Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method

Authors

  • Reza Ranjbar Ph.D. of Medical Bacteriology, Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran

Keywords:

uropathogenic E. coli, urinary tract infection, ERIC-PCR, molecular typing

Abstract

Introduction: Escherichia coli (E. coli) is the most common cause of urinary infections in hospitals. The aim of this study was to evaluate the ERIC-PCR method for molecular typing of uropathogenic E. coli strains isolated from hospitalized patients.

Methods: In a cross sectional study, 98 E. coli samples were collected from urine samples taken from patients admitted to Baqiyatallah Hospital from June 2014 to January 2015. The disk agar diffusion method was used to determine antibiotic sensitivity. DNA proliferation based on repetitive intergenic consensus was used to classify the E. coli strains. The products of proliferation were electrophoresed on 1.5% agarose gel, and their dendrograms were drawn. The data were analyzed by online Insillico software. 

Results: The method used in this research proliferated numerous bands (4-17 bands), ranging from 100 to 3000 base pairs. The detected strains were classified into six clusters (E1-E6) with 70% similarity between them.

Conclusion: In this study, uropathogenic E. coli strains belonged to different genotypic clusters. It was found that ERIC-PCR had good differentiation power for molecular typing of uropathogenic E. coli strains isolated from the patients in the study.

References

Kaper JB, Nataro JP, Mobley HL. Pathogenic escherichia coli. Nature Reviews Microbiology. 2004; 2(2):

-40. doi: 10.1038/nrmicro818.

Sheerin NS. Urinary tract infection. Medicine. 2011; 39(7): 384-9. doi: 10.1016/j.mpmed.2011.04.003.

Lee JB, Neild GH. Urinary tract infection. Medicine. 2007; 35(8): 423-8. doi:

1016/j.mpmed.2007.05.009.

Farshad S, Anvarinejad M, Tavana AM, Ranjbar R, Japoni A, Zadegan RM, et al. Molecular epidemiology

of Escherichia coli strains isolated from children with community acquired urinary tract infections. African

J Microbiol Res. 2011; 5(26): 4476-83. doi: 10.5897/AJMR11.285.

Momtaz H, Karimian A, Madani M, Safarpoor Dehkordi F, Ranjbar R, Sarshar M, et al. Uropathogenic

Escherichia coli in Iran: serogroup distributions, virulence factors and antimicrobial resistance properties.

Ann Clin Microbiol Antimicrob. 2013; 12(8). doi: 10.1186/1476-0711-12-8.

Farshad S, Ranjbar R, Japoni A, Hosseini M, Anvarinejad M, Mohammadzadegan R. Microbial

susceptibility, virulence factors, and plasmid profiles of uropathogenic Escherichia coli strains isolated

from children in Jahrom, Iran. Archives of Iranian medicine. 2012; 15(5): 312-6. doi: 012155/AIM.0013.

Anvarinejad M, Farshad S, Ranjbar R, Giammanco GM, Alborzi A, Japoni A. Genotypic analysis of E. coli

strains isolated from patients with cystitis and pyelonephritis. Iran Red Crescent Med J. 2012; 14(7): 408- 16. PMID: 22997556, PMCID: PMC3438433

Healy M, Huong J, Bittner T, Lising M, Frye S, Raza S, et al. Microbial DNA typing by automated

repetitive-sequence-based PCR. Journal of clinical microbiology. 2005; 43(1): 199-207. doi:

1128/JCM.43.1.199-207.

Hulton CS, Higgins CF, Sharp PM. ERIC sequences: a novel family of repetitive elements in the genomes

of Escherichia coli, Salmonella typhimurium and other enterobacteria. Mol Microbiol. 1991; 5(4): 825-34.

doi: 10.1111/j.1365-2958.1991.tb00755.x, PMID: 1713281.

Sharples GJ, Lloyd RG. A novel repeated DNA sequence located in the intergenic regions of bacterial

chromosomes. Nucleic Acids Res. 1990; 18(22): 6503-8. doi: 10.1093/nar/18.22.6503, PMCID:

PMC332602.

Meacham KJ, Zhang L, Foxman B, Bauer RJ, Marrs CF. Evaluation of genotyping large numbers of

Escherichia coli isolates by enterobacterial repetitive intergenic consensus-PCR. J Clin Microbiol. 2003;

(11): 5224-6. doi: 10.1128/JCM.41.11.5224-5226.2003.

Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia

coli: Evolution and implications for ERIC-PCR. Mol Biol Evol. 2006; 23(6): 1156-68. doi:

1093/molbev/msj125, PMID: 16533821.

Versalovic J, Koeuth T, Lupski R. Distribution of repetitive DNA sequences in eubacteria and application

to finerpriting of bacterial enomes. Nucleic Acids Research. 1991; 19(24): 6823-31. doi:

1093/nar/19.24.6823, PMCID: PMC329316.

