1887

Abstract

The enteric, pathogenic spirochaete colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus . Our study revealed that an additional isolate that was unable to be species typed against any other lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the as random mutation (/=1.02). Comparative genomics has informed diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.

  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2020-11-11
2021-10-21
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References

  1. Ludwig W, Euzeby J, Whitman WB. Draft taxonomic outline of the Bacteroidetes, Planctomycetes, chlamydiae, spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi and Gemmatimonadetes. wwwbergeysorg/outlines/ Bergeys_Vol_4_Outlinepdf01/05/12 ; 2008
  2. Hampson DJ. The spirochete Brachyspira pilosicoli, enteric pathogen of animals and humans. Clin Microbiol Rev 2018; 31: [View Article][PubMed]
    [Google Scholar]
  3. La T, Phillips ND, Hampson DJ. An investigation into the etiological agents of swine dysentery in Australian pig herds. PLoS One 2016; 11:e0167424 [View Article][PubMed]
    [Google Scholar]
  4. Mirajkar NS, Phillips ND, La T, Hampson DJ, Gebhart CJ. Characterization and recognition of Brachyspira hampsonii sp. nov., a novel intestinal spirochete that is pathogenic to pigs. J Clin Microbiol 2016; 54:2942–2949 [View Article][PubMed]
    [Google Scholar]
  5. Mushtaq M, Zubair S, Råsbäck T, Bongcam-Rudloff E, Jansson DS. Brachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics. BMC Microbiol 2015; 15:208 [View Article][PubMed]
    [Google Scholar]
  6. Osorio J, Carvajal A, Naharro G, Rubio P, La T et al. Identification of weakly haemolytic Brachyspira isolates recovered from pigs with diarrhoea in Spain and Portugal and comparison with results from other countries. Res Vet Sci 2013; 95:861–869 [View Article][PubMed]
    [Google Scholar]
  7. Mappley LJ, La Ragione RM, Woodward MJ. Brachyspira and its role in avian intestinal spirochaetosis. Vet Microbiol 2014; 168:245–260 [View Article][PubMed]
    [Google Scholar]
  8. Mirajkar NS, Bekele AZ, Chander YY, Gebhart CJ. Molecular epidemiology of novel pathogen "Brachyspira hampsonii" reveals relationships between diverse genetic groups, regions, host species, and other pathogenic and commensal Brachyspira species. J Clin Microbiol 2015; 53:2908–2918 [View Article][PubMed]
    [Google Scholar]
  9. Burch DGS, Strugnell BW, Steventon A, Watson EN, Harding C. Survey of 222 flocks in Great Britain for the presence of Brachyspira species and their effect on production. Proceedings of the 5th International Conference on Colonic Spirochaetal Infections in Animals and Humans Leon, Spain; 2009
  10. Hovind-Hougen K, Birch-Andersen A, Henrik-Nielsen R, Orholm M, Pedersen JO et al. Intestinal spirochetosis: morphological characterization and cultivation of the spirochete Brachyspira aalborgi gen. nov., sp. nov. J Clin Microbiol 1982; 16:1127–1136 [View Article][PubMed]
    [Google Scholar]
  11. Mikosza AS, Hampson DJ. Human intestinal spirochetosis: Brachyspira aalborgi and/or Brachyspira pilosicoli?. Anim Health Res Rev 2001; 2:101–110 [View Article][PubMed]
    [Google Scholar]
  12. Trivett-Moore NL, Gilbert GL, Law CL, Trott DJ, Hampson DJ. Isolation of Serpulina pilosicoli from rectal biopsy specimens showing evidence of intestinal spirochetosis. J Clin Microbiol 1998; 36:261–265 [View Article][PubMed]
