Original Article

Phylogenetic Analysis and Antimicrobial Resistance Profiles of Escherichia coli Strains Isolated from UTI-Suspected Patients


Background: Escherichia coli as one of the most predominant pathogens is the major cause of ‎urinary tract infections (UTI) worldwide. E. coli strains could be classified into distinct phylo-groups based on PCR method. Additionally, studying the antimicrobial resistance profiles of these strains is essential for finding the effective selection of treatment and evaluating the differences among resistance patterns of particular phylogenetic groups. This study aimed to determine the phylogroups of E. coli isolated from patients with UTI in Tehran, Iran.

Methods: The urine samples were collected from patients suspected to UTI from four hospitals in Tehran, Iran; Mofid, Vali-Asr, Bu-Ali and Tehran Heart Center (THC) Hospitals during 2014-2016. Assessing the ‎antimicrobial resistance profile of the identified strains was accomplished using ampicillin, ‎ceftriaxone, cefotaxime, and ceftazidime among β-lactam group; gentamicin, and ‎streptomycin among aminoglycosides; nalidixic acid and norfloxacin from quinolones; and ‎chloramphenicol disks. The phylogenetic characterization of 60 E. ‎coli isolates obtained from patients with UTI was done by triplex PCR method.

Results: E. coli strains showed high resistance toward streptomycin (93.33%), ampicillin (86.6%) and nalidixic acid (73.33%) while resistance against chloramphenicol showed the lowest (10%). The prevalent groups were B2 (n=50/60, 83%), followed by D (n=6/60, 10%), B1 (n=3/60‎‏‎, 5%), and A (n=1, 1.6%).

Conclusion: The most predominant phylogenetic group was B2 with the major frequent detected with ‎the major drug resistant (48%) compared to other Phylogenetic groups.

‎1.‎ Foxman B, Brown P (2003). Epidemiology of urinary tract infections: transmission and risk ‎factors, incidence, and costs. Infect Dis Clin North Am, 17(2):227-41.‎

‎2.‎ Johnson JR, Russo TA (2002). Extraintestinal pathogenic Escherichia coli:“the other bad E ‎coli”. J Lab Clin Med, 139(3):155-62.‎

‎3.‎ Russo TA, Johnson JR (2000). Proposal for a new inclusive designation for extraintestinal ‎pathogenic isolates of Escherichia coli: ExPEC. J Infect Dis, 181(5):1753-4.‎

‎4.‎ Martin GS, Mannino DM, Eaton S, Moss M (2003).The epidemiology of sepsis in the ‎United States from 1979 through 2000. N Engl J Med, 348(16):1546-54.‎

‎5.‎ Anvarinejad M, Farshad S, Ranjbar R, Giammanco G, Alborzi A, Japoni A ‎‎(2012).Genotypic analysis of E. coli strains isolated from patients with cystitis and ‎pyelonephritis. Iran Red Crescent Med J, 14(7):408.‎

‎6.‎ Basu S, Mukherjee SK, Hazra A, Mukherjee M (2013).Molecular characterization of ‎uropathogenic Escherichia coli: nalidixic acid and ciprofloxacin resistance, virulent factors ‎and phylogenetic background. J Clin Diagn Res, 7(12):2727.‎

‎7.‎ Ejrnæs K (2011).Bacterial characteristics of importance for recurrent urinary tract ‎infections caused by Escherichia coli. Dan Med Bull. 58(4):B4187.‎

‎8.‎ Santo E, Salvador MM, Marin JM (2007).Multidrug-resistant urinary tract isolates of ‎Escherichia coli from Ribeirão Preto, São Paulo, Brazil. Braz J Infect Dis 11(6):575-8.‎

‎9.‎ Hassan SA, Jamal SA, Kamal M (2011).Occurrence of multidrug resistant and ESBL ‎producing E. coli causing urinary tract infections. J Basic Appl Sci. 7(1):39-43.‎

‎10.‎ Ranjbar R, Sami M (2017).Genetic Investigation of Beta-Lactam Associated Antibiotic ‎Resistance Among Escherichia Coli Strains Isolated from Water Sources. Open Microbiol J, ‎‎11(1).‎

‎11.‎ Momtaz H, Karimian A, Madani M, Dehkordi FS, Ranjbar R, Sarshar M, et al. ‎‎(2013).Uropathogenic Escherichia coli in Iran: serogroup distributions, virulence factors ‎and antimicrobial resistance properties. Ann Clin Microbiol Antimicrob, 12(1):8.‎

