Skip to content
1887

Abstract

Isolates of spp. were cultured from water sources at five different sites in central Iowa in the Midwestern United States and characterized by whole-genome sequencing. Isolates were helix-shaped and motile. Genome sequence analyses determined that the isolates could be clearly distinguished from other species described in the genus a and included one species that belonged to the pathogen subclade P1, one species that belonged to the pathogen subclade P2 and three species that belonged to the saprophyte subclade S1. The names sp. nov. (type strain WS92.C1=NVSL-WS92.C1=KIT0303), sp. nov. (type strain WS58.C1=NVSL-WS58.C1=KIT0304), sp. nov. (type strain WS4.C2=NVSL.WS4.C2=KIT0305), sp. nov. (type strain WS39.C2=NVSL-WS39.C2=KIT0306) and sp. nov. (type strain WS60.C2=NVSL-WS60.C2=KIT0307) are proposed.

Funding
This study was supported by the:
  • U.S. Department of Agriculture
    • Principal Award Recipient: CamilaHamond
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License.
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006595
2025-01-07
2025-12-16

Metrics

Loading full text...

Full text loading...

/deliver/fulltext/ijsem/75/1/ijsem006595.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.006595&mimeType=html&fmt=ahah

References

  1. Bharti AR, Nally JE, Ricaldi JN, Matthias MA, Diaz MM et al. Leptospirosis: a zoonotic disease of global importance. Lancet Infect Dis 2003; 3:757–771 [View Article] [PubMed]
    [Google Scholar]
  2. Ellis WA. Animal leptospirosis. Curr Top Microbiol Immunol 2015; 387:99–137 [View Article] [PubMed]
    [Google Scholar]
  3. Hamond C, LeCount K, Anderson T, Putz EJ, Stuber T et al. Isolation and characterization of saprophytic and pathogenic strains of Leptospira from water sources in the Midwestern United States. Front Water 2024; 6: [View Article]
    [Google Scholar]
  4. 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 [View Article] [PubMed]
    [Google Scholar]
  5. Casanovas-Massana A, Hamond C, Santos LA, de Oliveira D, Hacker KP et al. Leptospira yasudae sp. nov. and Leptospira stimsonii sp. nov., two new species of the pathogenic group isolated from environmental sources. Int J Syst Evol Microbiol 2020; 70:1450–1456 [View Article] [PubMed]
    [Google Scholar]
  6. Korba AA, Lounici H, Kainiu M, Vincent AT, Mariet J-F et al. Leptospira ainlahdjerensis sp. nov., Leptospira ainazelensis sp. nov., Leptospira abararensis sp. nov. and Leptospira chreensis sp. nov., four new species isolated from water sources in Algeria. Int J Syst Evol Microbiol 2021; 71: [View Article]
    [Google Scholar]
  7. Parte AC, Sardà Carbasse J, Meier-Kolthoff JP, Reimer LC, Göker M. List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ. Int J Syst Evol Microbiol 2020; 70:5607–5612 [View Article] [PubMed]
    [Google Scholar]
  8. Fernandes LGV, Stone NE, Roe CC, Goris MGA, van der Linden H et al. Leptospira sanjuanensis sp. nov., a pathogenic species of the genus Leptospira isolated from soil in Puerto Rico. Int J Syst Evol Microbiol 2022; 72: [View Article] [PubMed]
    [Google Scholar]
  9. Dos Santos Ribeiro P, Carvalho NB, Aburjaile F, Sousa T, Veríssimo G et al. Environmental biofilms from an urban community in Salvador, Brazil, shelter previously uncharacterized saprophytic Leptospira. Microb Ecol 2023; 86:2488–2501 [View Article] [PubMed]
    [Google Scholar]
  10. Hornsby RL, Alt DP, Nally JE. Isolation and propagation of leptospires at 37 °C directly from the mammalian host. Sci Rep 2020; 10:9620 [View Article] [PubMed]
    [Google Scholar]
  11. Chakraborty A, Miyahara S, Villanueva SYAM, Saito M, Gloriani NG et al. A novel combination of selective agents for isolation of Leptospira species. Microbiol Immunol 2011; 55:494–501 [View Article] [PubMed]
    [Google Scholar]
  12. Hamond C, Adam EN, Stone NE, LeCount K, Anderson T et al. Identification of equine mares as reservoir hosts for pathogenic species of Leptospira. Front Vet Sci 2024; 11:1346713 [View Article] [PubMed]
    [Google Scholar]
  13. Nally JE, Whitelegge JP, Bassilian S, Blanco DR, Lovett MA. Characterization of the outer membrane proteome of Leptospira interrogans expressed during acute lethal infection. Infect Immun 2007; 75:766–773 [View Article] [PubMed]
    [Google Scholar]