    [Google Scholar]
  13. Smith JL. Colonic spirochetosis in animals and humans. J Food Prot 2005; 68:1525–1534 [View Article][PubMed]
    [Google Scholar]
  14. Hampson DJ, Oxberry SL, La T. Potential for zoonotic transmission of Brachyspira pilosicoli . Emerg Infect Dis 2006; 12:869–870 [View Article][PubMed]
    [Google Scholar]
  15. Koopman MB, Käsbohrer A, Beckmann G, van der Zeijst BA, Kusters JG. Genetic similarity of intestinal spirochetes from humans and various animal species. J Clin Microbiol 1993; 31:711–716 [View Article][PubMed]
    [Google Scholar]
  16. Neo E, La T, Phillips ND, Alikani MY, Hampson DJ. The pathogenic intestinal spirochaete Brachyspira pilosicoli forms a diverse recombinant species demonstrating some local clustering of related strains and potential for zoonotic spread. Gut Pathog 2013; 5:24 [View Article][PubMed]
    [Google Scholar]
  17. Trott DJ, Stanton TB, Jensen NS, Duhamel GE, Johnson JL et al. Serpulina pilosicoli sp. nov., the agent of porcine intestinal spirochetosis. Int J Syst Bacteriol 1996; 46:206–215 [View Article][PubMed]
    [Google Scholar]
  18. Le Roy CI, Mappley LJ, La Ragione RM, Woodward MJ, Claus SP. Brachyspira pilosicoli-induced avian intestinal spirochaetosis. Microb Ecol Health Dis 2015; 26:28853 [View Article][PubMed]
    [Google Scholar]
  19. Stephens CP, Hampson DJ. Intestinal spirochete infections of chickens: a review of disease associations, epidemiology and control. Anim Health Res Rev 2001; 2:83–91 [View Article][PubMed]
    [Google Scholar]
  20. Jansson DS, Persson M, Zimmerman U, Johansson KE. Phenotypic and genetic diversity among intestinal spirochaetes (genus Brachyspira) in free-living wild mallards (Anas platyrhynchos) sampled in southern Sweden. Syst Appl Microbiol 2011; 34:566–575 [View Article][PubMed]
    [Google Scholar]
  21. Oxberry SL, Trott DJ, Hampson DJ. Serpulina pilosicoli, waterbirds and water: potential sources of infection for humans and other animals. Epidemiol Infect 1998; 121:219–225 [View Article][PubMed]
    [Google Scholar]
  22. Shivaprasad HL, Duhamel GE. Cecal spirochetosis caused by Brachyspira pilosicoli in commercial turkeys. Avian Dis 2005; 49:609–613 [View Article][PubMed]
    [Google Scholar]
  23. Jansson DS, Bröjer C, Gavier-Widén D, Gunnarsson A, Fellström C. Brachyspira spp. (Serpulina spp.) in birds: a review and results from a study of Swedish game birds. Anim Health Res Rev 2001; 2:93–100 [View Article][PubMed]
    [Google Scholar]
  24. Webb DM, Duhamel GE, Mathiesen MR, Muniappa N, White AK. Cecal spirochetosis associated with Serpulina pilosicoli in captive juvenile ring-necked pheasants. Avian Dis 1997; 41:997–1002 [View Article][PubMed]
    [Google Scholar]
  25. Backhans A, Jansson DS, Aspán A, Fellström C. Typing of Brachyspira spp. from rodents, pigs and chickens on Swedish farms. Vet Microbiol 2011; 153:156–162 [View Article][PubMed]
    [Google Scholar]
  26. Backhans A, Johansson K-E, Fellström C. Phenotypic and molecular characterization of Brachyspira spp. isolated from wild rodents. Environ Microbiol Rep 2010; 2:720–727 [View Article][PubMed]
    [Google Scholar]
  27. Duhamel GE, Trott DJ, Muniappa N, Mathiesen MR, Tarasiuk K et al. Canine intestinal spirochetes consist of Serpulina pilosicoli and a newly identified group provisionally designated "Serpulina canis" sp. nov. J Clin Microbiol 1998; 36:2264–2270 [View Article][PubMed]
