Combining pangenome analysis to identify potential cross-protective antigens against avian pathogenic Escherichia coli

References

• Agterberg, M., Adriaanse, H., Barteling, S., van Maanen, K. & Tommassen, J. (1990). Protection of guinea-pigs against foot-and-mouth disease virus by immunization with a PhoE-FMDV hybrid protein. Vaccine, 8, 438–440.
   PubMed Web of Science ®Google Scholar
• Agterberg, M., Adriaanse, H., Lankhof, H., Meloen, R. & Tommassen, J. (1990). Outer membrane PhoE protein of Escherichia coli as a carrier for foreign antigenic determinants: immunogenicity of epitopes of foot-and-mouth disease virus. Vaccine, 8, 85–91.
   PubMed Web of Science ®Google Scholar
• Ariel, N., Zvi, A., Grosfeld, H., Gat, O., Inbar, Y., Velan, B., Cohen, S. & Shafferman, A. (2002). Search for potential vaccine candidate open reading frames in the Bacillus anthracis virulence plasmid pXO1: in silico and in vitro screening. Infection and Immunity, 70, 6817–6827.
   PubMed Web of Science ®Google Scholar
• Arp, L.H. (1980). Consequences of active or passive immunization of turkeys against Escherichia coli O78. Avian Diseases, 24, 808–815.
   PubMed Web of Science ®Google Scholar
• Bao, Y., Zhai, Z., Wang, S., Ma, J., Zhang, W. & Lu, C. (2013). Chaperonin GroEL: a novel phylogenetically conserved protein with strong immunoreactivity of avian pathogenic Escherichia coli isolates from duck identified by immunoproteomics. Vaccine, 31, 2947–2953.
   PubMed Web of Science ®Google Scholar
• Casey, W.T., Spink, N., Cia, F., Collins, C., Romano, M., Berisio, R., Bancroft, G.J. & McClean, S. (2016). Identification of an OmpW homologue in Burkholderia pseudomallei, a protective vaccine antigen against melioidosis. Vaccine, 34, 2616–2621.
   PubMed Web of Science ®Google Scholar
• Chakravarti, D.N., Fiske, M.J., Fletcher, L.D. & Zagursky, R.J. (2000). Application of genomics and proteomics for identification of bacterial gene products as potential vaccine candidates. Vaccine, 19, 601–612.
   PubMed Web of Science ®Google Scholar
• Clermont, O., Bonacorsi, S. & Bingen, E. (2000). Rapid and simple determination of the Escherichia coli phylogenetic group. Applied and Environmental Microbiology, 66, 4555–4558.
   PubMed Web of Science ®Google Scholar
• Clermont, O., Christenson, J.K., Denamur, E. & Gordon, D.M. (2013). The Clermont Escherichia coli phylo-typing method revisited: improvement of specificity and detection of new phylo-groups. Environmental Microbiology Reports, 5, 58–65.
   PubMed Web of Science ®Google Scholar
• Cloud, S.S., Rosenberger, J.K., Fries, P.A., Wilson, R.A. & Odor, E.M. (1985). In vitro and in vivo characterization of avian Escherichia coli. I. Serotypes, metabolic activity, and antibiotic sensitivity. Avian Diseases, 29, 1084–1093.
   PubMed Web of Science ®Google Scholar
• Deb, J.R. & Harry, E.G. (1978). Laboratory trials with inactivated vaccines against Escherichia coli (O2:K1) infection in fowls. Research in Veterinary Science, 24, 308–313.
   PubMed Web of Science ®Google Scholar
• Dissanayake, D.R., Octavia, S. & Lan, R. (2014). Population structure and virulence content of avian pathogenic Escherichia coli isolated from outbreaks in Sri Lanka. Veterinary Microbiology, 168, 403–412.
   PubMed Web of Science ®Google Scholar
• Donati, C. & Rappuoli, R. (2013). Reverse vaccinology in the 21st century: improvements over the original design. Annals of the New York Academy of Sciences, 1285, 115–132.
   PubMed Web of Science ®Google Scholar
• Doytchinova, I.A. & Flower, D.R. (2007). Vaxijen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8, 4.
   PubMed Web of Science ®Google Scholar
• Dziva, F. & Stevens, M.P. (2008). Colibacillosis in poultry: unravelling the molecular basis of virulence of avian pathogenic Escherichia coli in their natural hosts. Avian Pathology, 37, 355–366.
