This study examined the sequences of the two rRNA (rrn) operons of pathogenic non-cultivable treponemes, comprising 11 strains of T. pallidum ssp. pallidum (TPA), five strains of T. pallidum ssp. pertenue (TPE), two strains of T. pallidum ssp. endemicum (TEN), a simian Fribourg-Blanc strain and a rabbit T. paraluiscuniculi (TPc) strain. PCR was used to determine the type of 16S-23S ribosomal intergenic spacers in the rrn operons from 30 clinical samples belonging to five different genotypes. When compared with the TPA strains, TPc Cuniculi A strain had a 17 bp deletion, and the TPE, TEN and Fribourg-Blanc isolates had a deletion of 33 bp. Other than these deletions, only 17 heterogeneous sites were found within the entire region (excluding the 16S-23S intergenic spacer region encoding tRNA-Ile or tRNA-Ala). The pattern of nucleotide changes in the rrn operons corresponded to the classification of treponemal strains, whilst two different rrn spacer patterns (Ile/Ala and Ala/Ile) appeared to be distributed randomly across species/subspecies classification, time and geographical source of the treponemal strains. It is suggested that the random distribution of tRNA genes is caused by reciprocal translocation between repetitive sequences mediated by a recBCD-like system.

Department of Biology Faculty of Medicine Masaryk University Kamenice 5 Building A6 62500 Brno Czech Republic

The Genome Institute Washington University in St Louis 4444 Forest Park Avenue St Louis MO 63108 USA

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Acinas S. G., Marcelino L. A., Klepac-Ceraj V., Polz M. F. (2004). Divergence and redundancy of 16S rRNA sequences in genomes with multiple rrn operons. J Bacteriol 186, 2629–2635 10.1128/JB.186.9.2629-2635.2004 PubMed DOI PMC

Antón A. I., Martínez-Murcia A. J., Rodríguez-Valera F. (1998). Sequence diversity in the 16S–23S intergenic spacer region (ISR) of the rRNA operons in representatives of the Escherichia coli ECOR collection. J Mol Evol 47, 62–72 10.1007/PL00006363 PubMed DOI

Baseman J. B., Nichols J. C., Rumpp J. W., Hayes N. S. (1974). Purification of Treponema pallidum from infected rabbit tissue: resolution into two treponemal populations. Infect Immun 10, 1062–1067 PubMed PMC

Bunikis J., Garpmo U., Tsao J., Berglund J., Fish D., Barbour A. G. (2004). Sequence typing reveals extensive strain diversity of the Lyme borreliosis agents Borrelia burgdorferi in North America and Borrelia afzelii in Europe. Microbiology 150, 1741–1755 10.1099/mic.0.26944-0 PubMed DOI

Čejková D., Zobaníková M., Chen L., Pospíšilová P., Strouhal M., Qin X., Mikalová L., Norris S. J., Muzny D. M. & other authors (2012). 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 6, e1471 10.1371/journal.pntd.0001471 PubMed DOI PMC

Centurion-Lara A., Castro C., van Voorhis W. C., Lukehart S. A. (1996). Two 16S–23S ribosomal DNA intergenic regions in different Treponema pallidum subspecies contain tRNA genes. FEMS Microbiol Lett 143, 235–240 10.1111/j.1574-6968.1996.tb08486.x PubMed DOI

Comstedt P., Asokliene L., Eliasson I., Olsen B., Wallensten A., Bunikis J., Bergström S. (2009). Complex population structure of Lyme borreliosis group spirochete Borrelia garinii in subarctic Eurasia. PLoS ONE 4, e5841 10.1371/journal.pone.0005841 PubMed DOI PMC

Condon C., Philips J., Fu Z. Y., Squires C., Squires C. L. (1992). Comparison of the expression of the seven ribosomal RNA operons in Escherichia coli. EMBO J 11, 4175–4185 PubMed PMC

Darling A. E., Miklós I., Ragan M. A. (2008). Dynamics of genome rearrangement in bacterial populations. PLoS Genet 4, e1000128 10.1371/journal.pgen.1000128 PubMed DOI PMC

de Vries M. C., Siezen R. J., Wijman J. G., Zhao Y., Kleerebezem M., de Vos W. M., Vaughan E. E. (2006). Comparative and functional analysis of the rRNA-operons and their tRNA gene complement in different lactic acid bacteria. Syst Appl Microbiol 29, 358–367 10.1016/j.syapm.2005.11.010 PubMed DOI

Flasarová M., Šmajs D., Matějková P., Woznicová V., Heroldová-Dvoráková M., Votava M. (2006). [Molecular detection and subtyping of Treponema pallidum subsp. pallidum in clinical specimens]. Epidemiol Mikrobiol Imunol 55, 105–111 (in Czech). PubMed

Flasarová M., Pospíšilová P., Mikalová L., Vališová Z., Dastychová E., Strnadel R., Kuklová I., Woznicová V., Zákoucká H., Šmajs D. (2012). Sequencing-based molecular typing of Treponema pallidum strains in the Czech Republic: all identified genotypes are related to the sequence of the SS14 strain. Acta Derm Venereol 92, 669–674 PubMed

