Comparative analyses of Campylobacter concisusstrains reveal the genome of the reference strain BAA-1457 is not representative of the species

Gut Pathogens

Hazel Mitchell³  Karolina Janitz¹  Mark J Raftery⁴  Marc R Wilkins¹  Nandan P Deshpande²  Nadeem O Kaakoush³ 

[1] Ramaciotti Centre for Gene Function Analysis, The University of New South Wales, Sydney, NSW 2052, Australia;Systems Biology Initiative, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia;School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW 2052, Australia;Biological Mass Spectrometry Facility, The University of New South Wales, Sydney, NSW 2052, Australia

关键词: legionaminic acid;    pseudoaminic acid;    glycosylation;    comparative;    Campylobacter concisus;   

Others  :  833654
DOI  :  10.1186/1757-4749-3-15

 received in 2011-09-12, accepted in 2011-10-13,  发布年份 2011

【 摘 要 】

Background

Several studies have shown that significant genotypic heterogeneity exists among Campylobacter concisus strains. Recently, the genome of C. concisus UNSWCD, isolated from a patient with Crohn's disease, was sequenced.

Results

In this study, comparative analyses were performed between strain UNSWCD and BAA-1457, isolated from a patient with acute gastroenteritis. Searches between C. concisus UNSWCD and BAA-1457 showed that 76% of genes were homologues, whereas those between C. jejuni strains showed 90-91% to be homologues, indicating substantial variation exists within these two C. concisus genomes. More specific bidirectional homology searches identified 1593 genes that are shared between these strains, and 115 and 281 genes unique to UNSWCD and BAA-1457, respectively. Significantly, differences in the type of flagellin glycosylation pathways between the two strains were identified and confirmed by PCR. The protein profiles of UNSWCD, BAA-1457 and a further six strains of C. concisus were compared and analyzed bioinformatically, and this differentiated the strains into four clades. BAA-1457 was found to be highly divergent (average similarity: 56.8%) from the other seven strains (mean average similarity ± standard deviation: 64.7 ± 1.7%). Furthermore, searches for homologues of the 1593 proteins found to be common between UNSWCD and BAA-1457 were conducted against all available bacterial genomes, and 18 proteins were found to be unique to C. concisus, of which 6 were predicted to be secreted, and may represent good markers for detection of this species.

Conclusions

This study has elucidated several features that may be responsible for the heterogeneity that exists among C. concisus strains, and has determined that the strain BAA-1457 is genetically atypical to other C. concisus strains and is not a good candidate reference strain.

