Treponema pallidum strain DAL-1 is a human uncultivable pathogen causing the sexually transmitted disease syphilis. Strain DAL-1 was isolated from the amniotic fluid of a pregnant woman in the secondary stage of syphilis. Here we describe the 1,139,971 bp long genome of T. pallidum strain DAL-1 which was sequenced using two independent sequencing methods (454 pyrosequencing and Illumina). In rabbits, strain DAL-1 replicated better than the T. pallidum strain Nichols. The comparison of the complete DAL-1 genome sequence with the Nichols sequence revealed a list of genetic differences that are potentially responsible for the increased rabbit virulence of the DAL-1 strain.

Department of Biology Faculty of Medicine Masaryk University Brno Czech Republic

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Fraser CM, Norris SJ, Weinstock CM, White O, Sutton GG, Dodson R, Gwinn M, Hickey EK, Clayton R, Ketchum KA, et al. Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 1998; 281:375-388 10.1126/science.281.5375.375 PubMed DOI

Matějková P, Strouhal M, Šmajs D, Norris SJ, Palzkill T, Petrosino JF, Sodergren E, Norton JE, Singh J, Richmond TA, et al. Complete genome sequence of Treponema pallidum ssp pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol 2008; 8:76 10.1186/1471-2180-8-76 PubMed DOI PMC

Giacani L, Jeffrey BM, Molini BJ, Le HT, Lukehart SA, Centurion-Lara A, Rockey DD. Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain. J Bacteriol 2010; 192:2645-2646 10.1128/JB.00159-10 PubMed DOI PMC

Čejková D, Zobaníková M, Chen L, Pospíšilová P, Strouhal M, Qin X, Mikalová L, Norris SJ, Muzny DM, Gibbs RA, et al. Whole Genome Sequences of Three Treponema pallidum ssp. pertenue Strains: Yaws and Syphilis Treponemes Differ in Less than 0.2% of the Genome Sequence. PLoS Negl Trop Dis 2012; 6:e1471 10.1371/journal.pntd.0001471 PubMed DOI PMC

Šmajs D, Zobaníková M, Strouhal M, Čejková D, Dugan-Rocha S, Pospíšilová P, Norris SJ, Albert T, Qin X, Hallsworth-Pepin K, et al. Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: The loss of infectivity to humans is associated with genome decay. PLoS ONE 2011; 6:e20415 10.1371/journal.pone.0020415 PubMed DOI PMC

Šmajs D, Norris SJ, Weinstock GM. Genetic diversity in Treponema pallidum: Implications for pathogenesis, evolution and molecular diagnostics of syphilis and yaws. Infect Genet Evol 2012; 12:191-202 10.1016/j.meegid.2011.12.001 PubMed DOI PMC

Wendel GD, Sanchez PJ, Peters MT, Harstad TW, Potter LL, Norgard MV. Identification of Treponema pallidum in amniotic fluid and fetal blood from pregnancies complicated by congenital syphilis. Obstet Gynecol 1991; 78:890-895 PubMed DOI

Schaudin FR, Hoffmann E. Vorläufiger Bericht über das Vorkommen von Spirochäten in syphilitischen Krandkheitprodukten und bei Papillomen. Arb K Gesund 1905; 22:527-534

Miao RM, Fieldsteel AH. Genetic relationship between Treponema pallidum and Treponema pertenue, two noncultivable human pathogens. J Bacteriol 1980; 141:427-429 PubMed DOI PMC

Castellani A. Further observations on parangi (Yaws). BMJ 1905; 2:1330-1331 10.1136/bmj.2.2342.1330-a PubMed DOI PMC

Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547 10.1038/nbt1360 PubMed DOI PMC

Woese CR, Kandler O, Wheelis ML. Towards a Natural System of Organisms: Proposal for the Domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579 10.1073/pnas.87.12.4576 PubMed DOI PMC

Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.