Fraser C. M., Casjens S., Huang W. M., Sutton G. G., Clayton R., Lathigra R., White O., Ketchum K. A., Dodson R. & other authors (1997). Genomic sequence of a Lyme disease spirochaete, Borrelia burgdorferi. Nature 390, 580–586 10.1038/37551 PubMed DOI

Fraser C. M., Norris S. J., Weinstock G. M., White O., Sutton G. G., Dodson R., Gwinn M., Hickey E. K., Clayton R. & other authors (1998). Complete genome sequence of Treponema pallidum, the syphilis spirochete. Science 281, 375–388 10.1126/science.281.5375.375 PubMed DOI

Fribourg-Blanc A., Mollaret H. H. (1969). Natural treponematosis of the African primate. Primates Med 3, 113–121 PubMed

Fukunaga M., Okuzako N., Mifuchi I., Arimitsu Y., Seki M. (1992). Organization of the ribosomal RNA genes in Treponema phagedenis and Treponema pallidum. Microbiol Immunol 36, 161–167 PubMed

Gastinel P., Vaisman A., Hamelin A., Dunoyer F. (1963). [Study of a recently isolated strain of Treponema pertenue]. Prophyl Sanit Morale 35, 182–188 (in French). PubMed

Giacani L., Jeffrey B. M., Molini B. J., Le H. T., Lukehart S. A., Centurion-Lara A., Rockey D. D. (2010). Complete genome sequence and annotation of the Treponema pallidum subsp. pallidum Chicago strain. J Bacteriol 192, 2645–2646 10.1128/JB.00159-10 PubMed DOI PMC

Giacani L., Chattopadhyay S., Centurion-Lara A., Jeffrey B. M., Le H. T., Molini B. J., Lukehart S. A., Sokurenko E. V., Rockey D. D. (2012). Footprint of positive selection in Treponema pallidum subsp. pallidum genome sequences suggests adaptive microevolution of the syphilis pathogen. PLoS Negl Trop Dis 6, e1698 10.1371/journal.pntd.0001698 PubMed DOI PMC

Gürtler V. (1999). The role of recombination and mutation in 16S–23S rDNA spacer rearrangements. Gene 238, 241–252 10.1016/S0378-1119(99)00224-3 PubMed DOI

Gürtler V., Stanisich V. A. (1996). New approaches to typing and identification of bacteria using the 16S–23S rDNA spacer region. Microbiology 142, 3–16 10.1099/13500872-142-1-3 PubMed DOI

Hanincová K., Liveris D., Sandigursky S., Wormser G. P., Schwartz I. (2008). Borrelia burgdorferi sensu stricto is clonal in patients with early Lyme borreliosis. Appl Environ Microbiol 74, 5008–5014 10.1128/AEM.00479-08 PubMed DOI PMC

Hardy J. B., Hardy P. H., Oppenheimer E. H., Ryan S. J., Jr, Sheff R. N. (1970). Failure of penicillin in a newborn with congenital syphilis. JAMA 212, 1345–1349 10.1001/jama.1970.03170210051008 PubMed DOI

Harvey S., Hill C. W. (1990). Exchange of spacer regions between rRNA operons in Escherichia coli. Genetics 125, 683–690 PubMed PMC

Hashimoto J. G., Stevenson B. S., Schmidt T. M. (2003). Rates and consequences of recombination between rRNA operons. J Bacteriol 185, 966–972 10.1128/JB.185.3.966-972.2003 PubMed DOI PMC

Indra A., Blaschitz M., Kernbichler S., Reischl U., Wewalka G., Allerberger F. (2010). Mechanisms behind variation in the Clostridium difficile 16S–23S rRNA intergenic spacer region. J Med Microbiol 59, 1317–1323 10.1099/jmm.0.020792-0 PubMed DOI PMC

Kobayashi I. (1992). Mechanisms for gene conversion and homologous recombination: the double-strand break repair model and the successive half crossing-over model. Adv Biophys 28, 81–133 10.1016/0065-227X(92)90023-K PubMed DOI

Lan R. T., Reeves P. R. (1998). Recombination between rRNA operons created most of the ribotype variation observed in the seventh pandemic clone of Vibrio cholerae. Microbiology 144, 1213–1221 10.1099/00221287-144-5-1213 PubMed DOI

Lebuhn M., Bathe S., Achouak W., Hartmann A., Heulin T., Schloter M. (2006). Comparative sequence analysis of the internal transcribed spacer 1 of Ochrobactrum species. Syst Appl Microbiol 29, 265–275 10.1016/j.syapm.2005.11.003 PubMed DOI

Liao D. (2000). Gene conversion drives within genic sequences: concerted evolution of ribosomal RNA genes in bacteria and archaea. J Mol Evol 51, 305–317 PubMed