‎12.‎ Kõljalg S, Truusalu K, Stsepetova J, Pai K, Vainumäe I, Sepp E, et al. (2014).The ‎Escherichia coli phylogenetic group B2 with integrons prevails in childhood recurrent ‎urinary tract infections. Apmis. 122(5):452-8.‎

‎13.‎ Tajbakhsh E, Khamesipour F, Ranjbar R, Ugwu IC (2015). 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, 14(1):37.‎

‎14.‎ Farshad S, Ranijbar 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(5).‎

‎15.‎ Jahandeh N, Ranjbar R, Behzadi P, Behzadi E (2015). Uropathogenic Escherichia coli ‎virulence genes: invaluable approaches for designing DNA microarray probes. Cent ‎European J Urol, 68(4):452.‎

‎16.‎ Ranjbar R, Haghi-Ashtiani M, Jafari NJ, Abedini M (2009). The prevalence and ‎antimicrobial susceptibility of bacterial uropathogens isolated from pediatric patients. Iran J ‎Public Health, 38(2):134-8.‎

‎17.‎ Ranjbar R, Hosseini S, Zahraei-Salehi T, Kheiri R, Khamesipour F (2016). Investigation on ‎prevalence of Escherichia coli strains carrying virulence genes ipaH, estA, eaeA and bfpA ‎isolated from different water sources. Asian Pac J Trop Dis, 6(4):278-83.‎

‎18.‎ Khademestarki NS, Ranjbar R (2016). The phylogenetic study of Escherichia coli strains ‎isolated from clinical cases. J Pure Appl Microbio. 10(1):351-5.‎

‎19.‎ Ranjbar R, Karami A, Farshad S, Giammanco GM, Mammina C (2014). Typing methods ‎used in the molecular epidemiology of microbial pathogens: a how-to guide. New ‎Microbiol, 37(1):1-15.‎

‎20.‎ Ranjbar R, Farahani O (2017). The Prevalence of Plasmid-mediated Quinolone Resistance ‎Genes in Escherichia coli Isolated from Hospital Wastewater Sources in Tehran, Iran. Iran J ‎Public Health, 46(9):1285.‎

‎21.‎ Abdi S (2014). Frequency of bla TEM, bla SHV, bla CTX-M, and qnrA among Escherichia ‎coli isolated from urinary tract infection. Arch Clin Infect Dis, 9(1):1-5.‎

‎22.‎ Anvarinejad M, Farshad S, Alborzi A, Ranjbar R, Giammanco GM, Japoni A (2011). ‎Integron and genotype patterns of quinolones-resistant uropathogenic Escherichia coli. Afr J ‎Microbiol Res, 5(22):3736-70.‎

‎23.‎ Clermont O, Bonacorsi S, Bingen E (2000). Rapid and simple determination of ‎theEscherichia coli phylogenetic group. Appl Environ Microbiol, 66(10):4555-8.‎

‎24.‎ Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, et al. ‎‎(2008).Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. ‎BMC genomics. 9(1):560.‎

‎25.‎ Moissenet D, Salauze B, Clermont O, Bingen E, Arlet G, Denamur E, et al. (2010). ‎Meningitis caused by Escherichia coli producing TEM-52 extended-spectrum β-lactamase ‎within an extensive outbreak in a neonatal ward: epidemiological investigation and ‎characterization of the strain. J Clin Microbiol, 48(7):2459-63.‎

‎26.‎ Tenaillon O, Skurnik D, Picard B, Denamur E (2010). The population genetics of ‎commensal Escherichia coli. Nat Rev Microbiol, 8(3):207.‎

‎27.‎ Clermont O, Olier M, Hoede C, Diancourt L, Brisse S, Keroudean M, et al. (2011). Animal ‎and human pathogenic Escherichia coli strains share common genetic backgrounds. Infect ‎Genet Evol, 11(3):654-62.‎

‎28.‎ Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT (2011). ‎Genome sequencing of environmental Escherichia coli expands understanding of the ‎ecology and speciation of the model bacterial species. Proc Natl Acad Sci, 108(17):7200-5.‎

‎29.‎ Clermont O, Christenson JK, Denamur E, Gordon DM (2013). The Clermont Escherichia ‎coli phylo‐typing method revisited: improvement of specificity and detection of new phylo‐‎groups. Environ Microbiol Rep, 5(1):58-65.‎

‎30.‎ Alali WQ, Scott H, Harvey R, Norby B, Lawhorn D, Pillai S (2008). Longitudinal study of ‎antimicrobial resistance among Escherichia coli isolates from integrated multisite cohorts of ‎humans and swine. Appl. Environ. Microbiol, 74(12):3672-81.‎