Ludwig W, Euzeby J, Whitman WG. Draft taxonomic outline of the Bacteroidetes, Planctomycetes, Chlamydiae, Spirochaetes, Fibrobacteres, Fusobacteria, Acidobacteria, Verrucomicrobia, Dictyoglomi, and Gemmatimonadetes http://www.bergeys.org/outlines/Bergeys_Vol_4_Outline.pdf Taxonomic Outline 2008. DOI

Judicial Commission of the International Committee on Systematics of Prokaryotes The nomenclatural types of the orders Acholeplasmatales, Halanaerobiales, Halobacteriales, Methanobacteriales, Methanococcales, Methanomicrobiales, Planctomycetales, Prochlorales, Sulfolobales, Thermococcales, Thermoproteales and Verrucomicrobiales are the genera Acholeplasma, Halanaerobium, Halobacterium, Methanobacterium, Methanococcus, Methanomicrobium, Planctomyces, Prochloron, Sulfolobus, Thermococcus, Thermoproteus and Verrucomicrobium, respectively. Opinion 79. Int J Syst Evol Microbiol 2005; 55:517-518 10.1099/ijs.0.63548-0 PubMed DOI

Buchanan RE. Studies in the Nomenclature and Classification of the Bacteria: II. The Primary Subdivisions of the Schizomycetes. J Bacteriol 1917; 2:155-164 PubMed DOI PMC

Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420 10.1099/00207713-30-1-225 PubMed DOI

Swellengrebel NH. Sur la cytologie comparée des spirochètes et des spirilles. Ann Inst Pasteur (Paris) 1907; 21:562-586

Schaudinn F. Zur Kenntnis der Spirochaete pallida. Dtsch Med Wochenschr 1905; 31:1728 10.1055/s-0029-1188418 DOI

Smibert RM. Genus III. Treponema Schaudinn 1905, 1728. In: Buchanan RE, Gibbons NE (eds), Bergey's Manual of Determinative Bacteriology, Eighth Edition, The Williams and Wilkins Co., Baltimore, 1974, p. 175-184. DOI

Fieldsteel AH, Cox DL, Moeckli RA. Further studies on replication of virulent Treponema pallidum in tissue cultures of SFLEP cells. Infect Immun 1982; 35:449-455 PubMed DOI PMC

Baseman JB, Nichols JC, Hayes NS. Virulent Treponema pallidum - aerobe or anaerobe. Infect Immun 1976; 13:704-711 PubMed DOI PMC

Nichols JC, Baseman JB. Carbon sources utilized by virulent Treponema pallidum. Infect Immun 1975; 12:1044-1050 PubMed DOI PMC

Schiller NL, Cox CD. Catabolism of glucose and fatty acids by virulent Treponema pallidum. Infect Immun 1977; 16:60-68 PubMed DOI PMC

Turner TB, Hollander DH. Biology of the treponematoses based on studies carried out at the International Treponematosis Laboratory Center of the Johns Hopkins University under the auspices of the World Health Organization. Monogr Ser World Health Organ 1957; 35:3-266 PubMed

BAuA. Classification of Bacteria and Archaea in risk groups. www.baua.de TRBA 466 p. 349. DOI

Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al Gene ontology: tool for the unification of biology. Nat Genet 2000; 25(1):25-29. pmid: 10802651 PubMed PMC

Project RD.http://rdp.cme.msu.edu/treebuilderpub/treeHelp.jsp

Bruno WJ, Socci ND, Halpern AL. Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 2000; 17:189-197 10.1093/oxfordjournals.molbev.a026231 PubMed DOI

Som A. Theoretical foundation to estimate the relative efficiencies of the Jukes-Cantor+gamma model and the Jukes-Cantor model in obtaining the correct phylogenetic tree. Gene 2006; 385:103-110 10.1016/j.gene.2006.03.027 PubMed DOI

Jepsen OB, Hougen KH, Birch-Andersen A. Electron microscopy of Treponema pallidum Nichols. Acta Pathol Microbiol Scand 1968; 74:241-258 10.1111/j.1699-0463.1968.tb03477.x PubMed DOI

Fieldsteel AH, Cox DL, Moeckli RA. Cultivation of virulent Treponema pallidum in tissue culture. Infect Immun 1981; 32:908-915 PubMed DOI PMC

Norris SJ. Invitro cultivation of Treponema pallidum - independent confirmation. Infect Immun 1982; 36:437-439 PubMed DOI PMC

Wagner-Jauregg J. Über die Einwirkung der Malaria auf die progressive Paralyse. Psychiatr Neurol Wochenschr 1918; 20:132-134