   PubMed Web of Science ®Google Scholar
• Ewers, C., Janssen, T., Kiessling, S., Philipp, H.C. & Wieler, L.H. (2004). Molecular epidemiology of avian pathogenic Escherichia coli (APEC) isolated from colisepticemia in poultry. Veterinary Microbiology, 104, 91–101.
   PubMed Web of Science ®Google Scholar
• Ewers, C., Janssen, T. & Wieler, L.H. (2003). Avian pathogenic Escherichia coli (APEC). Berliner und Münchener Tierärztliche Wochenschrift, 116, 381–395.
   PubMed Web of Science ®Google Scholar
• Fernandes Filho, T., Favaro, C., Jr., Ingberman, M., Beirao, B.C., Inoue, A., Gomes, L. & Caron, L.F. (2013). Effect of spray Escherichia coli vaccine on the immunity of poultry. Avian Diseases, 57, 671–676.
   PubMed Web of Science ®Google Scholar
• Frommer, A., Freidlin, P.J., Bock, R.R., Leitner, G., Chaffer, M. & Heller, E.D. (1994). Experimental vaccination of young chickens with a live, non-pathogenic strain of Escherichia coli. Avian Pathology, 23, 425–433.
   PubMed Web of Science ®Google Scholar
• Ghunaim, H., Abu-Madi, M.A. & Kariyawasam, S. (2014). Advances in vaccination against avian pathogenic Escherichia coli respiratory disease: potentials and limitations. Veterinary Microbiology, 172, 13–22.
   PubMed Web of Science ®Google Scholar
• Gross, W.B. (1957). Pathological changes of an Escherichia coli infection in chickens and turkeys. American Journal of Veterinary Research, 18, 724–730.
   PubMed Web of Science ®Google Scholar
• Gyimah, J.E., Panigrahy, B. & Williams, J.D. (1986). Immunogenicity of an Escherichia coli multivalent pilus vaccine in chickens. Avian Diseases, 30, 687–689.
   PubMed Web of Science ®Google Scholar
• Gyimah, J.E., Panigrapy, B., Hall, C.F. & Williams, J.D. (1985). Immunogenicity of an oil-emulsified Escherichia coli bacterin against heterologous challenge. Avian Diseases, 29, 540–545.
   PubMed Web of Science ®Google Scholar
• Han, Y., Liu, Q., Willias, S., Liang, K., Li, P., Cheng, A. & Kong, Q. (2018). A bivalent vaccine derived from attenuated Salmonella expressing O-antigen polysaccharide provides protection against avian pathogenic Escherichia coli O1 and O2 infection. Vaccine, 36, 1038–1046.
   PubMed Web of Science ®Google Scholar
• Janssen, R., Wauben, M., van der Zee, R. & Tommassen, J. (1994). Immunogenicity of a mycobacterial T-cell epitope expressed in outer membrane protein PhoE of Escherichia coli. Vaccine, 12, 406–409.
   PubMed Web of Science ®Google Scholar
• Johnson, J.R., Porter, S.B., Zhanel, G., Kuskowski, M.A. & Denamur, E. (2012). Virulence of Escherichia coli clinical isolates in a murine sepsis model in relation to sequence type ST131 status, fluoroquinolone resistance, and virulence genotype. Infection and Immunity, 80, 1554–1562.
   PubMed Web of Science ®Google Scholar
• Kariyawasam, S., Wilkie, B.N. & Gyles, C.L. (2004). Construction, characterization, and evaluation of the vaccine potential of three genetically defined mutants of avian pathogenic Escherichia coli. Avian Diseases, 48, 287–299.
   PubMed Web of Science ®Google Scholar
• Kariyawasam, S., Wilkie, B.N., Hunter, D.B. & Gyles, C.L. (2002). Systemic and mucosal antibody responses to selected cell surface antigens of avian pathogenic Escherichia coli in experimentally infected chickens. Avian Diseases, 46, 668–678.
   PubMed Web of Science ®Google Scholar
• Krogh, A., Larsson, B., von Heijne, G. & Sonnhammer, E.L. (2001). Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. Journal of Molecular Biology, 305, 567–580.
   PubMed Web of Science ®Google Scholar
• Kurupati, P., Teh, B.K., Kumarasinghe, G. & Poh, C.L. (2006). Identification of vaccine candidate antigens of an ESBL producing Klebsiella pneumoniae clinical strain by immunoproteome analysis. Proteomics, 6, 836–844.
