1887

Abstract

is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn’s disease (CD) and ulcerative colitis (UC). Currently, only three complete genomes are available and more complete genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 . strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete genomes were analysed using bioinformatic tools. The enteric disease associations of plasmids were examined using 239 . strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete genomes in this study. Analysis of 16 complete genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding plasmids, genomospecies features, evolution, secretion systems and pathogenicity.

Funding
This study was supported by the:
  • Li Zhang , University of New South Wales , (Award PS46772)
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2020-10-28
2020-12-01
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References

  1. Zhang L, Budiman V, Day AS, Mitchell H, Lemberg DA et al. Isolation and detection of Campylobacter concisus from saliva of healthy individuals and patients with inflammatory bowel disease. J Clin Microbiol 2010; 48:2965–2967 [CrossRef][PubMed]
    [Google Scholar]
  2. Yeow M, Liu F, Ma R, Williams TJ, Riordan SM et al. Analyses of energy metabolism and stress defence provide insights into Campylobacter concisus growth and pathogenicity. Gut Pathog 2020; 12:13 [CrossRef][PubMed]
    [Google Scholar]
  3. Lee H, Ma R, Grimm MC, Riordan SM, Lan R et al. Examination of the anaerobic growth of Campylobacter concisus strains. Int J Microbiol 2014; 2014:476047 [CrossRef][PubMed]
    [Google Scholar]
  4. Zhang L, Man SM, Day AS, Leach ST, Lemberg DA et al. Detection and isolation of Campylobacter species other than C. jejuni from children with Crohn's disease. J Clin Microbiol 2009; 47:453–455 [CrossRef][PubMed]
    [Google Scholar]
  5. Mukhopadhya I, Thomson JM, Hansen R, Berry SH, El-Omar EM et al. Detection of Campylobacter concisus and other Campylobacter species in colonic biopsies from adults with ulcerative colitis. PLoS One 2011; 6:e21490-e [CrossRef][PubMed]
    [Google Scholar]
  6. Mahendran V, Riordan SM, Grimm MC, Tran TAT, Major J et al. Prevalence of Campylobacter species in adult Crohn's disease and the preferential colonization sites of Campylobacter species in the human intestine. PLoS One 2011; 6:e25417 [CrossRef][PubMed]
    [Google Scholar]
  7. Kirk KF, Nielsen HL, Thorlacius-Ussing O, Nielsen H. Optimized cultivation of Campylobacter concisus from gut mucosal biopsies in inflammatory bowel disease. Gut Pathog 2016; 8:27 [CrossRef][PubMed]
    [Google Scholar]
  8. Chandan JS, Thomas T. Inflammatory bowel disease and oral health. BDJ Team 2017; 4:17083 [CrossRef]
    [Google Scholar]
  9. Lindblom GB, Sjögren 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 [CrossRef][PubMed]
    [Google Scholar]
  10. Lastovica AJ, le Roux E. Efficient isolation of Campylobacteria from stools. J Clin Microbiol 2000; 38:2798–2800[PubMed]
    [Google Scholar]
  11. Nielsen HL, Ejlertsen T, Engberg J, Nielsen H. High incidence of Campylobacter concisus in gastroenteritis in North Jutland, Denmark: a population-based study. Clin Microbiol Infect 2013; 19:445–450 [CrossRef][PubMed]
    [Google Scholar]
  12. Macfarlane S, Furrie E, Macfarlane GT, Dillon JF. Microbial colonization of the upper gastrointestinal tract in patients with Barrett's esophagus. Clin Infect Dis 2007; 45:29–38 [CrossRef][PubMed]
    [Google Scholar]
  13. Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK et al. Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease. Sci Rep 2018; 8:1902 [CrossRef]
    [Google Scholar]
  14. Gemmell MR, Berry S, Mukhopadhya I, Hansen R, Nielsen HL et al. Comparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential. Emerg Microbes Infect 2018; 7:1–17 [CrossRef][PubMed]
    [Google Scholar]
  15. Ismail Y, Mahendran V, Octavia S, Day AS, Riordan SM et al. Investigation of the enteric pathogenic potential of oral Campylobacter concisus strains isolated from patients with inflammatory bowel disease. PLoS One 2012; 7:e38217 [CrossRef][PubMed]
    [Google Scholar]
  16. Istivan T. Molecular Characterisation of Campylobacter concisus: a Potential Etiological Agent of Gastroenteritis in Children School of Applied Sciences, RMIT University; 2005
    [Google Scholar]
