Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1

Abstract

Urinary tract infections (UTIs) are among the most common infections in humans, predominantly caused by uropathogenic Escherichia coli (UPEC). The diverse genomes of UPEC strains mostly impede disease prevention and control measures. In this study, we comparatively analyzed the whole genome sequence of a highly virulent UPEC strain, namely UPEC 26-1, which was isolated from urine sample of a patient suffering from UTI in Korea. Whole genome analysis showed that the genome consists of one circular chromosome of 5,329,753 bp, comprising 5064 protein-coding genes, 122 RNA genes (94 tRNA, 22 rRNA and 6 ncRNA genes), and 100 pseudogenes, with an average G+C content of 50.56%. In addition, we identified 8 prophage regions comprising 5 intact, 2 incomplete and 1 questionable ones and 63 genomic islands, suggesting the possibility of horizontal gene transfer in this strain. Comparative genome analysis of UPEC 26-1 with the UPEC strain CFT073 revealed an average nucleotide identity of 99.7%. The genome comparison with CFT073 provides major differences in the genome of UPEC 26-1 that would explain its increased virulence and biofilm formation. Nineteen of the total GIs were unique to UPEC 26-1 compared to CFT073 and nine of them harbored unique genes that are involved in virulence, multidrug resistance, biofilm formation and bacterial pathogenesis. The data from this study will assist in future studies of UPEC strains to develop effective control measures.

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Acknowledgements

This work was supported by research fund of Chungnam National University (2015). Also, it was supported by Chungnam National University Hospital Research Fund, 2013.

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Correspondence to Man Hwan Oh or Chul Hee Choi.

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Subhadra, B., Kim, D.H., Kim, J. et al. Complete genome sequence of uropathogenic Escherichia coli isolate UPEC 26-1. Genes Genom 40, 643–655 (2018). https://doi.org/10.1007/s13258-018-0665-5

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Keywords

  • UPEC
  • UTI
  • Genome annotation
  • Genome sequencing
  • Genomic islands
  • Pathogenic genes