1887

Abstract

Four spirochetes (F1, B21, Yale and AMB6-RJ) were isolated from environmental sources: F1 and B21 from soils of an urban slum community in Salvador (Brazil), Yale from river water in New Haven, Connecticut (USA) and AMB6-RJ from a pond in a horse farm in Rio de Janeiro (Brazil). Isolates were helix-shaped, aerobic, highly motile and non-virulent in a hamster model of infection. Draft genomes of the strains were obtained and analysed to determine the relatedness to other species of the genus Leptospira . The analysis of 498 core genes showed that strains F1/B21 and Yale/AMB6-RJ formed two distinct phylogenetic clades within the ‘Pathogens’ group (group I). The average nucleotide identity (ANI) values of strains F1/B21 and Yale/AMB6-RJ to other previously described Leptospira species were below <84 % and <82 %, respectively, which confirmed that these isolates should be classified as representatives of two novel species. Therefore, we propose Leptospira yasudae sp. nov. and Leptospira stimsonii sp. nov. as new species in the genus Leptospira . The type strains are F1 (=ATCC-TSD-163=KIT0259=CLEP00287) and Yale (=ATCC-TDS-162=KIT0258=CLEP00288), respectively.

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/content/journal/ijsem/10.1099/ijsem.0.003480
2019-06-11
2019-08-19
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References

