Draft Genome Sequence of a Canine Uropathogenic Escherichia coli Strain Isolated in New Zealand

Urinary tract infections (UTIs) affect about 150 million people each year, and uropathogenic Escherichia coli (UPEC) is the major causative agent (1). It was shown that UPEC isolates obtained from dogs with cystitis are able to invade human bladder epithelial cells and cause cytotoxicity, which emphasizes the zoonotic risk of canine UPEC isolates (2). In this report, we present the draft genome sequence of the isolate UPEC P50, which was isolated from a dog (12-year-old bull terrier) within a routine UTI diagnosis. This strain was isolated by culturing urine on MacConkey/sheep blood agar and identified as E. coli based on colony morphology on chromogenic UTI agar and using a Microbact 12A biochemical identification strip (Oxoid).

The genomic DNA was extracted from the overnight culture in 2xYT medium using the UltraClean microbial DNA isolation kit (Qiagen). The DNA sample was then submitted to the Massey Genome Service (Massey University, Palmerston North, New Zealand) for whole-genome shotgun sequencing using Illumina TruSeq Nano DNA library preparation and 2 × 300-base paired-end (PE) v3 sequencing on the Illumina MiSeq platform. The sequencing run generated 1,469,340 paired-end reads. The raw reads were trimmed to a quality cutoff value of Q30, and the short-length reads (<25 bases by default) were removed using SolexaQA⁺⁺ v3.1.7.1 (3). After quality trimming, 1,303,860 paired-end reads with an average length of 200 bases per read were used for genome assembly, equivalent to 50× coverage for the draft genome. De novo assembly was performed with SPAdes v3.13.0 in the --careful mode (4). The gaps in the contigs were filled using GapFiller v1.10 with default parameters (5). Any contigs having a high identity with the phiX (ΦX174) sequence or Homo sapiens sequences were removed. The P50 draft genome was then annotated using the NCBI Prokaryotic Genome Annotation Pipeline (6). The genome assembly metrics were obtained using QUAST v5.0.1 with default parameters (7). Overall, the UPEC P50 draft genome is 5,155,240 bp long with 5,247 genes, and the GC content is 50.41%. There are 246 contigs with an N₅₀ value of 314,239 bp, and the largest contig has 651,995 bp.

In silico analysis of the draft genome with SerotypeFinder server v2.0 (8), VirulenceFinder server v2.0 (9), and PathogenFinder server v1.1 (10) with default settings indicated that UPEC P50 has the O2:H1 serotype, possesses at least 10 virulence genes, including cnf1, ireA, iroN, iss, mchB, mchC, mchF, mcmA, pic, and vat, and has a high probability (P = 0.936) of causing human infections.

The UPEC P50 strain can be used as a model organism for studying the pathogenesis of UTIs and the genetics of biofilm formation and as a target for developing antibiotic therapies for treating UTIs and antibiotic-coated urinary catheters. The draft genome sequence of UPEC P50 would facilitate any precise genetic manipulation to support such types of research.

We thank New Zealand Veterinary Pathology Ltd. (Palmerston North, New Zealand) for isolating the E. coli P50 strain.