Investigation of phylogenetic diversity among Eschereshia coli isolates recovered from hospitalized patients

authors:

avatar Omid Pajand , avatar Khatereh Ghassemi , avatar Fatemeh Kamali , avatar Sahar Taghavipoor , avatar Zoya Hojabri , *

Koomesh: Vol.19, issue 1; 207-212
article type: issue_documents_importer
received: March 01, 2016
accepted: October 05, 2016

how to cite: Pajand O, Ghassemi K, Kamali F, Taghavipoor S, Hojabri Z. Investigation of phylogenetic diversity among Eschereshia coli isolates recovered from hospitalized patients. koomesh. 2024;19(1):e151338. 

Abstract

Introduction: Eschereshia coli (E.coli) as one of the major cause of infections in hospital settings can be classified into phylogenetic groups which are different in virulence, growth rates and antibiotic susceptibility patterns. In this study, we aimed to perform phylogenetic analysis in E.coli strains to understand association between phylogroups and antibiotic susceptibility patterns. Materials and Methods: Two hundred and sixty E. coli isolates recovered from hospitalized patients at Kosar teaching hospital in Semnan city, Iran were subjected to phylogenetic typing by a quadruplex PCR method. Antimicrobial susceptibility testing was also performed by disk agar diffusion method. Results: Phylogroup B2 was the most predominant phylogroup (38.4%) followed by A (14.8%), F (13.4%), D (9.3%), B1 (8.8%), C and E (4.6%), unknown (4.2%), and clade I (1.9%). We found 70.4% of our isolates were multiple drug resistant (MDR). The most and the least efficient antibiotics were meropenem and trimethoprime/sulfamethoxazole with 94.4% and 27.8% of susceptibility rates, respectively. Conclusion: Our results represent the high prevalence of MDR E. coli isolates with dominance of phylogroup B2. Phylogroup B2 not only could be considered as a virulent phylogroup but also as a genetic antibiotic resistance reservoir.

References

  • 1.

    Dobrindt U. (Patho-) genomics of Escherichia coli. Intern J Med Microb 2005; 295: 357-371.

  • 2.

    Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microb 2000; 66: 4555-4558.

  • 3.

    Carlos C, Pires MM, Stoppe NC, Hachich EM, Sato MI, Gomes TA, et al. Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microb 2010; 10: 1.

  • 4.

    Gordon DM. The influence of ecological factors on the distribution and the genetic structure of escherichia coli. EcoSal Plus 2004; 1.

  • 5.

    Lecointre G, Rachdi L, Darlu P, Denamur E. Escherichia coli molecular phylogeny using the incongruence length difference test. Mol Biol Evolu 1998; 15: 1685-1695.

  • 6.

    Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylotyping method revisited: improvement of specificity and detection of new phylogroups. Environ Microbiol Rep 2013; 5: 58-65.

  • 7.

    Ghenghesh KS, Elkateb E, Berbash N, Nada RA, Ahmed SF, Rahouma A, et al. Uropathogens from diabetic patients in Libya: virulence factors and phylogenetic groups of Escherichia coli isolates. J Med Microbiol 2009; 58: 1006-1014.

  • 8.

    Johnson JR, Kuskowski MA, O'bryan TT, Colodner R, Raz R. Virulence genotype and phylogenetic origin in relation to antibiotic resistance profile among Escherichia coli urine sample isolates from Israeli women with acute uncomplicated cystitis. Antimicrob Agents Chemother 2005; 49: 26-31.

  • 9.

    Zarinfar N, sharafkhah M, Amiri M, Rafeie M. Probiotic effects in prevention from ventilator-associated pneumonia. Koomesh 2016; 17: 803-813. (Persian).

  • 10.

    Koshi M. Methods in biochemical identification of bacteria. In Myers and KoshisManual of Diagnostic Procedures in Medical Microbiology and Immunology/Serology: Department of Clinical Microbiology, Christian Medical College; 2001; 95-202.

  • 11.