  1. Costa F, Hagan JE, Calcagno J, Kane M, Torgerson P et al. Global morbidity and mortality of leptospirosis: a systematic review. PLoS Negl Trop Dis 2015;9: e0003898 [CrossRef] [PubMed]
    [Google Scholar]
  2. Torgerson PR, Hagan JE, Costa F, Calcagno J, Kane M et al. Global burden of leptospirosis: estimated in terms of disability adjusted life years. PLoS Negl Trop Dis 2015;9: e0004122 [CrossRef] [PubMed]
    [Google Scholar]
  3. Picardeau M. Virulence of the zoonotic agent of leptospirosis: still terra incognita?. Nat Rev Microbiol 2017;15: 297– 307 [CrossRef] [PubMed]
    [Google Scholar]
  4. Ko AI, Goarant C, Picardeau M. Leptospira: the dawn of the molecular genetics era for an emerging zoonotic pathogen. Nat Rev Microbiol 2009;7: 736– 747 [CrossRef] [PubMed]
    [Google Scholar]
  5. Thibeaux R, Iraola G, Ferrés I, Bierque E, Girault D et al. Deciphering the unexplored Leptospira diversity from soils uncovers genomic evolution to virulence. Microb Genom 2018;4: [CrossRef] [PubMed]
    [Google Scholar]
  6. Thibeaux R, Girault D, Bierque E, Soupé-Gilbert ME, Rettinger A et al. Biodiversity of environmental Leptospira: improving identification and revisiting the diagnosis. Front Microbiol 2018;9: 816 [CrossRef] [PubMed]
    [Google Scholar]
  7. Vincent AT, Schiettekatte O, Goarant C, Neela VK, Bernet E et al. Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics. PLoS Negl Trop Dis 2019;13: e0007270 [CrossRef] [PubMed]
    [Google Scholar]
  8. Hagan JE, Moraga P, Costa F, Capian N, Ribeiro GS et al. Spatiotemporal determinants of urban leptospirosis transmission: four-year prospective cohort study of slum residents in Brazil. PLoS Negl Trop Dis 2016;10: e0004275 [CrossRef] [PubMed]
    [Google Scholar]
  9. Felzemburgh RD, Ribeiro GS, Costa F, Reis RB, Hagan JE et al. Prospective study of leptospirosis transmission in an urban slum community: role of poor environment in repeated exposures to the Leptospira agent. PLoS Negl Trop Dis 2014;8: e2927 [CrossRef] [PubMed]
    [Google Scholar]
  10. Schneider AG, Casanovas-Massana A, Hacker KP, Wunder EA, Begon M et al. Quantification of pathogenic Leptospira in the soils of a Brazilian urban slum. PLoS Negl Trop Dis 2018;12: e0006415 [CrossRef] [PubMed]
    [Google Scholar]
  11. Casanovas-Massana A, Costa F, Riediger IN, Cunha M, de Oliveira D et al. Spatial and temporal dynamics of pathogenic Leptospira in surface waters from the urban slum environment. Water Res 2018;130: 176– 184 [CrossRef] [PubMed]
    [Google Scholar]
  12. Chakraborty A, Miyahara S, Villanueva SY, Saito M, Gloriani NG et al. A novel combination of selective agents for isolation of Leptospira species. Microbiol Immunol 2011;55: 494– 501 [CrossRef] [PubMed]
    [Google Scholar]
  13. Johnson RC, Rogers P. Differentiation of pathogenic and saprophytic leptospires with 8-azaguanine. J Bacteriol 1964;88: 1618– 1623 [PubMed]
    [Google Scholar]
  14. Nikolenko SI, Korobeynikov AI, Alekseyev MA. BayesHammer: Bayesian clustering for error correction in single-cell sequencing. BMC Genomics 2013;14: S7 [CrossRef] [PubMed]
    [Google Scholar]
  15. Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 2012;19: 455– 477 [CrossRef] [PubMed]
    [Google Scholar]
  16. Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 2013;29: 1072– 1075 [CrossRef] [PubMed]
    [Google Scholar]
  17. Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep 2015;5: 8365 [CrossRef] [PubMed]
    [Google Scholar]
  18. Wattam AR, Davis JJ, Assaf R, Boisvert S, Brettin T et al. Improvements to PATRIC, the all-bacterial Bioinformatics Database and Analysis Resource Center. Nucleic Acids Res 2017;45: D535– D542 [CrossRef] [PubMed]
    [Google Scholar]
  19. Seemann T. barrnap 0.7 : rapid ribosomal RNA prediction. 2013; https://github.com/tseemann/barrnap
  20. Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update. Nucleic Acids Res 2016;44: W3– W10 [CrossRef] [PubMed]
    [Google Scholar]
  21. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004;32: 1792– 1797 [CrossRef] [PubMed]
    [Google Scholar]
  22. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W et al. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol 2010;59: 307– 321 [CrossRef] [PubMed]
    [Google Scholar]
  23. Morey RE, Galloway RL, Bragg SL, Steigerwalt AG, Mayer LW et al. Species-specific identification of Leptospiraceae by 16S rRNA gene sequencing. J Clin Microbiol 2006;44: 3510– 3516 [CrossRef] [PubMed]
    [Google Scholar]
  24. Bourhy P, Collet L, Brisse S, Picardeau M. Leptospira mayottensis sp. nov., a pathogenic species of the genus Leptospira isolated from humans. Int J Syst Evol Microbiol 2014;64: 4061– 4067 [CrossRef] [PubMed]
    [Google Scholar]
  25. 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]
  26. Katoh K, Misawa K, Kuma K, Miyata T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res 2002;30: 3059– 3066 [CrossRef] [PubMed]
    [Google Scholar]
  27. Stamatakis A. RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies. Bioinformatics 2014;30: 1312– 1313 [CrossRef] [PubMed]
    [Google Scholar]
  28. Konstantinidis KT, Tiedje JM. Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 2005;102: 2567– 2572 [CrossRef] [PubMed]
    [Google Scholar]
  29. Richter M, Rosselló-Móra R, Oliver Glöckner F, Peplies J. JSpeciesWS: a web server for prokaryotic species circumscription based on pairwise genome comparison. Bioinformatics 2016;32: 929– 931 [CrossRef] [PubMed]
    [Google Scholar]
  30. Richter M, Rosselló-Móra R. Shifting the genomic gold standard for the prokaryotic species definition. Proc Natl Acad Sci USA 2009;106: 19126– 19131 [CrossRef] [PubMed]
    [Google Scholar]
  31. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J et al. BLAST+: architecture and applications. BMC Bioinformatics 2009;10: 421 [CrossRef] [PubMed]
    [Google Scholar]
  32. Cock PJ, Chilton JM, Grüning B, Johnson JE, Soranzo N. NCBI BLAST+ integrated into Galaxy. Gigascience 2015;4: 39 [CrossRef] [PubMed]
    [Google Scholar]
  33. Adhikarla H, Wunder EA, Mechaly AE, Mehta S, Wang Z et al. Lvr, a signaling system that controls global gene regulation and virulence in pathogenic Leptospira. Front Cell Infect Microbiol 2018;8: 45 [CrossRef] [PubMed]
    [Google Scholar]
  34. Ko AI, Reis MG, Dourado CM, Johnson WD Jr, Riley LW et al. Urban epidemic of severe leptospirosis in Brazil. Lancet 1999;354: 820– 825
    [Google Scholar]
  35. Nascimento AL, Ko AI, Martins EA, Monteiro-Vitorello CB, Ho PL et al. Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J Bacteriol 2004;186: 2164– 2172 [CrossRef] [PubMed]
    [Google Scholar]
  36. Wunder EA, Figueira CP, Santos GR, Lourdault K, Matthias MA et al. Real-time PCR reveals rapid dissemination of Leptospira interrogans after intraperitoneal and conjunctival inoculation of hamsters. Infect Immun 2016;84: 2105– 2115 [CrossRef] [PubMed]
    [Google Scholar]
  37. Smythe LD, Smith IL, Smith GA, Dohnt MF, Symonds ML et al. A quantitative PCR (TaqMan) assay for pathogenic Leptospira spp. BMC Infect Dis 2002;2: 13 [CrossRef] [PubMed]
    [Google Scholar]
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