    [Google Scholar]
  28. Hidalgo A, Rubio P, Osorio J, Carvajal A. Prevalence of Brachyspira pilosicoli and "Brachyspira canis" in dogs and their association with diarrhoea. Vet Microbiol 2010; 146:356–360 [View Article][PubMed]
    [Google Scholar]
  29. Oxberry SL, Hampson DJ. Colonisation of pet shop puppies with Brachyspira pilosicoli . Vet Microbiol 2003; 93:167–174 [View Article][PubMed]
    [Google Scholar]
  30. Hampson DJ, Lester GD, Phillips ND, La T. Isolation of Brachyspira pilosicoli from weanling horses with chronic diarrhoea. Vet Rec 2006; 158:661–662 [View Article][PubMed]
    [Google Scholar]
  31. Duhamel GE. Comparative pathology and pathogenesis of naturally acquired and experimentally induced colonic spirochetosis. Anim Health Res Rev 2001; 2:3–18 [View Article][PubMed]
    [Google Scholar]
  32. Margawani KR, Robertson ID, Hampson DJ. Isolation of the anaerobic intestinal spirochaete Brachyspira pilosicoli from long-term residents and Indonesian visitors to Perth, Western Australia. J Med Microbiol 2009; 58:248–252 [View Article][PubMed]
    [Google Scholar]
  33. Caro-Quintero A, Ritalahti KM, Cusick KD, Löffler FE, Konstantinidis KT. The chimeric genome of Sphaerochaeta: nonspiral spirochetes that break with the prevalent dogma in spirochete biology. mBio 2012; 3: [View Article][PubMed]
    [Google Scholar]
  34. Bellgard MI, Wanchanthuek P, La T, Ryan K, Moolhuijzen P et al. Genome sequence of the pathogenic intestinal spirochete Brachyspira hyodysenteriae reveals adaptations to its lifestyle in the porcine large intestine. PLoS One 2009; 4:e4641 [View Article][PubMed]
    [Google Scholar]
  35. Wood DE, Salzberg SL. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biol 2014; 15:R46 [View Article][PubMed]
    [Google Scholar]
  36. Leimbach A. Bac-Genomics-Scripts: bovine E. coli mastitis comparative genomics edition. Genome Announc 2016
    [Google Scholar]
  37. Phillips ND, La T, Hampson DJ. A cross-sectional study to investigate the occurrence and distribution of intestinal spirochaetes (Brachyspira spp.) in three flocks of laying hens. Vet Microbiol 2005; 105:189–198 [View Article][PubMed]
    [Google Scholar]
  38. Mikosza AS, La T, de Boer WB, Hampson DJ. Comparative prevalences of Brachyspira aalborgi and Brachyspira (Serpulina) pilosicoli as etiologic agents of histologically identified intestinal spirochetosis in Australia. J Clin Microbiol 2001; 39:347–350 [View Article][PubMed]
    [Google Scholar]
  39. Coil D, Jospin G, Darling AE. A5-miseq: an updated pipeline to assemble microbial genomes from illumina MiSeq data. Bioinformatics 2015; 31:587–589 [View Article][PubMed]
    [Google Scholar]
  40. Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 2014; 30:2114–2120 [View Article][PubMed]
    [Google Scholar]
  41. Simpson JT, Durbin R. Efficient de novo assembly of large genomes using compressed data structures. Genome Res 2012; 22:549–556 [View Article][PubMed]
    [Google Scholar]
  42. Peng Y, Leung HCM, Yiu SM, Chin FYL. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 2012; 28:1420–1428 [View Article][PubMed]
    [Google Scholar]
  43. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013; 29:1072–1075 [View Article][PubMed]
    [Google Scholar]
  44. Inouye M, Dashnow H, Raven L-A, Schultz MB, Pope BJ et al. SRST2: rapid genomic surveillance for public health and hospital microbiology Labs. Genome Med 2014; 6:90 [View Article][PubMed]
