Sun, Dec 22, 2024
Volume 18, Issue 2 (Mar-Apr 2024)
mljgoums 2024, 18(2): 22-25 |
Back to browse issues page
Download citation:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
BibTeX | RIS | EndNote | Medlars | ProCite | Reference Manager | RefWorks
Send citation to:
karshenas A, yahya raiat R, zahraiee salehi T, asghari B, adabi M. Phylogenetic group determination and genetic diversity of Escherichia coli isolated from domestic animals’ stool specimens and human clinical samples. mljgoums 2024; 18 (2) :22-25
URL: http://mlj.goums.ac.ir/article-1-1627-en.html
URL: http://mlj.goums.ac.ir/article-1-1627-en.html
1- Department of Pathobiology, science and research branch, Islamic Azad University, Tehran, Iran
2- Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
3- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
4- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran ,maryam_adabi@yahoo.com
2- Department of Microbiology, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
3- Department of Microbiology, School of Medicine, Hamadan University of Medical Sciences, Hamadan, Iran
4- Infectious Ophthalmologic Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran ,
Abstract: (861 Views)
Background: Escherichia coli consists of a wide range of strains with huge diversity in their genome, distributed in nature and the alimentary tracts of animals and humans. This study analyzed the phylogenetic group determination and genetic diversity of E. coli strains isolated from domestic animals and human clinical samples.
Methods: Twenty E. coli isolates from domestic animals were analyzed for phylogenetic grouping. Also, 100 clinical samples and 20 animal samples were evaluated by the enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) technique. The results and the similarity between the strains were determined based on the Dice similarity coefficient in the SAHN program of the NTSYS-pc software.
Results: The frequency of phylogroups among animal samples were A = 5%, B1 = 65%, B2 = 20%, and D = 10%. Based on the ERIC-PCR results, the clinical strains were allocated into 19 clusters. Most strains were in the E7 cluster. Fifty percent of the E. coli isolated from animal specimens belonged to the E4 group, and the lowest number of strains was in the E3 and E5 (1 strain) groups.
Conclusion: The results confirmed the efficiency and usefulness of the ERIC-PCR tool for the identification and classification of bacteria. Also, we demonstrated the most phylogroup among animal samples.
Methods: Twenty E. coli isolates from domestic animals were analyzed for phylogenetic grouping. Also, 100 clinical samples and 20 animal samples were evaluated by the enterobacterial repetitive intergenic consensus–polymerase chain reaction (ERIC-PCR) technique. The results and the similarity between the strains were determined based on the Dice similarity coefficient in the SAHN program of the NTSYS-pc software.
Results: The frequency of phylogroups among animal samples were A = 5%, B1 = 65%, B2 = 20%, and D = 10%. Based on the ERIC-PCR results, the clinical strains were allocated into 19 clusters. Most strains were in the E7 cluster. Fifty percent of the E. coli isolated from animal specimens belonged to the E4 group, and the lowest number of strains was in the E3 and E5 (1 strain) groups.
Conclusion: The results confirmed the efficiency and usefulness of the ERIC-PCR tool for the identification and classification of bacteria. Also, we demonstrated the most phylogroup among animal samples.
Research Article: Research Article |
Subject:
Laboratory Sciences
Received: 2023/02/17 | Accepted: 2024/02/6 | Published: 2024/03/26 | ePublished: 2024/03/26
Received: 2023/02/17 | Accepted: 2024/02/6 | Published: 2024/03/26 | ePublished: 2024/03/26
References
1. Ardakani MA, Ranjbar R. Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method. Electronic physician. 2016;8:4:2291. [View at Publisher] [DOI] [PMID] [Google Scholar]
2. Rousset F, Cabezas-Caballero J, Piastra-Facon F, Fernández-Rodríguez J, Clermont O, Denamur E, et al. The impact of genetic diversity on gene essentiality within the Escherichia coli species. Nature microbiology. 2021; 6(3): 301-12 [View at Publisher] [DOI] [PMID] [Google Scholar]
3. Zoolkifli NW, Mutalib SA. Molecular typing among beef isolates of Escherichia coli using consensus repetitive intergenic enterobacteria-polymerase chain reaction (ERIC-PCR). AIP Conference Proceedings: American Institute of Physics; 2013: 654-9. [View at Publisher] [DOI] [Google Scholar]
