A comparative phylotyping analysis of E. coli originating from avian colibacillosis based on the Clermont triplex scheme and gyrA gene sequencing

Avian colibacillosis (AC) is frequently reported from poultry farms in the west of Iran. The aim of the present survey wasto evaluate the phylogeny of Escherichia coli isolated from AC through the Clermont triplex protocol and gyrA gene sequencing. Onehundred and fifty fresh carcasses suspected of having died from colibacillosis were sampled. The specimens were examined for E. coliisolation and identification. The extracted DNA repertoire of the isolates was subjected to phylogenetic analysis using Clermont triplexPCR. A DNA fragment of 1.8 kbp of the gyrA gene was amplified from a representative of each phylogroup or subgroup and the finalproduct was sequenced to depict a phylogenetic tree. In general, among 119 E. coli isolates, 31.93%, 6.72%, 34.45%, and 23.52% wereclustered in phylogroups A, B1, B2, and D, respectively. The phylogenetic assignment of the isolates based on the phylogenetic tree wascompletely uniform with the results of the triplex method. The outcome represents the segregation of avian pathogenic E. coli isolates tovarious phylogroups in the region. Moreover, the precise cluster analysis of E. coli based on gyrA sequencing confirms this method as arobust candidate for phylotyping of the bacterium.

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1. Obeng AS, Rickard H, Ndi O, Sexton M, Barton M. Antibiotic resistance, phylogenetic grouping and virulence potential of Escherichia coli isolated from the faeces of intensively farmed and free range poultry. Vet Microbiol 2012; 154: 305-315.
2. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 2000; 66: 4555-4558.
3. Picard B, Garcia JS, Gouriou S, Duriez P, Brahimi N, Bingen E, Elion J, Denamur E. The link between phylogeny and virulence in Escherichia coli extraintestinal infection. Infect Immun 1999; 67: 546-553.
4. Tenaillon O, Skurnik D, Picard B, Denamur E. The population genetics of commensal Escherichia coli. Nat Rev Microbiol 2010; 8: 207-217.
5. Abdelbaqi K, Menard A, Prouzet-Mauleon V, Bringaud F, Lehours P, Megraud F. Nucleotide sequence of the gyrA gene of Arcobacter species and characterization of human ciprofloxacin-resistant clinical isolates. FEMS Immunol Med Microbiol 2007; 49: 337-345.
6. Das S, Dash HR, Mangwani N, Chakraborty J, Kumari S. Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms. J Microbiol Methods 2014; 103, 80-100.
7. Menard A, Buissonniere A, Prouzet-Mauleon V, Sifre E, Megraud F. The GyrA encoded gene: a pertinent marker for the phylogenetic revision of Helicobacter genus. Syst Appl Microbiol 2016; 39: 77-87.
8. Shamsi H, Mardani K, Ownagh A. Phylogenetic analysis of Escherichia coli isolated from broilers with colibacillosis based on gyrA gene sequences. Can J Vet Res 2017; 81: 28-32.
9. Rayamajhi N, Kang SG, Lee DY, Kang ML, Lee SI, Park KY, Lee HS, Yoo HS. Characterization of TEM-, SHV- and AmpC-type beta-lactamases from cephalosporin-resistant Enterobacteriaceae isolated from swine. Int J Food Microbiol 2008; 124: 183-187.
10. Güler L, Gündüz K, Ok U. Virulence factors and antimicrobial susceptibility of Escherichia coli isolated from calves in Turkey. Zoonoses Public Health 2008; 55: 249-257.
11. Riffon R, Sayasith K, Khalil H, Dubreuil P, Drolet M, Lagace J. Development of a rapid and sensitive test for identification of major pathogens in bovine mastitis by PCR. J Clin Microbiol 2001; 39: 2584-2589.
12. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23: 2947-2948.
13. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30: 2725-2729.
14. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406-425.
15. Ghanbarpour R, Sami M, Salehi M, Ouromiei M. Phylogenetic background and virulence genes of Escherichia coli isolates from colisepticemic and healthy broiler chickens in Iran. Trop Anim Health Pro 2011; 43: 153-157.
16. Hassani B, Shayegh J, Ameghi A, Mikaili P, Mahmmudzadeh M. Phylogenic typing of Escherichia coli isolated from broilers with collibacillosis in Tabriz, North West of Iran. Arch Razi Inst 2013; 68: 43-46.
17. Kazemnia A, Ahmadi M, Dilmaghani M. Antibiotic resistance pattern of different Escherichia coli phylogenetic groups isolated from human urinary tract infection and avian colibacillosis. Iran Biomed J 2014; 18: 219-224.