    [Google Scholar]
  45. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article][PubMed]
    [Google Scholar]
  46. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article][PubMed]
    [Google Scholar]
  47. 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 [View Article][PubMed]
    [Google Scholar]
  48. Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article][PubMed]
    [Google Scholar]
  49. Rambaut A. FigTree, a graphical viewer of phylogenetic trees. http://tree.bio.ed.ac.uk/software/figtree . Inst Evol Biol Univ Edinburgh 2016
    [Google Scholar]
  50. Hadfield J, Croucher NJ, Goater RJ, Abudahab K, Aanensen DM et al. Phandango: an interactive viewer for bacterial population genomics. Bioinformatics 2017
    [Google Scholar]
  51. Treangen TJ, Ondov BD, Koren S, Phillippy AM. The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol 2014; 15:524 [View Article][PubMed]
    [Google Scholar]
  52. Rice P, Longden I, Bleasby A. EMBOSS: the European molecular biology open software suite. Trends Genet 2000; 16:276–277 [View Article][PubMed]
    [Google Scholar]
  53. Guindon S, Delsuc F, Dufayard J-F, Gascuel O. Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol 2009; 537:113–137 [View Article][PubMed]
    [Google Scholar]
  54. Popescu A-A, Huber KT, Paradis E. Ape 3.0: new tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics 2012; 28:1536–1537 [View Article][PubMed]
    [Google Scholar]
  55. Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res 2019; 47:D309–D314 [View Article][PubMed]
    [Google Scholar]
  56. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 2018; 9:5114 [View Article][PubMed]
    [Google Scholar]
  57. Pritchard L, Glover RH, Humphris S, Elphinstone JG, Toth IK. Genomics and taxonomy in diagnostics for food security: soft-rotting enterobacterial plant pathogens. Analytical Methods 2016; 8:12–24 [View Article]
    [Google Scholar]
  58. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci U S A 2009; 106:19126–19131 [View Article][PubMed]
    [Google Scholar]
  59. Wanchanthuek P, Bellgard MI, La T, Ryan K, Moolhuijzen P et al. The complete genome sequence of the pathogenic intestinal spirochete Brachyspira pilosicoli and comparison with other Brachyspira genomes. PLoS One 2010; 5:e11455 [View Article][PubMed]
    [Google Scholar]
  60. Casas V, Rodríguez-Asiain A, Pinto-Llorente R, Vadillo S, Carrascal M et al. Brachyspira hyodysenteriae and B. pilosicoli proteins recognized by sera of challenged pigs. Front Microbiol 2017; 8:723 [View Article][PubMed]
    [Google Scholar]
  61. Bakshi U, Sarkar M, Paul S, Dutta C. Assessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach - Identification of pathogen-specific and habitat-specific genes. Sci Rep 2016; 6:38648 [View Article][PubMed]
    [Google Scholar]
  62. Black M, Moolhuijzen P, Barrero R, La T, Phillips N et al. Analysis of multiple Brachyspira hyodysenteriae genomes confirms that the species is relatively conserved but has potentially important strain variation. PLoS One 2015; 10:e0131050 [View Article][PubMed]
    [Google Scholar]
  63. Håfström T, Jansson DS, Segerman B. Complete genome sequence of Brachyspira intermedia reveals unique genomic features in Brachyspira species and phage-mediated horizontal gene transfer. BMC Genomics 2011; 12:395 [View Article][PubMed]
    [Google Scholar]