    Wayne P. CLSI Performance standard of Antimicrobial Susceptibility Testing: Twenty-fourth International Supplement. CLSI Document M100-S24 Clinical and Laboratory Standard Institute. 2014.

  • 12.

    Hojabri Z, Rezaee M, Nahaei MR, Davodi M, Satarzadeh Tabrizi M, Ghazi M, et al. Comparison of in vitro activity of Doripenem versus old carbapenems against Pseudomonas aeruginosa clinical isolates from both CF and burn patients. Advan Pharm Bul 2013; 3: 121-125.

  • 13.

    Iranpour D, Hassanpour M, Ansari H, Tajbakhsh S, Khamisipour G, Najafi A. Phylogenetic Groups of Escherichia coli Strains from patients with urinary tract infection in iran based on the new clermont phylotyping method. BioMed Res Intern 2015; http://dx.doi.org/10.1155/2015/846219.

  • 14.

    Rahimi M, Tajbakhsh M, Razaghi M, Tajeddin E, Alebouyeh M, Rajabi Bazl M, Zali M. Frequency of -lactamase producing isolates of Escherichia coli and their diversity in enzyme activitiesamong the resistance isolates from patients with diarrhea and nosocomial infections in Tehran, Iran. Koomesh 2014; 15: 197-205. (Persian).

  • 15.

    Bashir S, Haque A, Sarwar Y, Ali A, Anwar MI. Virulence profile of different phylogenetic groups of locally isolated community acquired uropathogenic E. coli from Faisalabad region of Pakistan. Annals Clin Microbiol Antimicrob 2012; 11: 1.

  • 16.

    Bingen-Bidois M, Clermont O, Bonacorsi S, Terki M, Brahimi N, Loukil C, et al. Phylogenetic analysis and prevalence of urosepsis strains of Escherichia coli bearing pathogenicity island-like domains. Infect Immun 2002; 70: 3216-3226.

  • 17.

    Smati M, Clermont O, Le Gal F, Schichmanoff O, Jaurguy F, Eddi A, et al. Real-Time PCR for quantitative analysis of human commensal Escherichia coli populations reveals a high frequency of subdominant phylogroups. Appl Environ Microbiol 2013; 79: 5005-5012.

  • 18.

    Dubois D, Delmas J, Cady A, Robin F, Sivignon A, Oswald E, et al. Cyclomodulins in urosepsis strains of Escherichia coli. J Clin Microbiol 2010; 48: 2122-2129.

  • 19.

    Luo Y, Ma Y, Zhao Q, Wang L, Guo L, Ye L, et al. Similarity and divergence of phylogenies, antimicrobial susceptibilities, and virulence factor profiles of Escherichia coli isolates causing recurrent urinary tract infections that persist or result from reinfection. J Clin Microbiol 2012; 50: 4002-4007.

  • 20.

    Adib N, Ghanbarpour R, Solatzadeh H, Alizade H. Antibiotic resistance profile and virulence genes of uropathogenic Escherichia coli isolates in relation to phylogeny. Trop Biomed 2014; 31: 17-25.

  • 21.

    Nowrouzian FL, Adlerberth I, Wold AE. Enhanced persistence in the colonic microbiota of Escherichia coli strains belonging to phylogenetic group B2: role of virulence factors and adherence to colonic cells. Microb Infect 2006; 8: 834-840.##[22 Sannes MR, Kuskowski MA, Owens K, Gajewski A, Johnson JR. Virulence factor profiles and phylogenetic background of Escherichia coli isolates from veterans with bacteremia and uninfected control subjects. J Infect Dis 2004; 190: 2121-2128.

  • 22.

    Walk ST, Alm EW, Calhoun LM, Mladonicky JM, Whittam TS. Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ Microbiol 2007; 9: 2274-2288.

  • 23.

    Vila J, Simon K, Ruiz J, Horcajada JP, Velasco M, Barranco M, et al. Are quinolone-resistant uropathogenic Escherichia coli less virulent? J Infect Disea 2002; 186: 1039-1042##.