Detection of pap, fim, sfa and afa Genes in Eschreshia Coli Strains Isolated from Patients with Urinary Tract Infection by Multiplex-PCR in Kerman, Iran

Document Type : Original Article


1 MSc Department of Microbiology.Department of Microbiology, School of Basic Sciences, Sirjan Branch, Islamic Azad University, Sirjan, Iran.

2 Assistant Professor of Microbiology. Department of Microbiology, School of Basic Sciences, Saveh Branch, Islamic Azad University, Saveh, Iran.


Background and Objective: Urinary tract infection is the second most common infection in the human body. Among the causes of urinary tract infections, E. coli is one of the most common urinary tract pathogens in both genders.
Subjects and Methods: In this study, 200 urine samples to detect E. coli were cultured. Isolates were identified by standard biochemical tests and DNA extracted from isolates confirmed to determine the genes papEF, fimH, afaBC and sfa/focDE by Multiplex-PCR (Multiplex-polymerase chain reaction) method.
Results: In total, 110 E. coli strains from urine samples cultured were identified. The genotype virulence genes showed that 42.5 % of the isolates at least one of the four acuity type gene. PapEF gene with 21.81 % was the most frequent gene. While sfa and focDE genes had 4.54 and 2.77 % frequencies respectively. Thirty two samples (29.09%) had both fimH and afaBC genes.
Conclusion: Urinary tract infections are considered as a widespread health concern that is consistent with different geographic regions. The reason for the difference in results with other studies can be due to the difference in sample isolation regions.