4. Stoppe NdC, Silva JS, Carlos C, Sato MI, Saraiva AM, Ottoboni LM, et al. Worldwide phylogenetic group patterns of Escherichia coli from commensal human and wastewater treatment plant isolates. Frontiers in microbiology. 2017;8:2512. [View at Publisher] [DOI] [PMID] [Google Scholar]
5. Coura FM, Diniz Sde A, Silva MX, Mussi JM, Barbosa SM, Lage AP, et al. Phylogenetic Group Determination of Escherichia coli Isolated from Animals Samples. Scientific World Journal. 2015; 2015: 258424. [View at Publisher] [DOI] [PMID] [Google Scholar]
6. Ranjbar R, Tabatabaee A, Behzadi P, Kheiri R. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) genotyping of Escherichia coli strains isolated from different animal stool specimens. Iranian journal of pathology. 2017; 12(1): 25. [View at Publisher] [DOI] [PMID] [Google Scholar]
7. Mainil J. Escherichia coli virulence factors. Veterinary immunology and immunopathology. 2013;152:1-2:2-12. [View at Publisher] [DOI] [PMID] [Google Scholar]
8. Movahedi M, Zarei O, Hazhirkamal M, Karami P, Shokoohizadeh L, Taheri M. Molecular typing of Escherichia coli strains isolated from urinary tract infection by ERIC-PCR. Gene Reports. 2021; 23: 101058. [View at Publisher] [DOI]
9. 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. [View at Publisher] [DOI] [PMID] [Google Scholar]
10. Helalat H, Rezatofighi SE, Ardakani MR, Dos Santos LF, Badouei MA. Genotypic and phenotypic characterization of enteroaggregative Escherichia coli (EAEC) isolates from diarrheic children: An unresolved diagnostic paradigm exists. Iranian journal of basic medical sciences. 2020; 23(7): 915. [View at Publisher] [DOI] [PMID] [Google Scholar]
11. Ghorbani AR, Khoshbakht R, Kaboosi H, Shirzad-Aski H, Ghadikolaii FP. Phylogenetic relationship and virulence gene profiles of avian pathogenic and uropathogenic Escherichia coli isolated from avian colibacillosis and human urinary tract infections (UTIs). Iranian Journal of Veterinary Research. 2021;22(3):203. [View at Publisher] [DOI] [PMID] [Google Scholar]
12. Bourne JA, Chong WL, Gordon DM. Genetic structure, antimicrobial resistance and frequency of human associated Escherichia coli sequence types among faecal isolates from healthy dogs and cats living in Canberra, Australia. PLoS One. 2019;14(3):e0212867. [View at Publisher] [DOI] [PMID] [Google Scholar]
13. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Applied and environmental microbiology. 2000; 66(10):4555. [View at Publisher] [DOI] [PMID] [Google Scholar]
14. Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal Escherichia coli. Nature reviews microbiology. 2010; 8(3): 207-17. [View at Publisher] [DOI] [PMID] [Google Scholar]
15. Johnson JR, Stell AL. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. The Journal of infectious diseases. 2000;181:1:261-72. [View at Publisher] [DOI] [PMID] [Google Scholar]
16. Anvarinejad M, Farshad S, Ranjbar R, Giammanco G, Alborzi A, Japoni A. Genotypic analysis of E. coli strains isolated from patients with cystitis and pyelonephritis. Iranian Red Crescent Medical Journal. 2012; 14(7): 408. [View at Publisher] [Google Scholar]
17. Momtaz H, Karimian A, Madani M, Dehkordi FS, Ranjbar R, Sarshar M, et al. Uropathogenic Escherichia coli in Iran: serogroup distributions, virulence factors and antimicrobial resistance properties. Annals of clinical microbiology and antimicrobials. 2013;12:1:1-12. [View at Publisher] [DOI] [PMID] [Google Scholar]
18. 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. Journal of clinical microbiology. 2003; 41(11): 5224. [View at Publisher] [DOI] [PMID] [Google Scholar]
19. Versalovic J, Schneider M, De Bruijn F, Lupski JR. Genomic fingerprinting of bacteria using repetitive sequence-based polymerase chain reaction. Methods in molecular and cellular biology. 1994; 5(1): 25-40. [View at Publisher] [Google Scholar]
20. Wilson LA, Sharp PM. Enterobacterial repetitive intergenic consensus (ERIC) sequences in Escherichia coli: Evolution and implications for ERIC-PCR. Molecular biology and evolution. 2006; 23(6): 1156-68. [View at Publisher] [DOI] [PMID] [Google Scholar]
21. Jain P, Bepari AK, Sen PK, Rafe T, Imtiaz R, Hossain M. High prevalence of multiple antibiotic resistance in clinical E. coli isolates from Bangladesh and prediction of molecular resistance determinants using WGS of an XDR isolate. Scientific reports. 2021; 11(1): 22859. [View at Publisher] [DOI] [PMID] [Google Scholar]