18. Alizade H, Ghanbarpour R, Jajarami M, Askari A. Phylogenetic typing and molecular detection of virulence factors of avian pathogenic Escherichia coli isolated from colibacillosis cases in Japanese quail. Vet Res Forum 2017; 8: 55-58.
19. Jafari RA, Motamedi H, Maleki E, Ghanbarpour R, Mayahi M. Phylogenetic typing and detection of extended-spectrum β-lactamases in Escherichia coli isolates from broiler chickens in Ahvaz, Iran. Vet Res Forum 2016; 7: 227-233.
20. Gordon DM, Clermont O, Tolley H, Denamur E. Assigning Escherichia coli strains to phylogenetic groups: multi-locus sequence typing versus the PCR triplex method. Environ Microbiol 2008; 10: 2484-2496.
21. Bingen E, Picard B, Brahimi N, Mathy S, Desjardins P, Elion J, Denamur E. Phylogenetic analysis of Escherichia coli strains causing neonatal meningitis suggests horizontal gene transfer from a predominant pool of highly virulent B2 group strains. J Infect Dis 1998; 177: 642-650.
22. Rodriguez-Siek KE, Giddings CW, Doetkott C, Johnson TJ, Fakhr MK, Nolan LK. Comparison of Escherichia coli isolates implicated in human urinary tract infection and avian colibacillosis. Microbiology 2005; 151: 2097-2110.
23. Herzer PJ, Inouye S, Inouye M, Whittam TS. Phylogenetic distribution of branched RNA-linked multicopy singlestranded DNA among natural isolates of Escherichia coli. J Bacteriol 1990; 1722: 6175-6181.
24. Bingen E, Denamur E, Elion J. Use of ribotyping in epidemiological surveillance of nosocomial outbreaks. Clin Microbiol Rev 1994; 7: 311-317.
25. Günaydin E, Müştak HK, Önat K, diker KS. Evaluation of virulence factors and phylogrouping of Escherichia coli strains isolated from acute bovine mastitis in Turkey. Kafkas Univ Vet Fak 2017; 23: 431-435.
26. Müştak HK, Gunaydin E, Kaya IB, Salar MO, Babacan O, Onat K, Ata Z, Diker KS. Phylo-typing of clinical Escherichia coli isolates originating from bovine mastitis and canine pyometra and urinary tract infection by means of quadruplex PCR. Vet Q 2015; 35: 194-199.
27. Giray B, Uçar FB, Aydemir SŞ. Genotypic analysis of Escherichia coli strains that cause urosepsis in the Aegean region. Turk J Med Sci 2016; 46: 1518-1527.
28. Maiden MC. Multilocus sequence typing of bacteria. Annu Rev Microbiol 2006; 60: 561-588.
29. López VHM, Serrano IQ, Delgado PDPM, Rodríguez LEV, Olague-Marchán M, Rodríguez SHS, Luna MAL, de la Torre AF, Santoyo RMR. Genes of virulence and phylogenetic group in isolates of avian pathogenic Escherichia coli. Arch Med 2017; 9: 1-5.
30. Wang XM, Liao XP, Zhang WJ, Jiang HX, Sun J, Zhang MJ, He XF, Lao DX, Liu YH. Prevalence of serogroups, virulence genotypes, antimicrobial resistance, and phylogenetic background of avian pathogenic Escherichia coli in south of China. Foodborne Pathog Dis 2010; 7: 1099-1106.
31. Stromberg ZR, Johnson JR, Fairbrother JM, Kilbourne J, Van Goor A, Curtiss RR, Mellata M. Evaluation of Escherichia coli isolates from healthy chickens to determine their potential risk to poultry and human health. PLoS One 2017; 12: e0180599.
32. Carlos C, Pires MM, Stoppe NC, Hachich EM, Sato MI, Gomes TA, Amaral LA, Ottoboni LM. Escherichia coli phylogenetic group determination and its application in the identification of the major animal source of fecal contamination. BMC Microbiol 2010; 10: 161.
33. Barzan M, Rad M, Hashemi Tabar GR, Azizzadeh M. Phylogenetic analysis of Escherichia coli isolated from healthy and diarrhoeic calves in Mashhad, Iran. Bulgarian J Vet Med 2016; 20: 11-18.
34. Clermont O, Christenson JK, Denamur E, Gordon DM. The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environ Microbiol Rep 2013; 5: 58-65.
35. 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 Int 2015 2015; 1-7.
36. Logue CM, Wannemuehler Y, Nicholson BA, Doetkott C, Barbieri NL, Nolan LK. Comparative analysis of phylogenetic assignment of human and avian ExPEC and fecal commensal Escherichia coli using the (previous and revised) Clermont phylogenetic typing methods and its impact on avian pathogenic Escherichia coli (APEC) classification. Fron Microbiol 2017; 8: 283.