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rpoB gene sequencing for phylogenetic analysis of avian pathogenic Escherichia coli

  • Kwon, Hyuk-Joon (Laboratory of Poultry Clinical Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University) ;
  • Seong, Won-Jin (Laboratory of Avian Diseases, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University) ;
  • Kim, Tae-Eun (BioPOA Co.) ;
  • Won, Yong-Jin (Division of EcoScience, Ewha Womans University) ;
  • Kim, Jae-Hong (Research Institute for Veterinary Science, College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University)
  • Received : 2014.11.06
  • Accepted : 2015.01.08
  • Published : 2015.03.31

Abstract

The present study was conducted to determine the full rpoB and eight house-keeping gene sequences of 78 and 35, respectively, avian pathogenic E. coli (APEC) strains. Phylogenetic comparison with 66 E. coli and Shigella strains from GenBank and EMBL was also conducted. Based on the full rpoB sequence, 50 different rpoB sequence types (RSTs) were identified. RST 1 was assigned to a major RST that included 34.7% (50/144) of the analyzed strains. RST 2 to RST 50 were then assigned to other strains with higher nucleotide sequence similarity to RST 1 in order. RST 1, 11, and 23 were mixed with APEC along with human commensal and pathogenic strains while RST 2, 6, 9, 13-15, 22, 24, 25, 33, 34, 36, and 41 were unique to APEC strains. Only five APEC strains grouped into RST 32 and 47, which contained human pathogenic E. coli (HPEC). Thus, most of the APEC strains had genetic backgrounds different from HPEC strains. However, the minor APEC strains similar to HPEC should be considered potential zoonotic risks. The resolution power of multi-locus sequence typing (MLST) was better than RST testing. Nevertheless, phylogenetic analysis of rpoB was simpler and more economic than MLST.