22. Sharp PM. Insertions within ERIC sequences. Molecular microbiology. 1997;24:6:1314-5. [View at Publisher] [DOI] [PMID] [Google Scholar]
23. Bakhshi B, Afshari N, Fallah F. Enterobacterial repetitive intergenic consensus (ERIC)-PCR analysis as a reliable evidence for suspected Shigella spp. outbreaks. brazilian journal of microbiology. 2018; 49(3): 529-33. [View at Publisher] [DOI:10.1016/j.bjm.2017.01.014] [PMID] [Google Scholar]
24. Bakhtiari S, Mahmoudi H, Seftjani SK, Amirzargar MA, Ghiasvand S, Ghaffari ME, et al. Antibiotic resistance pattern and phylogenetic groups of the uropathogenic Escherichia coli isolates from urinary tract infections in Hamedan, west of Iran. Iranian Journal of Microbiology. 2020;12(5):388. [View at Publisher] [DOI:10.18502/ijm.v12i5.4598] [PMID] [Google Scholar]
25. Mahon CR, Lehman DC, Manuselis G. Textbook of diagnostic microbiology-e-book. Elsevier Health Sciences. 2018. [View at Publisher] [Google Scholar]
26. Adabi M, Talebi-Taher M, Arbabi L, Afshar M, Fathizadeh S, Minaeian S, et al. Spread of efflux pump overexpressing-mediated fluoroquinolone resistance and multidrug resistance in Pseudomonas aeruginosa by using an efflux pump inhibitor. Infection & chemotherapy. 2015;47:2:98. [View at Publisher] [DOI:10.3947/ic.2015.47.2.98] [PMID] [Google Scholar]
27. Fox JT, Renter DG, Sanderson MW, Thomson DU, Lechtenberg KF, Nagaraja T. Evaluation of culture methods to identify bovine feces with high concentrations of Escherichia coli O157. Applied and environmental microbiology. 2007;73(16):5253. [View at Publisher] [DOI:10.1128/AEM.00554-07] [PMID] [Google Scholar]
28. 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. Iranian journal of Microbiology. 2013;5:2:126. [View at Publisher] [PMID] [Google Scholar]
29. Lewis JS, II MH, Wickes B, Patterson JE, Jorgensen JH. First report of the emergence of CTX-M-type extended-spectrum -lactamases (ESBLs) as the predominant ESBL isolated in a US health care system. Antimicrobial agents and chemotherapy. 2007;51:11:4015. [View at Publisher] [DOI:10.1128/AAC.00576-07] [PMID] [Google Scholar]
30. Gordon DM, Clermont O, Tolley H, Denamur E. Assigning Escherichia coli strains to phylogenetic groups: multi‐locus sequence typing versus the PCR triplex method. Environmental microbiology. 2008;10:10:2484-96. [View at Publisher] [DOI:10.1111/j.1462-2920.2008.01669.x] [PMID] [Google Scholar]
31. Gordon DM, Cowling A. The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology. 2003;149(12):3575-86. [View at Publisher] [DOI:10.1099/mic.0.26486-0] [PMID] [Google Scholar]
32. Nakazato G, Campos TAd, Stehling EG, Brocchi M, Silveira WDd. Virulence factors of avian pathogenic Escherichia coli (APEC). Pesquisa Veterinária Brasileira. 2009;29:7:479-86. [View at Publisher] [DOI:10.1590/S0100-736X2009000700001] [Google Scholar]
33. Selander RK, Caugant DA, Ochman H, Musser JM, Gilmour MN, Whittam TS. Methods of multilocus enzyme electrophoresis for bacterial population genetics and systematics. Applied and environmental microbiology. 1986;51:5:873. [View at Publisher] [DOI:10.1128/aem.51.5.873-884.1986] [PMID] [Google Scholar]
34. Escobar-Páramo P, Clermont O, Blanc-Potard A-B, Bui H, Le Bouguénec C, Denamur E. A specific genetic background is required for acquisition and expression of virulence factors in Escherichia coli. Molecular biology and evolution. 2004;21:6:1085-94. [View at Publisher] [DOI:10.1093/molbev/msh118] [PMID] [Google Scholar]
35. 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 microbiology. 2010;10:1:1-10. [View at Publisher] [DOI:10.1186/1471-2180-10-161] [PMID] [Google Scholar]
36. Blahna MT, Zalewski CA, Reuer J, Kahlmeter G, Foxman B, Marrs CF. The role of horizontal gene transfer in the spread of trimethoprim-sulfamethoxazole resistance among uropathogenic Escherichia coli in Europe and Canada. Journal of Antimicrobial Chemotherapy. 2006;57:4:666-72. [View at Publisher] [DOI:10.1093/jac/dkl020] [PMID] [Google Scholar]
37. Alyamani EJ, Khiyami AM, Booq RY, Majrashi MA, Bahwerth FS, Rechkina E. The occurrence of ESBL-producing Escherichia coli carrying aminoglycoside resistance genes in urinary tract infections in Saudi Arabia. Annals of clinical microbiology and antimicrobials. 2017;16:1:1-13. [View at Publisher] [DOI:10.1186/s12941-016-0177-6] [PMID] [Google Scholar]
Send email to the article author
| Rights and permissions | |
 |
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License. |
Enamad
This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.