‎31.‎ Usein C-R, Grigore LA, Georgescu RM, Bãltoiu MC, Condei M, Teleman MD ‎‎(2011).Phylogenetic background and extraintestinal virulence genotypes of Escherichia coli ‎vaginal strains isolated from adult women. Rev Romana Med Lab 2011; 19 (1): 37. 45.‎

‎32.‎ Skjøt-Rasmussen L, Ejrnæs K, Lundgren B, Hammerum AM, Frimodt-Møller N (2012). ‎Virulence factors and phylogenetic grouping of Escherichia coli isolates from patients with ‎bacteraemia of urinary tract origin relate to sex and hospital-vs. community-acquired origin. ‎Int J Med Microbiol, 302(3):129-34.‎

‎33.‎ Rijavec M, Müller-Premru M, Zakotnik B, Žgur-Bertok D (2008). Virulence factors and ‎biofilm production among Escherichia coli strains causing bacteraemia of urinary tract ‎origin. J. Med. Microbiol, 57(11):1329-34.‎

‎34.‎ Kanamaru S, Kurazono H, Nakano M, Terai A, Ogawa O, Yamamoto S (2006).Subtyping ‎of uropathogenic Escherichia coli according to the pathogenicity island encoding ‎uropathogenic‐specific protein: Comparison with phylogenetic groups. Int J Urol, ‎‎13(6):754-60.‎

‎35.‎ Johnson JR, Kuskowski MA, Owens K, Gajewski A, Winokur PL (2003). Phylogenetic ‎origin and virulence genotype in relation to resistance to fluoroquinolones and/or extended-‎spectrum cephalosporins and cephamycins among Escherichia coli isolates from animals ‎and humans. J. Infect. Dis, 188(5):759-68.‎

‎36.‎ Hancock V, Nielsen EM, Krag L, Engberg J, Klemm P (2009). Comparative analysis of ‎antibiotic resistance and phylogenetic group patterns in human and porcine urinary tract ‎infectious Escherichia coli. Apmis. 117(11):786-90.‎

‎37.‎ Zhao L, Chen X, Zhu X, Yang W, Dong L, Xu X, et al. (2009). Prevalence of virulence ‎factors and antimicrobial resistance of uropathogenic Escherichia coli in Jiangsu province ‎‎(China). Urology, 74(3):702-7.‎

‎38.‎ Johnson JR, Owens K, Gajewski A, Kuskowski MA (2005). Bacterial characteristics in ‎relation to clinical source of Escherichia coli isolates from women with acute cystitis or ‎pyelonephritis and uninfected women. J. Clin. Microbiol, 43(12):6064-72.‎

‎39.‎ Moreno E, Prats G, Sabaté M, Pérez T, Johnson JR, Andreu A (2006). Quinolone, ‎fluoroquinolone and trimethoprim/sulfamethoxazole resistance in relation to virulence ‎determinants and phylogenetic background among uropathogenic Escherichia coli. J. ‎Antimicrob. Chemother, 57(2):204-11.‎

‎40.‎ Liu Y, Liu G, Liu W, Liu Y, Ali T, Chen W, et al. (2014). Phylogenetic group, virulence ‎factors and antimicrobial resistance of Escherichia coli associated with bovine mastitis. Res ‎Microbiol, 165(4):273-7.‎

‎41.‎ Borsari AG, Bucher B, Brazzola P, Simonetti GD, Dolina M, Bianchetti MG (2008). ‎Susceptibility of Escherichia coli strains isolated from outpatient children with community-‎acquired urinary tract infection in southern Switzerland. Clin. Ther, 30(11):2090-5.‎

‎42.‎ Caracciolo A, Bettinelli A, Bonato C, Isimbaldi C, Tagliabue A, Longoni L, et al. (2011). ‎Antimicrobial resistance among Escherichia coli that cause childhood community-acquired ‎urinary tract infections in Northern Italy. Ital J Pediatr, 37(1):3.‎

IssueVol 49 No 9 (2020) QRcode
SectionOriginal Article(s)
DOI https://doi.org/10.18502/ijph.v49i9.4094
Escherichia coli phylo-group Triplex PCR; Urinary tract infections (UTI)

Rights and permissions
Creative Commons License This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.
How to Cite
RANJBAR R, NAZARI S, FARAHANI O. Phylogenetic Analysis and Antimicrobial Resistance Profiles of Escherichia coli Strains Isolated from UTI-Suspected Patients. Iran J Public Health. 2020;49(9):1743-1749.