Norris SJ, Edmondson DG. Invitro culture system to determine MICS and MBSC of antimicrobial agents against Treponema pallidum subsp. pallidum (Nichols strain). AAC 1988; 32:68-74 PubMed DOI PMC

Stamm LV, Bergen HL. A point mutation associated with bacterial macrolide resistance is present in both 23S rRNA genes of an erythromycin-resistant Treponema pallidum clinical isolate. AAC 2000; 44(3):806-807. pmcid: 89774 PubMed DOI PMC

Matějková P, Flasarová M, Zakoucká H, Borek M, Křemenová S, Arenberger P, Woznicová V, Weinstock GM, Šmajs D. Macrolide treatment failure in a case of secondary syphilis: a novel A2059G mutation in the 23S rRNA gene of Treponema pallidum subsp pallidum. J Med Microbiol 2009; 58:832-836 10.1099/jmm.0.007542-0 PubMed DOI

Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2010; 38(Database issue):D346-D354 10.1093/nar/gkp848 PubMed DOI PMC

Baseman JB, Nichols JC, Rumpp JW, Hayes NS. Purification of Treponema pallidum from infected rabbit tissue - resolution into two treponemal populations. Infect Immun 1974; 10:1062-1067 PubMed DOI PMC

Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829 10.1101/gr.074492.107 PubMed DOI PMC

DOE Joint Genome Institute http://img.jgi.doe.gov/

Brinkman MB, McGill MA, Pettersson J, Rogers A, Matejkova P, Smajs D, Weinstock GM, Norris SJ, Palzkill T. A novel Treponema pallidum antigen, TP0136, is an outer membrane protein that binds human fibronectin. Infect Immun 2008; 76:1848-1857 10.1128/IAI.01424-07 PubMed DOI PMC

LaFond RE, Centurion-Lara A, Godornes C, Van Voorhis WC, Lukehart SA. TprK sequence diversity accumulates during infection of rabbits with Treponema pallidum subsp. pallidum Nichols strain. Infect Immun 2006; 74:1896-1906 10.1128/IAI.74.3.1896-1906.2006 PubMed DOI PMC

Centurion-Lara A, Godornes C, Castro C, Van Voorhis WC, Lukehart SA. The tprK gene is heterogeneous among Treponema pallidum strains and has multiple alleles. Infect Immun 2000; 68:824-831 10.1128/IAI.68.2.824-831.2000 PubMed DOI PMC

Centurion-Lara A, Sun ES, Barrett LK, Castro C, Lukehart SA, Van Voorhis WC. Multiple alleles of Treponema pallidum repeat gene D in Treponema pallidum isolates. J Bacteriol 2000; 182:2332-2335 10.1128/JB.182.8.2332-2335.2000 PubMed DOI PMC

LaFond RE, Centurion-Lara A, Godornes C, Rompalo AM, Van Voorhis WC, Lukehart SA. Sequence diversity of Treponema pallidum subsp. pallidum tprK in human syphilis lesions and rabbit-propagated isolates. J Bacteriol 2003; 185:6262-6268 10.1128/JB.185.21.6262-6268.2003 PubMed DOI PMC

Leader BT, Hevner K, Molini BJ, Barrett LK, Van Voorhis WC, Lukehart SA. Antibody responses elicited against the Treponema pallidum repeat proteins differ during infection with different isolates of Treponema pallidum subsp. pallidum. Infect Immun 2003; 71:6054-6057 10.1128/IAI.71.10.6054-6057.2003 PubMed DOI PMC

Palmer GH, Bankhead T, Lukehart SA. 'Nothing is permanent but change' - antigenic variation in persistent bacterial pathogens. Cell Microbiol 2009; 11:1697-1705 10.1111/j.1462-5822.2009.01366.x PubMed DOI PMC

Giacani L, Molini B, Godornes C, Barrett L, Van Voorhis W, Centurion-Lara A, Lukehart SA. Quantitative analysis of tpr gene expression in Treponema pallidum isolates: Differences among isolates and correlation with T-cell responsiveness in experimental syphilis. Infect Immun 2007; 75:104-112 10.1128/IAI.01124-06 PubMed DOI PMC

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