   PubMed Web of Science ®Google Scholar
• Kwaga, J.K., Allan, B.J., Hurk, J., Seida, H. & Potter, A.A. (1994). A carAB mutant of avian pathogenic Escherichia coli serogroup O2 is attenuated and effective as a live oral vaccine against colibacillosis in turkeys. Infection and Immunity, 62, 3766.
   PubMed Web of Science ®Google Scholar
• Lynne, A.M., Kariyawasam, S., Wannemuehler, Y., Johnson, T.J., Johnson, S.J., Sinha, A.S., Lynne, D.K., Moon, H.W., Jordan, D.M., Logue, C.M., Foley, S.L. & Nolan, L.K. (2012). Recombinant Iss as a potential vaccine for avian colibacillosis. Avian Diseases, 56, 192–199.
   PubMed Web of Science ®Google Scholar
• Maiti, B., Shetty, M., Shekar, M., Karunasagar, I. & Karunasagar, I. (2012). Evaluation of two outer membrane proteins, Aha1 and OmpW of Aeromonas hydrophila as vaccine candidate for common carp. Veterinary Immunology and Immunopathology, 149, 298–301.
   PubMed Web of Science ®Google Scholar
• Matter, L.B., Barbieri, N.L., Nordhoff, M., Ewers, C. & Horn, F. (2011). Avian pathogenic Escherichia coli MT78 invades chicken fibroblasts. Veterinary Microbiology, 148, 51–59.
   PubMed Web of Science ®Google Scholar
• McNally, A., Oren, Y., Kelly, D., Pascoe, B., Dunn, S., Sreecharan, T., Vehkala, M., Välimäki, N., Prentice, M.B., Ashour, A., Avram, O., Pupko, T., Dobrindt, U., Literak, I., Guenther, S., Schaufler, K., Wieler, L.H., Zhiyong, Z., Sheppard, S.K., McInerney, J.O. & Corander, J. (2016). Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations. PLoS Genetics, 12, e1006280.
   PubMed Web of Science ®Google Scholar
• Melamed, D., Leitner, G. & Heller, E.D. (1991). A vaccine against avian colibacillosis based on ultrasonic inactivation of Escherichia coli. Avian Diseases, 35, 17–22.
   PubMed Web of Science ®Google Scholar
• Montigiani, S., Falugi, F., Scarselli, M., Finco, O., Petracca, R., Galli, G., Mariani, M., Manetti, R., Agnusdei, M., Cevenini, R., Donati, M., Nogarotto, R., Norais, N., Garaguso, I., Nuti, S., Saletti, G., Rosa, D., Ratti, G. & Grandi, G. (2002). Genomic approach for analysis of surface proteins in Chlamydia pneumoniae. Infection and Immunity, 70, 368–379.
   PubMed Web of Science ®Google Scholar
• Moulin, M.D. & Fairbrother, J.M. (1999). Avian pathogenic Escherichia coli (APEC). Veterinary Research, 30, 299.
   PubMed Web of Science ®Google Scholar
• Nakae, M., Sugahara, Y., Sasaki, H., Yasui, H. & Shibasaki, K. (1997). Serotypes and drug susceptibility of Pseudomonas aeruginosa isolated from clinical specimens. The Japanese Journal of Antibiotics, 50, 187–194.
   PubMedGoogle Scholar
• Page, A.J., Cummins, C.A., Hunt, M., Wong, V.K., Reuter, S., Holden, M.T., Fookes, M., Falush, D., Keane, J.A. & Parkhill, J. (2015). Roary: rapid large-scale prokaryote Pan genome analysis. Bioinformatics (Oxford, England), 31, 3691–3693.
   PubMed Web of Science ®Google Scholar
• Panigraphy, B., Gyimah, J.E., Hall, C.F. & Williams, J.D. (1984). Immunogenic potency of an oil-emulsified Escherichia coli bacterin. Avian Diseases, 28, 475–481.
   PubMed Web of Science ®Google Scholar
• Pilatti, L., Paiva, J.D., Rojas, T., Leite, J.L., Conceição, R.A., Nakazato, G. & Wanderley, D. (2016). The virulence factor ychO has a pleiotropic action in an avian pathogenic Escherichia coli (APEC) strain. BMC Microbiology, 16, 35.
