded by HHS | National Institutes of Health (NIH) (RC4-AI092828). This work, including the efforts of Evgeni Sokurenko, was funded by HHS | National Institutes of Health (NIH) (R01AI106007). This work, including the efforts of Paal Skytt Andersen, was funded by Augustinus Fonden (Augustinus Foundation).