1-Eslami M, Najar Peerayeh S. Phenotypic and genotypic identification of TEM, PER and VEB beta lactamase genes in the clinical Escherichia coli strains. Arak medical university journal. 2012; 15(1); 1-9.
2-Foxman B. Epidemiology of urinary tract infections. In: morbidity and economic costs. Dis Mon. 2003; 49: 53-70.
3-Klumpp J, Weiser C, Sengupta S, Forrestal G, Batler A, Schaeffer J. Uropathogenic E. coli potentiates type I pilus-induced apoptosis by suppressing NF-KB.Infect Immun.2001. 6689-96.
4-Salyers A, Whitt D. Bacterial pathogenesis.In : A molecular approach. 2thed.Washington DC.AMS
Press; 2002.534-542.
5-West DM, Sprigings KA, Cassar C, Wakeley PR, Sawyer J, and Davies RH. Rapid detection of Escherichia coli virulence factor gene using multiplex real-time TaqMan1 PCR assays. Vet Microbiol. 2007; 122: 323–33.
6-Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, Elion J, and Denamur E. The Link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun. 2009; 546–553.
7-Bekal S, Brousseau R, Masson L, Prefontaine G, Fairbrother J, and Harel J. Rapid identification of Escherichia coli pathotypes by virulence gene detection with DNAmicroarrays. J Clin Microbiol. 2003; 2113–2125.
8-Ulett G, Mabbett A, Fung Kh, Webb R, and Schembri M. The role of F9 fimbriae of uropathogenic Escherichia coli in biofilm formation. J Microbiol. 2007; 2321-2331.
9-Schwan W, Lee J, Lenard F, Matthews B, andBeck M. Osmolarity and pH growth conditions regulate fim gene transcription and Type 1 pilus expression in uropathogenic Escherichia coli. Infect Immun. 2002; 1391–1402.
10-Welch RA, Burland V, Plunkett G, Redford P, Roesch P, Rasko D, et al. Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Esherichia coli . Pans. 2002; 17020-17024.
11-Raksha R, Srinivasa H, and Macaden RS. Occurrence and characterization of uropathogenic Escherichia coli urinary tract infections. Indian J Med Microbiol. 2003; 21(2): 102- 107.
12-Matiuzzi da Costa M, Drescher G,Maboni F,Weber Sh, de Avila Botton S, Henning Vainstein M, Schrank IS, and Castagna de Vargas A. Virulence factors and antimicrobial resistance of Escherichia coli isolated from urinary tract of swine in southern of brazile . Brazilian J Microbiol. 2008; 39:741-743.
13-Sorsa J. Characterization of genomic diversity in extraintestinal pathogenic Escherichia coli (ExPEC) and development of a diagnostic DNA microarray for the differentiation of ExPEC isolates causing urinary tract infections. Acad Disser Gene Microbiol. 2007; 1-16.
14-Santo E, Macedo C, and Marin JM. Virulence factors of uropathogenic Escherichia coli from a university hospital in ribeirao preto, sao paulo, brazile. Inst Med Trop Sao Paulo. 2006; 48(4):185-188.
15-Snyder J, Haugen B, Lockatell CV, Maroncle N, Hagan E, Johnson D, Welch R, and Mobley H. Coordinate expression of fimbriae in uropathogenic Escherichia coli. Infect Immun. 2005; 7588–7596.
16-Alex P, Stouracova K, Hamric J, and Rychlik I. Gene typing of the colonization K88 (F4) in enterotoxigenic E.coli strains isolated from diarrhoeic piglets. Vet Med- Czech .2001; 46-49.
17-Birosova E, Siegfried L, Kmetova M, Makara A, Ostro A, Gresova A, et al. Detection of virulence factors in ahaemolytic Escherichia coli strains isolated from various clinical materials. Clin Microbiol Infect. 2004; 10: 569–573.
18-Blanco M, Leonel L, Blanco J, Dahbi Gh, Mora A, Cecilia L, GonzŁ„lez E, and Blanco J. Serotypes, virulence genes, and PFGE patterns of enteropathogenic Escherichia coli isolated fromCuban pigs with diarrhea. Int Microbiol. 2006; 9:53-60.
19-Mulvey M. Adhesion and entry of uropathogenic Escherichia coli. Cell Microbiol. 2002; 4(5): 257–271.
20-Riberio M, Yano Tand Silva Leite D. Genotypic characterization of virulence factors in Escherichia coli strains from patients with cystitis. Inst Med trop Sao Paulo. 2008; 50(5):255-260.
21-Miyazaki J, Ba-Thein W, Kumao T, Obata Yasuoka M, Akaza H, and Hayshi H. Type 1, P and S fimbriae, and afimbrial adhesin I are not essential for uropathogenic Escherichia coli to adhere to and invade bladder epithelial cells. Immunol Med Microbiol. 2002; 33: 23-26.
22-Soderhall M. The importance of Escherichia coli fimbriae in urinary tract infection. Department of Nephrology. 2001; 1-8.
23-Murray PR, Rosenthal KS, Pfaller MA. Medical microbiology: with student consult. 7th ed. Philadelphia, PA: Saunders; 2012.
24-Karimian A, Momtaz H, Madani M. Detection of uropathogenic Escherichia coli virulence factors in patients with urinary tract infections in Iran. Afr J Microbiol Res 2012; 6(39): 6811-6.
25-Yamamoto S, Terai A, Yuri K, Kurazono H, Takeda Y, and Yoshida O. Detection of urovirulence factors in Escherichia coli by multiplex polymerase chain reaction. FEMS Immunol Med Microbiol 1995; 12(2): 85-90.
26-Hosseini F, Goudarzi M, Bambaea B, Moradibid Hendi S. Molecular study of the impact of solid surface on type one fimbriae phase variation in E. coli serogroups O44 causing urinary tract infection. Kerman medical university journal. 2009; 16(3): 215-223. [In Persian]
27-Terai A, Yamamoto S, Mitsumori K, Okada Y, Kurazono H, Takeda Y, et al. Escherichia coli virulence factors and serotypes in acute bacterial prostatitis. Int J Urol 1997; 4(3): 289-94.
28-Gunther NW, Snyder JA, Lockatell V, Blomfield I, Johnson DE, Mobley HL. Assessment of virulence of uropathogenic Escherichia coli type 1 fimbrial mutants in which the invertible element is phase-locked on or off. Infect Immun 2002; 70(7): 3344-54.
29-Ishitoya S, Yamamoto S, Mitsumori K, Ogawa O, Terai A. Non-secretor status is associated with female acute uncomplicated pyelonephritis. BJU Int 2002; 89(9): 851-4.
30-Farshad S, Emamghoraishi F, Japoni A. Association of virulent genes hly, sfa, cnf-1 and pap with antibiotic sensitivity in Escherichia coli strains isolated from children with community-acquired UTI. Iran Red Crescent Med J 2010; 12(1): 33-7.
31-Tiba MR, Yano T, Leite DS. Genotypic characterization of virulence factors in Escherichia coli strains from patients with cystitis. Rev Inst Med Trop Sao Paulo 2008;
50(5): 255-60.
32-Arisoy M, Aysev D, Ekim M, Ozel D, Kose SK, Ozsoy ED, et al. Detection of virulence factors of Escherichia coli from children by multiplex polymerase chain reaction. Int J Clin Pract 2006; 60(2): 170-3.
33-Blanco M, Blanco JE, Rodriguez E, Abalia I, Alonso MP, and Blanco J. Detection of virulence genes in uropathogenic Escherichia coli by polymerase chain reaction (PCR): comparison with results obtained using phenotypic methods. Journal of Microbiological Methods 1997; 31(12): 37-43.
34-Arabi Sh, Tohidi F, Naderi S, Nazemi A. The common fimbarie genotyping in uropathogenic Escherichia coli. Annals of Biological Research 2012; 3(10): 4951-4.
35-Nazemi A, Naderi M, Jafarpour M, Miri Nargesi MS, Sharifi S. Distribution of fimbriae genes encoding in E.coli isolated from patients with urinary tract infection. Laboratory Journal. 2011; 4(2): 121-129.