   PubMed Web of Science ®Google Scholar
• Pizza, M., Scarlato, V., Masignani, V., Giuliani, M.M., Arico, B., Comanducci, M., Jennings, G.T., Baldi, L., Bartolini, E., Capecchi, B., Galeotti, C.L., Luzzi, E., Manetti, R., Marchetti, E., Mora, M., Nuti, S., Ratti, G., Santini, L., Savino, S., Scarselli, M., Storni, E., Zuo, P., Broeker, M., Hundt, E., Knapp, B., Blair, E., Mason, T., Tettelin, H., Hood, D.W., Jeffries, A.C., Saunders, N.J., Granoff, D.M., Venter, J.C., Moxon, E.R., Grandi, G. & Rappuoli, R. (2000). Identification of vaccine candidates against serogroup B meningococcus by whole-genome sequencing. Science, 287, 1816–1820.
   PubMed Web of Science ®Google Scholar
• Rabie, N.S. & Amin Girh, Z.M.S. (2020). Bacterial vaccines in poultry. Bulletin of the National Research Centre, 44, 15.
   PubMedGoogle Scholar
• Rasko, D.A., Rosovitz, M.J., Myers, G.S., Mongodin, E.F., Fricke, W.F., Gajer, P., Crabtree, J., Sebaihia, M., Thomson, N.R., Chaudhuri, R., Henderson, I.R., Sperandio, V. & Ravel, J. (2008). The pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates. Journal of Bacteriology, 190, 6881–6893.
   PubMed Web of Science ®Google Scholar
• Seemann, T. (2014). Prokka: rapid prokaryotic genome annotation. Bioinformatics, 30, 2068–2069.
   PubMed Web of Science ®Google Scholar
• Szmolka, A. & Nagy, B. (2013). Multidrug resistant commensal Escherichia coli in animals and its impact for public health. Frontiers in Microbiology, 4, 258.
   PubMed Web of Science ®Google Scholar
• Tommassen, J., Agterberg, M., Janssen, R. & Spierings, G. (1993). Use of the enterobacterial outer membrane protein PhoE in the development of new vaccines and DNA probes. Zentralblatt Für Bakteriologie International Journal of Medical Microbiology, 278, 396–406.
   PubMedGoogle Scholar
• Vandekerchove, D., De Herdt, P., Laevens, H. & Pasmans, F. (2004). Colibacillosis in caged layer hens: characteristics of the disease and the aetiological agent. Avian Pathology, 33, 117–125.
   PubMed Web of Science ®Google Scholar
• Wizemann, T.M., Heinrichs, J.H., Adamou, J.E., Erwin, A.L., Kunsch, C., Choi, G.H., Barash, S.C., Rosen, C.A., Masure, H.R. & Tuomanen, E. (2001). Use of a whole genome approach to identify vaccine molecules affording protection against Streptococcus pneumoniae infection. Infection and Immunity, 69, 1593–1598.
   PubMed Web of Science ®Google Scholar
• Yaguchi, K., Ohgitani, T., Noro, T., Kaneshige, T. & Shimizu, Y. (2009). Vaccination of chickens with liposomal inactivated avian pathogenic Escherichia coli (APEC) vaccine by eye drop or coarse spray administration. Avian Diseases, 53, 245–249.
   PubMed Web of Science ®Google Scholar
• Yang, J.N., Wang, C., Guo, C., Peng, X.X. & Li, H. (2011). Outer membrane proteome and its regulation networks in response to glucose concentration changes in Escherichia coli. Molecular Biosystems, 7, 3087–3093.
   PubMedGoogle Scholar
• Yasmin, H. & Yaqoub, A. (2018). Identification of cross-protective potential antigens against pathogenic Brucella spp. through combining Pan-genome analysis with reverse vaccinology. Journal of Immunology Research, 2018, 1474517.
   PubMed Web of Science ®Google Scholar
• Yu, N.Y., Wagner, J.R., Laird, M.R., Melli, G., Rey, S., Lo, R., Dao, P., Sahinalp, S.C., Ester, M., Foster, L.J. & Brinkman, F.S. (2010). PSORTb 3.0: improved protein subcellular localization prediction with refined localization subcategories and predictive capabilities for all prokaryotes. Bioinformatics, 26, 1608–1615.
   PubMed Web of Science ®Google Scholar
• Zhu Ge, X., Jiang, J., Pan, Z., Hu, L., Wang, S., Wang, H., Leung, F.C., Dai, J. & Fan, H. (2014). 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, 9, e112048.
   PubMed Web of Science ®Google Scholar