【 授权许可】

   
2011 Kaakoush et al; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

• [1]Vandamme P, Dewhirst FE, Paster BJ, On SLW: Campylobacter. In Bergey's Manual of Systematic Bacteriology. Edited by Brenner DJ, Krieg NR, Staley JT. New York: Springer; 2005:1147-1168.
• [2]Aabenhus R, Permin H, Andersen LP: Characterization and subgrouping of Campylobacter concisus strains using protein profiles, conventional biochemical testing and antibiotic susceptibility. Eur J Gastroenterol Hepatol 2005, 17:1019-1024.
• [3]Aabenhus R, Permin H, On SL, Andersen LP: Prevalence of Campylobacter concisus in diarrhoea of immunocompromised patients. Scand J Infect Dis 2002, 34:248-252.
• [4]Engberg J, Bang DD, Aabenhus R, Aarestrup FM, Fussing V, Gerner-Smidt P: Campylobacter concisus: an evaluation of certain phenotypic and genotypic characteristics. Clin Microbiol Infect 2005, 11:288-295.
• [5]Engberg J, On SL, Harrington CS, Gerner-Smidt P: Prevalence of Campylobacter, Arcobacter, Helicobacter, and Sutterella spp. in human fecal samples as estimated by a reevaluation of isolation methods for Campylobacters. J Clin Microbiol 2000, 38:286-291.
• [6]Lastovica AJ, le Roux E: Efficient isolation of campylobacteria from stools. J Clin Microbiol 2000, 38:2798-2799.
• [7]Lindblom GB, Sjogren E, Hansson-Westerberg J, Kaijser B: Campylobacter upsaliensis, C. sputorum sputorum and C. concisus as common causes of diarrhoea in Swedish children. Scand J Infect Dis 1995, 27:187-188.
• [8]Maher M, Finnegan C, Collins E, Ward B, Carroll C, Cormican M: Evaluation of culture methods and a DNA probe-based PCR assay for detection of Campylobacter species in clinical specimens of feces. J Clin Microbiol 2003, 41:2980-2986.
• [9]Man SM, Zhang L, Day AS, Leach ST, Lemberg DA, Mitchell H: Campylobacter concisus and other Campylobacter species in children with newly diagnosed Crohn's disease. Inflamm Bowel Dis 2009, 16:1008-1016.
• [10]Musmanno RA, Russi M, Figura N, Guglielmetti P, Zanchi A, Signori R, Rossolini A: Unusual species of campylobacters isolated in the Siena Tuscany area, Italy. New Microbiol 1998, 21:15-22.
• [11]Zhang L, Man SM, Day AS, Leach ST, Lemberg DA, Dutt S, Stormon M, Otley A, O'Loughlin EV, Magoffin A, Ng PH, Mitchell H: Detection and isolation of Campylobacter species other than C. jejuni from children with Crohn's disease. J Clin Microbiol 2009, 47:453-455.
• [12]Matsheka MI, Elisha BG, Lastovica AL, On SL: Genetic heterogeneity of Campylobacter concisus determined by pulsed field gel electrophoresis-based macrorestriction profiling. FEMS Microbiol Lett 2002, 211:17-22.
• [13]Vandamme P, Falsen E, Pot B, Hoste B, Kersters K, De Ley J: Identification of EF group 22 campylobacters from gastroenteritis cases as Campylobacter concisus. J Clin Microbiol 1989, 27:1775-1781.
• [14]Man SM, Kaakoush NO, Leach ST, Nahidi L, Lu HK, Norman J, Day AS, Zhang L, Mitchell HM: Host attachment, invasion, and stimulation of proinflammatory cytokines by Campylobacter concisus and other non-Campylobacter jejuni Campylobacter species. J Infect Dis 2010, 202:1855-1865.
• [15]De Melo MA, Gabbiani G, Pechere JC: Cellular events and intracellular survival of Campylobacter jejuni during infection of HEp-2 cells. Infect Immun 1989, 57:2214-2222.
• [16]Konkel ME, Joens LA: Adhesion to and invasion of HEp-2 cells by Campylobacter spp. Infect Immun 1989, 57:2984-2990.
• [17]Oelschlaeger TA, Guerry P, Kopecko DJ: Unusual microtubule-dependent endocytosis mechanisms triggered by Campylobacter jejuni and Citrobacter freundii. Proc Natl Acad Sci USA 1993, 90:6884-6888.
• [18]Deshpande NP, Kaakoush NO, Mitchell H, Janitz K, Raftery MJ, Li SS, Wilkins MR: Sequencing and Validation of the Genome of a Campylobacter concisus Reveals Intra-Species Diversity. PLoS One 2011, 6:e22170.
• [19]Man SM, Kaakoush NO, Octavia S, Mitchell H: The internal transcribed spacer region, a new tool for use in species differentiation and delineation of systematic relationships within the Campylobacter genus. Appl Environ Microbiol 2010, 76:3071-3081.
• [20]Pukatzki S, Ma AT, Revel AT, Sturtevant D, Mekalanos JJ: Type VI secretion system translocates a phage tail spike-like protein into target cells where it cross-links actin. Proc Natl Acad Sci USA 2007, 104:15508-15513.