  17. Miller WG, Chapman MH, Yee E, On SLW, McNulty DK et al. Multilocus sequence typing methods for the emerging Campylobacter Species C. hyointestinalis, C. lanienae, C. sputorum, C. concisus, and C. curvus . Front Cell Infect Microbiol 2012; 2:45 [CrossRef][PubMed]
    [Google Scholar]
  18. Mahendran V, Octavia S, Demirbas OF, Sabrina S, Ma R et al. Delineation of genetic relatedness and population structure of oral and enteric Campylobacter concisus strains by analysis of housekeeping genes. Microbiology 2015; 161:1600–1612 [CrossRef][PubMed]
    [Google Scholar]
  19. Chung HKL, Tay A, Octavia S, Chen J, Liu F et al. Genome analysis of Campylobacter concisus strains from patients with inflammatory bowel disease and gastroenteritis provides new insights into pathogenicity. Sci Rep 2016; 6:38442 [CrossRef][PubMed]
    [Google Scholar]
  20. Nielsen HL, Nielsen H, Torpdahl M. Multilocus sequence typing of Campylobacter concisus from Danish diarrheic patients. Gut Pathog 2016; 8:44 [CrossRef][PubMed]
    [Google Scholar]
  21. Wang Y, Liu F, Zhang X, Chung HKL, Riordan SM et al. Campylobacter concisus genomospecies 2 is better adapted to the human gastrointestinal tract as compared with Campylobacter concisus genomospecies 1. Front Physiol 2017; 8:543 [CrossRef][PubMed]
    [Google Scholar]
  22. Liu F, Ma R, Tay CYA, Octavia S, Lan R et al. Genomic analysis of oral Campylobacter concisus strains identified a potential bacterial molecular marker associated with active Crohn's disease. Emerg Microbes Infect 2018; 7:1–14 [CrossRef][PubMed]
    [Google Scholar]
  23. Tanner ACR, Badger S, Lai C-H, Listgarten MA, Visconti RA et al. Wolinella gen. nov., Wolinella succinogenes (Vibrio succinogenes 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 [CrossRef]
    [Google Scholar]
  24. Lu H, Giordano F, Ning Z. Oxford nanopore MinION sequencing and genome assembly. Genomics Proteomics Bioinformatics 2016; 14:265–279 [CrossRef]
    [Google Scholar]
  25. Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics 2018; 34:3094–3100 [CrossRef][PubMed]
    [Google Scholar]
  26. Okonechnikov K, Conesa A, García-Alcalde F. Qualimap 2: advanced multi-sample quality control for high-throughput sequencing data. Bioinformatics 2016; 32:btv566–4 [CrossRef][PubMed]
    [Google Scholar]
  27. Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH et al. Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Res 2017; 27:722–736 [CrossRef][PubMed]
    [Google Scholar]
  28. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [CrossRef][PubMed]
    [Google Scholar]
  29. Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 2017; 13:e1005595 [CrossRef][PubMed]
    [Google Scholar]
  30. Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S et al. Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 2015; 31:3691–3693 [CrossRef][PubMed]
    [Google Scholar]
  31. Frost LS, Leplae R, Summers AO, Toussaint A. Mobile genetic elements: the agents of open source evolution. Nat Rev Microbiol 2005; 3:722–732 [CrossRef][PubMed]
    [Google Scholar]
  32. Mahendran V, Tan YS, Riordan SM, Grimm MC, Day AS et al. The prevalence and polymorphisms of zonula occluden toxin gene in multiple Campylobacter concisus strains isolated from saliva of patients with inflammatory bowel disease and controls. PLoS One 2013; 8:e75525 [CrossRef][PubMed]
    [Google Scholar]
  33. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [CrossRef][PubMed]
    [Google Scholar]
  34. Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics 2015; 31:3350–3352 [CrossRef][PubMed]
    [Google Scholar]
  35. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S et al. NCBI blast: a better web interface. Nucleic Acids Res 2008; 36:W5–W9 [CrossRef][PubMed]
    [Google Scholar]
  36. Käll L, Krogh A, Sonnhammer ELL. Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res 2007; 35:W429–W432 [CrossRef][PubMed]
    [Google Scholar]
  37. Chen L, Zheng D, Liu B, Yang J, VFDB JQ. Hierarchical and refined dataset for big data analysis-10 years on. Nucleic Acids Res 2016; 2016:D694–697
    [Google Scholar]
  38. Deshpande NP, Kaakoush NO, Wilkins MR, Mitchell HM. Comparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association. BMC Genomics 2013; 14:585 [CrossRef][PubMed]
    [Google Scholar]
  39. Huq M, Van TTH, Gurtler V, Elshagmani E, Allemailem KS et al. The ribosomal RNA operon (rrn) of Campylobacter concisus supports molecular typing to genomospecies level. Gene Rep 2017; 6:8–14 [CrossRef]
    [Google Scholar]
