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.
Similar content being viewed by others
References
Alikhan NF, Petty NK, Ben Zakour NL, Beatson SA (2011) BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons. BMC Genom 12:402
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410
Alva V, Nam SZ, Söding J, Lupas AN (2016) The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis. Nucleic Acids Res 44:W410–W415
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, Formsma K, Gerdes S, Glass EM, Kubal M et al (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genom 9:75
Bergsten G, Wullt B, Svanborg C (2005) Escherichia coli, fimbriae, bacterial persistence and host response induction in the human urinary tract. Int J Med Microbiol 295:487–502
Brenner DJ (1984) Family I. Enterobacteriaceae Rahn 1937, Nom. fam. cons. Opin. 15, Jud. Com. 1958, 73; Ewing, Farmer, and Brenner 1980, 674; Judicial Commission 1981, 104. In: Krieg NR, Holt JG (eds) Bergey’s manual of systematic bacteriology, 1st edn. The Williams & Wilkins Co., Baltimore, pp 408–420
Cloud-Hansen KA, Peterson SB, Stabb EV, Goldman WE, McFall-Ngai MJ, Handelsman J (2006) Breaching the great wall: peptidoglycan and microbial interactions. Nat Rev Microbiol 4:710–716
Delcher AL, Bratke KA, Powers EC, Salzberg SL (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23:673–679
Dhillon BK, Laird MR, Shay JA, Winsor GL, Lo R, Nizam F, Pereira SK, Waglechner N, McArthur AG, Langille MG et al (2015) IslandViewer 3: more flexible, interactive genomic island discovery, visualization and analysis. Nucleic Acids Res 43:W104–W108
Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32:1792–1797
Escherich T (1886) Die Darmbakterien des Säuglings und ihre Beziehungen zur Physiologie der Verdauung. Ferdinand Enke, Stuttgart, pp 63–74
Farshad S, Ranjbar R, Japoni A, Hosseini M, Anvarinejad M, Mohammadzadegan R (2012) Microbial susceptibility, virulence factors, and plasmid profiles of uropathogenic Escherichia coli strains isolated from children in Jahrom, Iran. Arch Iran Med 15:312–316
Foxman B (2010) The epidemiology of urinary tract infection. Nat Rev Urol 7:653–660
Foxman B, Brown P (2003) Epidemiology of urinary tract infections: transmission and risk factors, incidence, and costs. Infect Dis Clin North Am 17:227–241
Fukiya S, Mizoguchi H, Tobe T, Mori H (2004) Extensive genomic diversity in pathogenic Escherichia coli and Shigella Strains revealed by comparative genomic hybridization microarray. J Bacteriol 186:3911–3921
Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57
Käll L, Krogh A, Sonnhammer EL (2007) Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server. Nucleic Acids Res 35:W429–W432
Kim DH, Choi CH (2017) Clonal and Virulence distribution of Uropathogenic Escherichia coli Isolated from Children in Korea. J Bacteriol Virol 7:54–63
Kim YC, Tarr AW, Penfold CN (2014) Colicin import into E. coli cells: a model system for insights into the import mechanisms of bacteriocins. Biochim Biophys Acta 1843:1717–1731
Kulkarni R, Dhakal BK, Slechta ES, Kurtz Z, Mulvey MA, Thanassi DG (2009) Roles of putative type II secretion and type IV pilus systems in the virulence of uropathogenic Escherichia coli. PLoS One 4:e4752
Kurtz S, Phillippy A, Delcher AL, Smoot M, Schumway M, Antonescu C, Salzberg SL (2004) Versatile and open software for comparing large genomes. Genome Biol 5:R12
Lagesen K, Hallin P, Rodland EA, Staerfeldt HH, Rognes T, Ussery DW (2007) RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res 35:3100–3108
Lee JH, Subhadra B, Son YJ, Kim DH, Park HS, Kim JM, Koo SH, Oh MH, Kim HJ, Choi CH (2016) Phylogenetic group distributions, virulence factors and antimicrobial resistance properties of uropathogenic Escherichia coli strains isolated from patients with urinary tract infections in South Korea. Lett Appl Microbiol 62:84–90
Lloyd AL, Rasko DA, Mobley HL (2007) Defining genomic islands and uropathogen-specific genes in uropathogenic Escherichia coli. J Bacteriol 189:3532–3546
Lloyd AL, Henderson TA, Vigil PD, Mobley HL (2009) Genomic islands of uropathogenic Escherichia coli contribute to virulence. J Bacteriol 191:3469–3481
Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964
Marchler-Bauer A, Derbyshire MK, Gonzales NR, Lu S, Chitsaz F, Geer LY, Geer RC, He J, Gwadz M, Hurwitz DI et al (2015) CDD: NCBI’s conserved domain database. Nucleic Acids Res 43:D222–D226
Møller TSB, Overgaard M, Nielsen SS, Bortolaia V, Sommer MOA, Guardabassi L, Olsen JE (2016) Relation between tetR and tetA expression in tetracycline resistant Escherichia coli. BMC Microbiol 16:39
Mulvey MA (2002) Adhesion and entry of uropathogenic Escherichia coli. Cell Microbiol 4:257–271
Mutschler H, Meinhart A (2011) Epsilon/zeta systems: their role in resistance, virulence, and their potential for antibiotic development. J Mol Med (Berl) 89:1183–1194
Oliveira FA, Paludo KS, Arend LN, Farah SM, Pedrosa FO, Souza EM, Surek M, Picheth G, Fadel-Picheth CM (2011) Virulence characteristics and antimicrobial susceptibility of uropathogenic Escherichia coli strains. Genet Mol Res 10:4114–4125
Scheutz F, Strockbine NA (2005) Genus I. Escherichia Castellani and Chalmers 1919. In: Brenner DJ, Krieg NR, Staley JT (eds) Bergey’s manual of systematic bacteriology. Springer, New York, pp 607–624
Sun Z, Shi J, Liu C, Jin Y, Li K, Chen R, Jin S, Wu W (2014) PrtR homeostasis contributes to Pseudomonas aeruginosa pathogenesis and resistance against ciprofloxacin. Infect Immun 82:1638–1647
Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631–637
Vila J, Pal T (2010) Update on antibacterial resistance in low-income countries: factors favoring the emergence of resistance. Open Infect Dis J 4:38–54
Welch RA (2005) 3.3.3 The genus Escherichia. In: Dworkin M, Falkow S, Rosenberg E, Schleifer K-H, Stackebrandt E (eds) The prokaryotes, 3rd edn. Springer, Berlin, pp 62–71
Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J et al (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99:17020–17024
Withman B, Gunasekera TS, Beesetty P, Agans R, Paliy O (2013) Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea. Infect Immun 81:80–89
Wood JM, Bremer E, Csonka LN, Kraemer R, Poolman B, van der Heide T, Smith LT (2001) Osmosensing and osmoregulatory compatible solute accumulation by bacteria. Comp Biochem Physiol A Mol Integr Physiol 130:437–460
Yamada M, Nakazawa A (1984) Factors necessary for the export process of colicin E1 across cytoplasmic membrane of Escherichia coli. Eur J Biochem 140:249–255
Zhou Y, Liang Y, Lynch KH, Dennis JJ, Wishart DS (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39:W347–W352
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.
Author information
Authors and Affiliations
Corresponding authors
Ethics declarations
Conflict of interest
All authors declare that they have no conflict of interest.
Ethical approval
The article does not contain any studies with human participants performed by any of the authors.
Electronic supplementary material
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
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
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13258-018-0665-5