Versalovic J, Schneider M, De Bruijn FJ, Lupski JR. Genomic fingerprinting of bacteria using repetitive

sequence-based polymerase chain reaction. Methods in molecular and cellular biology. 1994; 5(1): 25-40.

Performance standards for antimicrobial susceptibility testing twenty second informational supplement

USA: Clinical and Laboratory Standards Institute. 2013

da Silveira WD, Ferreira A, Lancellotti M, Barbosa IA, Leite DS, de Castro AF, et al. Clonal relationships

among avian Escherichia coli isolates determined by enterobacterial repetitive intergenic consensus

(ERIC)–PCR. Veterinary Microbiology. 2002; 89(4): 323-8. doi: 10.1016/S0378-1135(02)00256-0.

Prabhu V, Isloor S, Balu M, Suryanarayana VVS, Rathnamma D. Genotyping by ERIC-PCR of Escherichia

coli isolated from bovine mastitis cases. Indian Journal of Biotechnology. 2010; 9(3): 298-301.

Ramazanzadeh R, Zamani S, Zamani S. Genetic diversity in clinical isolates of Escherichia coli by

enterobacterial repetitive intergenic consensus (ERIC)–PCR technique in Sanandaj hospitals. Iran J

Microbiol. 2013; 5(2): 126. PMID: 23825729, PMCID: PMC3696847.

Lang XY, Zhang YL, Jiang HT, Liu J, NI HB. Development of an enterobacterial repetitive intergenic

consensus polymerase chain reaction (ERIC-PCR) to detect and genotype enterotoxigenic Escherichia coli

of calf origin. Afr J Microbiol Res. 2013; 7(31): 4001-5. doi: 10.5897/AJMR2013.5748.

Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C.Typing methods used in the molecular

epidemiology of microbial pathogens: a how-to guide. New Microbiol. 2014; 37(1):1-15. PMid: 24531166

Ranjbar R, Naghoni A, Yousefi S, Ahmadi A, Jonaidi N, Panahi Y. The Study of Genetic Relationship

Among Third Generation Cephalosporin-resistant Salmonella enterica Strains by ERIC-PCR. Open

Microbiol J. 2013; 7:142-5. Doi: 10.2174/1874285801307010142, PMid: 24358066, PMCid: PMC3866615

Ranjbar R, Mirsaeed Ghazi F.Antibiotic Sensitivity Patterns and Molecular Typing of Shigella sonnei

Strains Using ERIC-PCR. Iran J Public Health. 2013; 42(10):1151-7. PMid: 26060624, PMCid:

PMC4436544

Ranjbar R, Rahbar M, Naghoni A, Farshad S, Davari A, Shahcheraghi F. A cholera outbreak associated

with drinking contaminated well water. Arch Iran Med. 2011; 14(5):339-40. PMid: 21888459

Ranjbar R, Hosseini MJ, Kaffashian AR, Farshad S. An outbreak of shigellosis due to Shigella flexneri

serotype 3a in a prison in Iran. Arch Iran Med. 2010; 13(5):413-6. PMid: 20804308

Pourshafie MR, Bakhshi B, Ranjbar R, Sedaghat M, Sadeghifard N, Zaemi Yazdi J, Parzadeh M, Raesi J.

Dissemination of a single Vibrio cholerae clone in cholera outbreaks during 2005 in Iran. J Med Microbiol.

; 56(Pt 12):1615-9. Doi: 10.1099/jmm.0.47218-0, PMid: 18033829

Khakabimamaghani S, Najafi A, Ranjbar R, Raam M.GelClust: a software tool for gel electrophoresis

images analysis and dendrogram generation.Comput Methods Programs Biomed. 2013; 111(2):512-8. Doi:

1016/j.cmpb.2013.04.013, PMid: 23727299

Tajbakhsh E, Khamesipour F, Ranjbar R, Ugwu IC. Prevalence of class 1 and 2 integrons in multi-drug

resistant Escherichia coli isolated from aquaculture water in Chaharmahal Va Bakhtiari province, Iran. Ann

Clin Microbiol Antimicrob. 2015 Jul 31; 14:37. Doi: 10.1186/s12941-015-0096-y, PMid: 26227260,

PMCid: PMC4521343

Jahandeh N, Ranjbar R, Behzadi P, Behzadi E. Uropathogenic Escherichia coli virulence genes: invaluable

approaches for designing DNA microarray probes. Cent European J Urol. 2015; 68(4):452-8. PMid:

, PMCid: PMC4742438

Behzadi P, Najafi A, Behzadi E, Ranjbar R. Microarray long oligo probe designing for Escherichia coli: an

in-silico DNA marker extraction. Cent European J Urol. 2016; 69(1):105-11. PMid: 27123336, PMCid:

PMC4846717

Ranjbar, R, Haghi-Ashtiani, MT, Jafari, NJ, Abedini, M. The prevalence and antimicrobial susceptibility

of bacterial uropathogens isolated from pediatric patients. Iran J Publ Health. 2009; 38 (2): 134-138

Published

2022-03-07

Issue

Section

Articles