In silico analysis of virulence associated genes in genomes of Escherichia coli strains causing colibacillosis in poultry

Open access


Introduction: Colibacillosis – the most common disease of poultry, is caused mainly by avian pathogenic Escherichia coli (APEC). However, thus far, no pattern to the molecular basis of the pathogenicity of these bacteria has been established beyond dispute. In this study, genomes of APEC were investigated to ascribe importance and explore the distribution of 16 genes recognised as their virulence factors.

Material and Methods: A total of 14 pathogenic for poultry E. coli strains were isolated, and their DNA was sequenced, assembled de novo, and annotated. Amino acid sequences from these bacteria and an additional 16 freely available APEC amino acid sequences were analysed with the DIFFIND tool to define their virulence factors.

Results: The DIFFIND tool enabled quick, reliable, and convenient assessment of the differences between compared amino acid sequences from bacterial genomes. The presence of 16 protein sequences indicated as pathogenicity factors in poultry resulted in the generation of a heatmap which categorises genomes in terms of the existence and similarity of the analysed protein sequences.

Conclusion: The proposed method of detection of virulence factors using the capabilities of the DIFFIND tool may be useful in the analysis of similarities of E. coli and other sequences deriving from bacteria. Phylogenetic analysis resulted in reliable segregation of 30 APEC strains into five main clusters containing various virulence associated genes (VAGs).

1. Barnes H.J., Nolan L.K., Vaillancourt J.P.: Colibacillosis, In: Diseases of poultry, Blackwell Publishing, Ames, 2008, pp. 691–732.

2. Dho-Moulin M., Fairbrother J. M.: Avian pathogenic Escherichia coli (APEC). Vet Res 1999, 30, 299–316.

3. Dziva F., Stevens M.P.: Colibacillosis in poultry: unravelling the molecular basis of virulence of avian pathogenic Escherichia coli in their natural hosts. Avian Pathol 2008, 37, 355–366.

4. Ewers C., Janßen T., Kießling S., Philipp H.C., Wieler L.H.: Rapid detection of virulence-associated genes in avian pathogenic Escherichia coli by multiplex polymerase chain reaction. Avian Dis 2005, 49, 269–273.

5. Ge X.Z., Jiang J., Pan Z., Hu L., Wang S., Wang H., Fan H.: Comparative genomic analysis shows that avian pathogenic Escherichia coli isolate IMT5155 (O2:K1:H5; ST complex 95, ST140) shares close relationship with ST95 APEC O1: K1 and human ExPEC O18:K1 strains. PloS One 2014, 9, e112048.

6. Giufré M., Accogli M., Graziani C., Busani L., Cerquetti M.: Whole-genome sequences of multidrug-resistant Escherichia coli strains sharing the same sequence type (ST410) and isolated from human and avian sources in Italy. Genome Announc 2015, 3, e00757–15.

7. Hejair H.M., Ma J., Zhu Y., Sun M., Dong W., Zhang Y., Yao H.: Role of outer membrane protein T in pathogenicity of avian pathogenic Escherichia coli. Res Vet Sci 2017, 115, 109–116.

8. Hunter J.D.: Matplotlib: A 2D Graphics Environment, Computing in Science and Engineering. 2007, doi:10.1109/MCSE.2007.55.

9. ISO: International Organization for Standardization, PN-ISO 7251:2006 - Microbiology of food and animal feeding stuffs – Horizontal method for the detection and enumeration of presumptive Escherichia coli – Most probable number technique. 2006, 1–18.

10. Jakobsen L., Garneau P., Kurbasic A., Bruant G., Stegger M., Harel J., Jensen K.S., Brousseau R., Hammerum A.M., Frimodt-Møller N.: Microarray-based detection of extended virulence and antimicrobial resistance gene profiles in phylogroup B2 Escherichia coli of human, meat, and animal origin. J Med Microbiol 2011, 60, 1502–1511.

11. Johnson T.J., Kariyawasam S., Wannemuehler Y., Mangiamele P., Johnson S.J., Doetkott C., Nolan L.K.: 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.

12. Johnson T.J., Wannemuehler Y., Doetkott C., Johnson S.J., Rosenberger S.C., Nolan L.K.: Identification of minimal predictors of avian pathogenic Escherichia coli virulence for use as a rapid diagnostic tool. J Clin Microbiol 2008, 46, 3987–3996.

13. Jones E., Oliphant T., Peterson P.: SciPy: open source scientific tools for Python, 2001. [Online; accessed 2017-11-07].

14. Köhler C.D., Dobrindt U.: What defines extraintestinal pathogenic Escherichia coli?. Zentralbl Bakteriol 2011, 301, 642–647.

15. Krawczyk B., Samet A., Leibner J., Śledzińska A., Kur J.: Evaluation of a PCR melting profile (PCR MP) technique for bacterial strain differentiation. J Clin Microbiol 2006, 44, 2327–2332.