Keywords

References

  1. Adekambi T, Drancourt M, Raoult D. The rpoB gene as a tool for clinical microbiologists. Trends Microbiol 2009, 17, 37-45. https://doi.org/10.1016/j.tim.2008.09.008
  2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215, 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2
  3. Bidet P, Mahjoub-Messai F, Blanco J, Blanco J, Dehem M, Aujard Y, Bingen E, Bonacorsi S. Combined multilocus sequence typing and O serogrouping distinguishes Escherichia coli subtypes associated with infant urosepsis and/or meningitis. J Infect Dis 2007, 196, 297-303. https://doi.org/10.1086/518897
  4. 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. https://doi.org/10.1086/514217
  5. Clermont O, Bonacorsi S, Bingen E. Rapid and simple determination of the Escherichia coli phylogenetic group. Appl Environ Microbiol 2000, 66, 4555-4558. https://doi.org/10.1128/AEM.66.10.4555-4558.2000
  6. Dho-Moulin M, Fairbrother JM. Avian pathogenic Escherichia coli (APEC). Vet Res 1999, 30, 299-316.
  7. Dissanayake DR, Wijewardana TG, Gunawardena GA, Poxton IR. Distribution of lipopolysaccharide core types among avian pathogenic Escherichia coli in relation to the major phylogenetic groups. Vet Microbiol 2008, 132, 355-363. https://doi.org/10.1016/j.vetmic.2008.05.024
  8. Dozois CM, Dho-Moulin M, Brée A, Fairbrother JM, Desautels C, Curtiss R 3rd. Relationship between the Tsh autotransporter and pathogenicity of avian Escherichia coli and localization and analysis of the Tsh genetic region. Infect Immun 2000, 68, 4145-4154. https://doi.org/10.1128/IAI.68.7.4145-4154.2000
  9. Ewers C, Antao EM, Diehl I, Philipp HC, Wieler LH. Intestine and environment of the chicken as reservoirs for extraintestinal pathogenic Escherichia coli strains with zoonotic potential. Appl Environ Microbiol 2009, 75, 184-192. https://doi.org/10.1128/AEM.01324-08
  10. 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 Prod 2011, 43, 153-157. https://doi.org/10.1007/s11250-010-9667-2
  11. Gross WG, Gyles CL. Diseases due to Escherichia coli in Poultry. In: Gyles CL (ed.). Escherichia coli in Domestic Animal and Humans. pp. 237-259, CAB International, Wallingford, 1994.
  12. Herrera L, Jimenez S, Valverde A, Garcia-Aranda MA, Saez-Nieto JA. Molecular analysis of rifampicin-resistant Mycobacterium tuberculosis isolated in Spain (1996-2001). Description of new mutations in the rpoB gene and review of the literature. Int J Antimicrob Agents 2003, 21, 403-408. https://doi.org/10.1016/S0924-8579(03)00036-0
  13. Jaureguy F, Landraud L, Passet V, Diancourt L, Frapy E, Guigon G, Carbonnelle E, Lortholary O, Clermont O, Denamur E, Picard B, Nassif X, Brisse S. Phylogenetic and genomic diversity of human bacteremic Escherichia coli strains. BMC Genomics 2008, 9, 560. https://doi.org/10.1186/1471-2164-9-560
  14. Jeong YW, Kim TE, Kim JH, Kwon HJ. Pathotyping avian pathogenic Escherichia coli strains in Korea. J Vet Sci 2012, 13, 145-152. https://doi.org/10.4142/jvs.2012.13.2.145
  15. Johnson JR, Delavari P, Stell AL, Whittam TS, Carlino U, Russo TA. Molecular comparison of extraintestinal Escherichia coli isolates of the same electrophoretic lineages from humans and domestic animals. J Infect Dis 2001, 183, 154-159. https://doi.org/10.1086/317662
  16. Johnson JR, Owens KL, Clabots CR, Weissman SJ, Cannon SB. Phylogenetic relationships among clonal groups of extraintestinal pathogenic Escherichia coli as assessed by multi-locus sequence analysis. Microbes Infect 2006, 8, 1702-1713. https://doi.org/10.1016/j.micinf.2006.02.007
  17. Johnson JR, Stell AL, O'Bryan TT, Kuskowski M, Nowicki B, Johnson C, Maslow JN, Kaul A, Kavle J, Prats G. Global molecular epidemiology of the O15: K52:H1 extraintestinal pathogenic Escherichia coli clonal group: evidence of distribution beyond Europe. J Clin Microbiol 2002, 40, 1913-1923. https://doi.org/10.1128/JCM.40.6.1913-1923.2002
  18. Johnson TJ, Kariyawasam S, Wannemuehler Y, Mangiamele P, Johnson SJ, Doetkott C, Skyberg JA, Lynne AM, Johnson JR, Nolan LK. The genome sequence of avian pathogenic Escherichia coli strain O1:K1:H7 shares strong similarities with human extraintestinal pathogenic E. coli genomes. J Bacteriol 2007, 189, 3228-3236. https://doi.org/10.1128/JB.01726-06