  40. Cornelius AJ, Miller WG, Lastovica AJ, On SLW, French NP et al. Complete genome sequence of Campylobacter concisus ATCC 33237T and draft genome Sequences for an additional eight well-characterized C. concisus strains. Genome Announc 2017; 5:e00711–00717 [CrossRef][PubMed]
    [Google Scholar]
  41. Kirk KF, Méric G, Nielsen HL, Pascoe B, Sheppard SK et al. Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease. Sci Rep 2018; 8:1902 [CrossRef][PubMed]
    [Google Scholar]
  42. Kumar S, Stecher G, Tamura K. mega7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [CrossRef][PubMed]
    [Google Scholar]
  43. Edgar RC. Muscle: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792–1797 [CrossRef][PubMed]
    [Google Scholar]
  44. Aramaki T, Blanc-Mathieu R, Endo H, Ohkubo K, Kanehisa M et al. KofamKOALA: KEGG ortholog assignment based on profile HMM and adaptive score threshold. bioRxiv 2019; 602110:
    [Google Scholar]
  45. Darling ACE, Mau B, Blattner FR, Perna NT. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Genome Res 2004; 14:1394–1403 [CrossRef][PubMed]
    [Google Scholar]
  46. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal omega. Mol Syst Biol 2011; 7:539 [CrossRef][PubMed]
    [Google Scholar]
  47. Espinosa M, Cohen S, Couturier M, Del Solar G, Diaz-Orejas R et al. Plasmid replication and copy number control. The horizontal gene pool: bacterial plasmids and gene spread ; 20001–47
  48. Utter B, Deutsch DR, Schuch R, Winer BY, Verratti K et al. Beyond the chromosome: the prevalence of unique extra-chromosomal bacteriophages with integrated virulence genes in pathogenic Staphylococcus aureus . PLoS One 2014; 9:e100502 [CrossRef][PubMed]
    [Google Scholar]
  49. Wu Z, Sahin O, Shen Z, Liu P, Miller WG et al. Multi-omics approaches to deciphering a hypervirulent strain of Campylobacter jejuni . Genome Biol Evol 2013; 5:2217–2230 [CrossRef][PubMed]
    [Google Scholar]
  50. Zong Z. Complete sequence of pJIE186-2, a plasmid carrying multiple virulence factors from a sequence type 131 Escherichia coli O25 strain. Antimicrob Agents Chemother 2013; 57:597–600 [CrossRef][PubMed]
    [Google Scholar]
  51. Cornélie S, Hoebeke J, Schacht A-M, Bertin B, Vicogne J et al. Direct evidence that Toll-like receptor 9 (TLR9) functionally binds plasmid DNA by specific cytosine-phosphate-guanine motif recognition. J Biol Chem 2004; 279:15124–15129 [CrossRef][PubMed]
    [Google Scholar]
  52. Murayama SY, Seki C, Sakata H, Sunaoshi K, Nakayama E et al. Capsular type and antibiotic resistance in Streptococcus agalactiae isolates from patients, ranging from newborns to the elderly, with invasive infections. Antimicrob Agents Chemother 2009; 53:2650–2653 [CrossRef][PubMed]
    [Google Scholar]
  53. Brunings AM, Gabriel DW. Xanthomonas citri: breaking the surface. Mol Plant Pathol 2003; 4:141–157 [CrossRef][PubMed]
    [Google Scholar]
  54. Green ER, Mecsas J. Bacterial secretion systems: an overview. Microbiol Spectr 2016; 4:213–239 [CrossRef][PubMed]
    [Google Scholar]
  55. Bleumink-Pluym NMC, van Alphen LB, Bouwman LI, Wösten MMSM, van Putten JPM. Identification of a functional type VI secretion system in Campylobacter jejuni conferring capsule polysaccharide sensitive cytotoxicity. PLoS Pathog 2013; 9:e1003393 [CrossRef][PubMed]
    [Google Scholar]
  56. Ugarte-Ruiz M, Stabler RA, Domínguez L, Porrero MC, Wren BW et al. Prevalence of type VI secretion system in Spanish Campylobacter jejuni isolates. Zoonoses Public Health 2015; 62:497–500 [CrossRef][PubMed]
    [Google Scholar]
  57. Bartonickova L, Sterzenbach T, Nell S, Kops F, Schulze J et al. Hcp and VgrG 1 are secreted components of the Helicobacter hepaticus type VI secretion system and VgrG 1 increases the bacterial colitogenic potential. Cell Microbiol 2013; 15:992–1011 [CrossRef][PubMed]
    [Google Scholar]
  58. Noreen Z, Jobichen C, Abbasi R, Seetharaman J, Sivaraman J et al. Structural basis for the pathogenesis of Campylobacter jejuni Hcp1, a structural and effector protein of the Type VI Secretion System. Febs J 2018; 285:4060–4070 [CrossRef][PubMed]
    [Google Scholar]
  59. Zhang L. Oral Campylobacter species: Initiators of a subgroup of inflammatory bowel disease?. World J Gastroenterol 2015; 21:9239–9244 [CrossRef][PubMed]
    [Google Scholar]
  60. Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics 2011; 27:1009–1010 [CrossRef][PubMed]
    [Google Scholar]
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