16. Lutful Kabir S.M.: Avian colibacillosis and salmonellosis: a closer look at epidemiology, pathogenesis, diagnosis, control, and public health concerns. Int J Environ Res Public Health 2010, 7, 89–114.

17. Maciel J.F., Matter L.B., Trindade M.M., Camillo G., Lovato M., Avila Boton S., Vargas A.C. Virulence factors and antimicrobial susceptibility profile of extraintestinal Escherichia coli from an avian colisepticemia outbreak. Microb Pathog 2017, 103, 119–122.

18. Maluta R.P., Nicholson B., Logue C.M., Nolan L.K., Rojas T.C., da Silveira W.D.: Complete genomic sequence of an avian pathogenic Escherichia coli strain of serotype O7:HNT. Genome Announc 2016, 4, e01611–15.

19. Mangiamele P., Nicholson B., Wannemuehler Y., Seemann T., Logue C.M., Li G., Nolan L.K.: Complete genome sequence of the avian pathogenic Escherichia coli strain APEC O78. Genome Announc 2013, 1, e00026–13.

20. Marciniak B., Borówka P., Strapagiel D.: DIFFIND – The sequence difference Finder, 2017. doi: 10.5281/zenodo.556162.

21. Marciniak B., Strapagiel D.: FA_TOOL – simple command line tool for fasta file editing, 2016.

22. Marciniak B., Borówka P., Strapagiel D.: Pycdhit. 2016.

23. McKerns M., Aivazis M.: Pathos: a framework for heterogeneous computing. 2010.

24. McPeake S.J.W., Smyth J.A., Ball H.J.: Characterisation of avian pathogenic Escherichia coli (APEC) associated with colisepticaemia compared to faecal isolates from healthy birds. Vet Microbiol 2005, 245–253.

25. Nakazato G., Campos T.A.D., Stehling E.G., Brocchi M., Silveira W.D.D.: Virulence factors of avian pathogenic Escherichia coli (APEC). Pesqui Vet Bras 2009, 29, 479–486.

26. Nicholson B.A., Wannemuehler Y.M., Logue C.M., Li G., Nolan L.K.: Complete genome sequence of the avian-pathogenic Escherichia coli strain APEC O18. Genome Announc 2016, 4, e01213–16.

27. Nurk S., Bankevich A., Antipov D., Gurevich A., Korobeynikov A., Lapidus A., Prjibelsky A., Pyshkin A., Sirotkin A., Sirotkin Y., Stepanauskas R., McLean J., Lasken R., Clingenpeel S.R., Woyke T., Tesler G., Alekseyev M.A., Pevzner P.A.: Assembling genomes and mini-metagenomes from highly chimeric reads. In: Research in computational molecular biology, Springer Verlag, Heidelberg, Germany, 2013, pp. 158–170.

28. Rodriguez-Siek K.E., Giddings C.W., Doetkott C., Johnson T.J., Fakhr M.K., Nolan L.K. Comparison of Escherichia coli isolates implicated in human urinary tract infections and avian colibacillosis. Microbiology 2005, 151, 2097–2110.

29. Rojas T.C.G., Maluta R.P., Parizzi L.P., Koenigkan L.V., Yang J., Yu J., da Silveira W.D.: Genome sequences of avian pathogenic Escherichia coli strains isolated from Brazilian commercial poultry. Genome Announc 2013, 1, e00110–13.

30. Ronco T., Stegger M., Andersen P.S., Pedersen K., Li L., Thøfner I.C., Olsen R.H.: Draft genome sequences of two avian pathogenic Escherichia coli strains of clinical importance, E44 and E51. Genome Announc 2016, 4, e00768–16.

31. Silveira F., Maluta R.P., Tiba M.R., Paiva J.B., Guastalli E.A.L., Silveira W.D.: Comparison between avian pathogenic (APEC) and avian fecal (AFEC) Escherichia coli isolated from different regions in Brazil. Vet J 2016, 217, 65–67.

32. Wang X., Wei L., Wang B., Zhang R., Liu C., Bi D., Tan C.: Complete genome sequence and characterization of avian pathogenic Escherichia coli field isolate ACN001. Stand Genomic Sci 2016, 11, 13.

Journal of Veterinary Research

formerly Bulletin of the Veterinary Institute in Pulawy

Journal Information

IMPACT FACTOR J Vet Res 2018: 0,829
5-year IMPACT FACTOR: 0,938

CiteScore 2018: 0.68

SCImago Journal Rank (SJR) 2018: 0.291
Source Normalized Impact per Paper (SNIP) 2018: 0.501

Cited By


All Time Past Year Past 30 Days
Abstract Views 0 0 0
Full Text Views 410 264 18
PDF Downloads 209 152 12