Draft genome sequence of a Uropathogenic Escherichia coli (UPEC) isolate (ST38 O1:H15) from Pakistan, an emerging MDR sequence type with a high virulence profile

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• Subashchandrabose S, Mobley HLT. Virulence and Fitness Determinants of Uropathogenic Escherichia coli. Microbiology Spectrum. 2015;3(4). • Chattaway MA, Jenkins C, Ciesielczuk H, Day M, DoNascimento V, Day M, et al. Evidence of Evolving Extraintestinal Enteroaggregative Escherichia coli ST38 Clone. Emerg Infect Dis. 2014;20(11):1935-7. • Clinical and Labaratory Stadards Institute, Performance Standards for Antimicrobial Susceptibility Testing; Twenty-Fourth Informational Supplement. Institute, Wayne, PA; 2015. M100(S24). • Ali I, Rafaque Z, Ahmed S, Malik S, Dasti JI. Prevalence of multi-drug resistant uropathogenic Escherichia coli in Potohar region of Pakistan. Asian Pacific Journal of Tropical Biomedicine. 2016;6(1):60-6. • Elsinghorst EA. Measurement of invasion by gentamicin resistance. Methods Enzymol. 236: Academic Press; 1994. p. 405-20. • Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455-77. • Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29(8):1072-5. • [8] Wattam AR, Abraham D, Dalay O, Disz TL, Driscoll T, Gabbard JL, et al. PATRIC, the bacterial bioinformatics database and analysis resource. Nucleic Acids Res. 2014;42(D1):D581-D91. • Bi D, Xu Z, Harrison EM, Tai C, Wei Y, He X, et al. ICEberg: a web-based resource for integrative and conjugative elements found in Bacteria. Nucleic Acids Res. 2012;40(Database issue):D621-D6. • Varani AM, Siguier P, Gourbeyre E, Charneau V, Chandler M. ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes. Genome Biol. 2011;12(3):R30. • Jolley KA, Maiden MCJ. BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics. 2010;11(1):595. • Joensen KG, Tetzschner AMM, Iguchi A, Aarestrup FM, Scheutz F. Rapid and Easy In Silico Serotyping of Escherichia coli Isolates by Use of Whole-Genome Sequencing Data. J Clin Microbiol. 2015;53(8):2410-26. • Carattoli A, Zankari E, Garcia-Fernandez A, Voldby Larsen M, Lund O, Villa L, et al. In silico detection and typing of plasmids using PlasmidFinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58(7):3895-903. • Alghoribi MF, Gibreel TM, Farnham G, Al Johani SM, Balkhy HH, Upton M: Antibiotic-resistant ST38, ST131 and ST405 strains are the leading uropathogenic Escherichia coli clones in Riyadh, Saudi Arabia. J Antimicrob Chemother. 2015, 70:2757-2762. • Abe CM, Salvador FA, Falsetti IN, Vieira MA, Blanco J, Blanco JE, Blanco M, Machado AM, Elias WP, Hernandes RT, et al.: Uropathogenic Escherichia coli (UPEC) strains may carry virulence properties of diarrhoeagenic E. coli. FEMS Immunol Med Microbiol. 2008, 52:397-406. • Arndt D, Grant JR, Marcu A, Sajed T, Pon A, Liang Y, et al. PHASTER: a better, faster version of the PHAST phage search tool. Nucleic Acids Res. 2016;44(W1):W16-W21. • Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(suppl_2):W52-W7.