  14. Wick RR. Filtlong; 2021 https://github.com/rrwick/Filtlong
  15. Wick RR, Judd LM, Cerdeira LT, Hawkey J, Méric G et al. Trycycler: consensus long-read assemblies for bacterial genomes. Genome Biol 2021; 22:266 [View Article] [PubMed]
    [Google Scholar]
  16. Li H. Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences. Bioinformatics 2016; 32:2103–2110 [View Article] [PubMed]
    [Google Scholar]
  17. Vaser R, Šikić M. Time- and memory-efficient genome assembly with Raven. Nat Comput Sci 2021; 1:332–336 [View Article] [PubMed]
    [Google Scholar]
  18. Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol 2019; 37:540–546 [View Article] [PubMed]
    [Google Scholar]
  19. Wick RR, Holt KE. Polypolish: short-read polishing of long-read bacterial genome assemblies. PLOS Comput Biol 2022; 18:e1009802 [View Article] [PubMed]
    [Google Scholar]
  20. Durbin R, De Sanctis B, Blumer M. Rotate: a command-line program to rotate circular DNA sequences to start at a given position or string. Wellcome Open Res 2023; 8:401 [View Article] [PubMed]
    [Google Scholar]
  21. Li W, O’Neill KR, Haft DH, DiCuccio M, Chetvernin V et al. RefSeq: expanding the Prokaryotic Genome Annotation Pipeline reach with protein family model curation. Nucleic Acids Res 2021; 49:D1020–D1028 [View Article] [PubMed]
    [Google Scholar]
  22. Haft DH, DiCuccio M, Badretdin A, Brover V, Chetvernin V et al. RefSeq: an update on prokaryotic genome annotation and curation. Nucleic Acids Res 2018; 46:D851–D860 [View Article] [PubMed]
    [Google Scholar]
  23. Tatusova T, DiCuccio M, Badretdin A, Chetvernin V, Nawrocki EP et al. NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 2016; 44:6614–6624 [View Article] [PubMed]
    [Google Scholar]
  24. Seemann T. Barrnap; 2018 https://github.com/tseemann/barrnap
  25. 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 [View Article] [PubMed]
    [Google Scholar]
  26. 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]
  27. Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol 2020; 37:1530–1534 [View Article] [PubMed]
    [Google Scholar]
  28. Kalyaanamoorthy S, Minh BQ, Wong TKF, von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods 2017; 14:587–589 [View Article] [PubMed]
    [Google Scholar]
  29. Hoang DT, Chernomor O, von Haeseler A, Minh BQ, Vinh LS. UFBoot2: improving the ultrafast bootstrap approximation. Mol Biol Evol 2018; 35:518–522 [View Article]
    [Google Scholar]
  30. Letunic I, Bork P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res 2021; 49:W293–W296 [View Article] [PubMed]
    [Google Scholar]
  31. Perrin A, Rocha EPC. PanACoTA: a modular tool for massive microbial comparative genomics. NAR Genom Bioinform 2021; 3:lqaa106 [View Article] [PubMed]
    [Google Scholar]
  32. Steenwyk JL, Buida TJ III, Li Y, Shen X-X, Rokas A. ClipKIT: a multiple sequence alignment trimming software for accurate phylogenomic inference. PLOS Biol 2020; 18:e3001007 [View Article] [PubMed]
    [Google Scholar]
  33. Steenwyk JL, Buida TJ III, Labella AL, Li Y, Shen X-X et al. PhyKIT: a broadly applicable UNIX shell toolkit for processing and analyzing phylogenomic data. Bioinformatics 2021; 37:2325–2331 [View Article] [PubMed]
    [Google Scholar]
  34. Mo YK, Lanfear R, Hahn MW, Minh BQ. Updated site concordance factors minimize effects of homoplasy and taxon sampling. Bioinformatics 2023; 39: [View Article]
    [Google Scholar]
  35. Lee I, Ouk Kim Y, Park SC, Chun J. OrthoANI: an improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  36. Larralde M. A Python implementation of the OrthoANI algorithm for nucleotide identity measurement; 2021 https://github.com/althonos/orthoani
  37. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P et al. DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 2007; 57:81–91 [View Article] [PubMed]
    [Google Scholar]
  38. 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]
  39. Dikken H, Kmety E. Serological typing methods of leptospires. Methods Microbiol 1978; 11:259–307 [View Article]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006595
Loading
/content/journal/ijsem/10.1099/ijsem.0.006595
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An error occurred
Approval was partially successful, following selected items could not be processed due to error