  64. Lin C, den Bakker HC, Suzuki H, Lefébure T, Ponnala L et al. Complete genome sequence of the porcine strain Brachyspira pilosicoli P43/6/78(T.). Genome Announc 2013; 1: [View Article][PubMed]
    [Google Scholar]
  65. Mappley LJ, Black ML, AbuOun M, Darby AC, Woodward MJ et al. Comparative genomics of Brachyspira pilosicoli strains: genome rearrangements, reductions and correlation of genetic compliment with phenotypic diversity. BMC Genomics 2012; 13:454 [View Article][PubMed]
    [Google Scholar]
  66. Mirajkar NS, Johnson TJ, Gebhart CJ. Complete Genome Sequence of Brachyspira hyodysenteriae Type Strain B-78 (ATCC 27164). Genome Announc 2016; 4: [View Article][PubMed]
    [Google Scholar]
  67. Pati A, Sikorski J, Gronow S, Munk C, Lapidus A et al. Complete genome sequence of Brachyspira murdochii type strain (56-150). Stand Genomic Sci 2010; 2:260–269 [View Article][PubMed]
    [Google Scholar]
  68. Stanton TB, Postic D, Jensen NS. Serpulina alvinipulli sp. nov., a new Serpulina species that is enteropathogenic for chickens. Int J Syst Bacteriol 1998; 48 Pt 3:669–676 [View Article][PubMed]
    [Google Scholar]
  69. Hampson DJ, Wang P. Colonic spirochetes: what has genomics taught us?. Curr Top Microbiol Immunol 2018; 415:273–294 [View Article][PubMed]
    [Google Scholar]
  70. Stanton TB, Fournié-Amazouz E, Postic D, Trott DJ, Grimont PA et al. Recognition of two new species of intestinal spirochetes: Serpulina intermedia sp. nov. and Serpulina murdochii sp. nov. Int J Syst Bacteriol 1997; 47:1007–1012 [View Article][PubMed]
    [Google Scholar]
  71. Zuerner RL, Stanton TB, Minion FC, Li C, Charon NW et al. Genetic variation in Brachyspira: chromosomal rearrangements and sequence drift distinguish B. pilosicoli from B. hyodysenteriae . Anaerobe 2004; 10:229–237 [View Article][PubMed]
    [Google Scholar]
  72. Stanton TB, Trott DJ, Lee JI, McLaren AJ, Hampson DJ et al. Differentiation of intestinal spirochaetes by multilocus enzyme electrophoresis analysis and 16S rRNA sequence comparisons. FEMS Microbiol Lett 1996; 136:181–186 [View Article][PubMed]
    [Google Scholar]
  73. Atyeo RF, Oxberry SL, Hampson DJ. Pulsed-field gel electrophoresis for sub-specific differentiation of Serpulina pilosicoli (formerly 'Anguillina coli'). FEMS Microbiol Lett 1996; 141:77–81 [View Article][PubMed]
    [Google Scholar]
  74. Neo E, La T, Phillips ND, Hampson DJ. Multiple locus variable number tandem repeat analysis (MLVA) of the pathogenic intestinal spirochaete Brachyspira pilosicoli . Vet Microbiol 2013; 163:299–304 [View Article][PubMed]
    [Google Scholar]
  75. González-Torres P, Rodríguez-Mateos F, Antón J, Gabaldón T. Impact of homologous recombination on the evolution of prokaryotic core genomes. MBio 2019; 10:e02494-18 [View Article][PubMed]
    [Google Scholar]
  76. Råsbäck T, Johansson K-E, Jansson DS, Fellström C, Alikhani MY et al. Development of a multilocus sequence typing scheme for intestinal spirochaetes within the genus Brachyspira . Microbiology 2007; 153:4074–4087 [View Article][PubMed]
    [Google Scholar]
  77. Vos M, Didelot X. A comparison of homologous recombination rates in bacteria and archaea. Isme J 2009; 3:199–208 [View Article][PubMed]
    [Google Scholar]
  78. Lee BJ, Hampson DJ. Lipo-oligosaccharide profiles of Serpulina pilosicoli strains and their serological cross-reactivities. J Med Microbiol 1999; 48:411–415 [View Article][PubMed]
    [Google Scholar]
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