  19. Johnson TJ, Wannemuehler Y, Johnson SJ, Stell AL, Doetkott C, Johnson JR, Kim KS, Spanjaard L, Nolan LK. Comparison of extraintestinal pathogenic Escherichia coli strains from human and avian sources reveals a mixed subset representing potential zoonotic pathogens. Appl Environ Microbiol 2008, 74, 7043-7050. https://doi.org/10.1128/AEM.01395-08
  20. Lan R, Alles MC, Donohoe K, Martinez MB, Reeves PR. Molecular evolutionary relationships of enteroinvasive Escherichia coli and Shigella spp. Infect Immun 2004, 72, 5080-5088. https://doi.org/10.1128/IAI.72.9.5080-5088.2004
  21. Le Gall T, Clermont O, Gouriou S, Picard B, Nassif X, Denamur E, Tenaillon O. Extraintestinal virulence is a coincidental by-product of commensalism in B2 phylogenetic group Escherichia coli strains. Mol Biol Evol 2007, 24, 2373-2384. https://doi.org/10.1093/molbev/msm172
  22. Leopold SR, Magrini V, Holt NJ, Shaikh N, Mardis ER, Cagno J, Ogura Y, Iguchi A, Hayashi T, Mellmann A, Karch H, Besser TE, Sawyer SA, Whittam TS, Tarr PI. A precise reconstruction of the emergence and constrained radiations of Escherichia coli O157 portrayed by backbone concatenomic analysis. Proc Natl Acad Sci U S A 2009, 106, 8713-8718. https://doi.org/10.1073/pnas.0812949106
  23. Lukjancenko O, Wassenaar TM, Ussery DW. Comparison of 61 sequenced Escherichia coli genomes. Microb Ecol 2010, 60, 708-720. https://doi.org/10.1007/s00248-010-9717-3
  24. Maiden MCJ, Bygraves JA, Feil E, Morelli G, Russell JE, Urwin R, Zhang Q, Zhou J, Zurth K, Caugant DA, Feavers IM, Achtman M, Spratt BG. Multilocus sequence typing: a portable approach to the identification of clones within populations of pathogenic microorganisms. Proc Natl Acad Sci U S A 1998, 95, 3140-3145. https://doi.org/10.1073/pnas.95.6.3140
  25. Manges AR, Johnson JR, Foxman B, O'Bryan TT, Fullerton KE, Riley LW. Widespread distribution of urinary tract infections caused by a multidrug-resistant Escherichia coli clonal group. N Engl J Med 2001, 345, 1007-1013. https://doi.org/10.1056/NEJMoa011265
  26. Martínez JA, Soto S, Fabrega A, Almela M, Mensa J, Soriano A, Marco F, Jimenez de Anta MT, Vila J. Relationship of phylogenetic background, biofilm production, and time to detection of growth in blood culture vials with clinical variables and prognosis associated with Escherichia coli bacteremia. J Clin Microbiol 2006, 44, 1468-1474. https://doi.org/10.1128/JCM.44.4.1468-1474.2006
  27. Pupo GM, Lan R, Reeves PR. Multiple independent origins of Shigella clones of Escherichia coli and convergent evolution of many of their characteristics. Proc Natl Acad Sci U S A 2000, 97, 10567-10572. https://doi.org/10.1073/pnas.180094797
  28. Ron EZ. Host specificity of septicemic Escherichia coli:human and avian pathogens. Curr Opin Microbiol 2006, 9, 28-32. https://doi.org/10.1016/j.mib.2005.12.001
  29. Russo TA, Johnson JR. Proposal for a new inclusive designation for extraintestinal pathogenic isolates of Escherichia coli: ExPEC. J Infect Dis 2000, 181, 1753-1754. https://doi.org/10.1086/315418
  30. Selander RK, Caugant DA, Whittam TS. Genetic structure and variation in natural populations of Escherichia coli. In: Neidhardt FC, Ingraham JL (eds.). Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. Vol. 1. pp. 1625-1648, American Society for Microbiology, Washington, D.C., 1987.
  31. Seong WJ, Kwon HJ, Kim TE, Lee DY, Park MS, Kim JH. Molecular serotyping of Salmonella enterica by complete rpoB gene sequencing. J Microbiol 2012, 50, 962-969. https://doi.org/10.1007/s12275-012-2547-x
  32. Wirth T, Falush D, Lan R, Colles F, Mensa P, Wieler LH, Karch H, Reeves PR, Maiden MCJ, Ochman H, Achtman M. Sex and virulence in Escherichia coli: an evolutionary perspective. Mol Microbiol 2006, 60, 1136-1151. https://doi.org/10.1111/j.1365-2958.2006.05172.x
  33. Zhao L, Gao S, Huan H, Xu X, Zhu X, Yang W, Gao Q, Liu X. Comparison of virulence factors and expression of specific genes between uropathogenic Escherichia coli and avian pathogenic E. coli in a murine urinary tract infection model and a chicken challenge model. Microbiology 2009, 155, 1634-1644. https://doi.org/10.1099/mic.0.024869-0