• [21]Pukatzki S, McAuley SB, Miyata ST: The type VI secretion system: translocation of effectors and effector-domains. Curr Opin Microbiol 2009, 12:11-17.
• [22]Kaakoush NO, Man SM, Lamb S, Raftery MJ, Wilkins MR, Kovach Z, Mitchell H: The secretome of Campylobacter concisus. FEBS J 2010, 277:1606-1617.
• [23]Uzzau S, Fasano A: Cross-talk between enteric pathogens and the intestine. Cell Microbiol 2000, 2:83-89.
• [24]Fasano A, Fiorentini C, Donelli G, Uzzau S, Kaper JB, Margaretten K, Ding X, Guandalini S, Comstock L, Goldblum SE: Zonula occludens toxin modulates tight junctions through protein kinase C-dependent actin reorganization, in vitro. J Clin Invest 1995, 96:710-720.
• [25]Hossain MM, Nakamoto H: Role for the cyanobacterial HtpG in protection from oxidative stress. Curr Microbiol 2003, 46:70-76.
• [26]Desai BV, Morrison DA: An unstable competence-induced protein, CoiA, promotes processing of donor DNA after uptake during genetic transformation in Streptococcus pneumoniae. J Bacteriol 2006, 188:5177-5186.
• [27]Abeyrathne PD, Daniels C, Poon KK, Matewish MJ, Lam JS: Functional characterization of WaaL, a ligase associated with linking O-antigen polysaccharide to the core of Pseudomonas aeruginosa lipopolysaccharide. J Bacteriol 2005, 187:3002-3012.
• [28]Yuan Y, Crane DD, Simpson RM, Zhu YQ, Hickey MJ, Sherman DR, Barry CE: The 16-kDa alpha-crystallin (Acr) protein of Mycobacterium tuberculosis is required for growth in macrophages. Proc Natl Acad Sci USA 1998, 95:9578-9583.
• [29]Wilkinson KA, Stewart GR, Newton SM, Vordermeier HM, Wain JR, Murphy HN, Horner K, Young DB, Wilkinson RJ: Infection biology of a novel alpha-crystallin of Mycobacterium tuberculosis: Acr2. J Immunol 2005, 174:4237-4243.
• [30]Stewart GR, Newton SM, Wilkinson KA, Humphreys IR, Murphy HN, Robertson BD, Wilkinson RJ, Young DB: The stress-responsive chaperone alpha-crystallin 2 is required for pathogenesis of Mycobacterium tuberculosis. Mol Microbiol 2005, 55:1127-1137.
• [31]Stewart JN, Rivera HN, Karls R, Quinn FD, Roman J, Rivera-Marrero CA: Increased pathology in lungs of mice after infection with an alpha-crystallin mutant of Mycobacterium tuberculosis: changes in cathepsin proteases and certain cytokines. Microbiology 2006, 152:233-244.
• [32]Ewing CP, Andreishcheva E, Guerry P: Functional characterization of flagellin glycosylation in Campylobacter jejuni 81-176. J Bacteriol 2009, 191:7086-7093.
• [33]Guerry P, Ewing CP, Schirm M, Lorenzo M, Kelly J, Pattarini D, Majam G, Thibault P, Logan S: Changes in flagellin glycosylation affect Campylobacter autoagglutination and virulence. Mol Microbiol 2006, 60:299-311.
• [34]Logan SM: Flagellar glycosylation - a new component of the motility repertoire? Microbiology 2006, 152:1249-1262.
• [35]Schoenhofen IC, McNally DJ, Brisson JR, Logan SM: Elucidation of the CMP-pseudaminic acid pathway in Helicobacter pylori: synthesis from UDP-N-acetylglucosamine by a single enzymatic reaction. Glycobiology 2006, 16:8C-14C.
• [36]Schoenhofen IC, Vinogradov E, Whitfield DM, Brisson JR, Logan SM: The CMP-legionaminic acid pathway in Campylobacter: biosynthesis involving novel GDP-linked precursors. Glycobiology 2009, 19:715-725.
• [37]Istivan TS, Coloe PJ, Fry BN, Ward P, Smith SC: Characterization of a haemolytic phospholipase A(2) activity in clinical isolates of Campylobacter concisus. J Med Microbiol 2004, 53:483-493.
• [38]Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M: Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 2005, 21:3674-3676.
• [39]Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y: KEGG for linking genomes to life and the environment. Nucleic Acids Res 2008, 36:D480-484.
• [40]Stothard P, Wishart DS: Circular genome visualization and exploration using CGView. Bioinformatics 2005, 21:537-539.
• [41]Tanner ACR, Badger S, Lai C-H, Listgarten MA, Visconti RA, Socransky SS: Wolinella gen. nov., Wolinella succinogenes (Vibrio succinogens Wolin et al.) comb. nov., and description of Bacteroides gracilis sp. nov., Wolinella recta sp. nov., Campylobacter concisus sp nov., and Eikenella corrodens from humans with periodontal disease. Int J Syst Bacteriol 1981, 31:432-445.