Liska S. L., Perine P. L., Hunter E. F., Crawford J. A., Feeley J. C. (1982). Isolation and transportation of Treponema pertenue in golden hamsters. Curr Microbiol 7, 41–43 10.1007/BF01570978 DOI

Liu H., Rodes B., Chen C.-Y., Steiner B. (2001). New tests for syphilis: rational design of a PCR method for detection of Treponema pallidum in clinical specimens using unique regions of the DNA polymerase I gene. J Clin Microbiol 39, 1941–1946 10.1128/JCM.39.5.1941-1946.2001 PubMed DOI PMC

Liveris D., Wormser G. P., Nowakowski J., Nadelman R., Bittker S., Cooper D., Varde S., Moy F. H., Forseter G. & other authors (1996). Molecular typing of Borrelia burgdorferi from Lyme disease patients by PCR-restriction fragment length polymorphism analysis. J Clin Microbiol 34, 1306–1309 PubMed PMC

Martin D. P., Lemey P., Lott M., Moulton V., Posada D., Lefeuvre P. (2010). rdp3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26, 2462–2463 10.1093/bioinformatics/btq467 PubMed DOI PMC

Matějková P., Strouhal M., Šmajs D., Norris S. J., Palzkill T., Petrosino J. F., Sodergren E., Norton J. E., Singh J. & other authors (2008). Complete genome sequence of Treponema pallidum ssp. pallidum strain SS14 determined with oligonucleotide arrays. BMC Microbiol 8, 76 10.1186/1471-2180-8-76 PubMed DOI PMC

Matějková P., Flasarová M., Zákoucká H., Boˇrek M., Kremenová S., Arenberger P., Woznicová V., Weinstock G. M., Šmajs D. (2009). 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 58, 832–836 10.1099/jmm.0.007542-0 PubMed DOI

Nei M., Rooney A. P. (2005). Concerted and birth-and-death evolution of multigene families. Annu Rev Genet 39, 121–152 10.1146/annurev.genet.39.073003.112240 PubMed DOI PMC

Nichols H. J., Hough W. H. (1913). Demonstration of Spirochaeta pallida in the cerebrospinal fluid: from a patient with nervous relapse following the use of salvarsan. JAMA 60, 108–110 10.1001/jama.1913.04340020016005 DOI

Pei A., Nossa C. W., Chokshi P., Blaser M. J., Yang L., Rosmarin D. M., Pei Z. (2009). Diversity of 23S rRNA genes within individual prokaryotic genomes. PLoS ONE 4, e5437 10.1371/journal.pone.0005437 PubMed DOI PMC

Pei A. Y., Oberdorf W. E., Nossa C. W., Agarwal A., Chokshi P., Gerz E. A., Jin Z., Lee P., Yang L. & other authors (2010). Diversity of 16S rRNA genes within individual prokaryotic genomes. Appl Environ Microbiol 76, 3886–3897 10.1128/AEM.02953-09 PubMed DOI PMC

Petes T. D., Hill C. W. (1988). Recombination between repeated genes in microorganisms. Annu Rev Genet 22, 147–168 10.1146/annurev.ge.22.120188.001051 PubMed DOI

Petit M.-A. (2005). Mechanisms of homologous recombination in bacteria. In The Dynamic Bacterial Genome, pp. 3–32 Edited by Mullany P. New York: Cambridge University Press; 10.1017/CBO9780511541544.001 DOI

Pillay A., Liu H., Chen C.-Y., Holloway B., Sturm A. W., Steiner B., Morse S. A. (1998). Molecular subtyping of Treponema pallidum subspecies pallidum. Sex Transm Dis 25, 408–414 10.1097/00007435-199809000-00004 PubMed DOI

Posada D., Crandall K. A. (2001). Evaluation of methods for detecting recombination from DNA sequences: computer simulations. Proc Natl Acad Sci U S A 98, 13757–13762 10.1073/pnas.241370698 PubMed DOI PMC

Rozen S., Skaletsky H. (2000). Primer3 on the WWW for general users and for biologist programmers. Methods Mol Biol 132, 365–386 PubMed

Sadeghifard N., Gürtler V., Beer M., Seviour R. J. (2006). The mosaic nature of intergenic 16S–23S rRNA spacer regions suggests rRNA operon copy number variation in Clostridium difficile strains. Appl Environ Microbiol 72, 7311–7323 10.1128/AEM.01179-06 PubMed DOI PMC

Saitou N., Nei M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406–425 PubMed

Santoyo G., Romero D. (2005). Gene conversion and concerted evolution in bacterial genomes. FEMS Microbiol Rev 29, 169–183 PubMed

Sawyer S. (1989). Statistical tests for detecting gene conversion. Mol Biol Evol 6, 526–538 PubMed

Schwartz J. J., Gazumyan A., Schwartz I. (1992). rRNA gene organization in the Lyme disease spirochete, Borrelia burgdorferi. J Bacteriol 174, 3757–3765 PubMed PMC

Seshadri R., Myers G. S., Tettelin H., Eisen J. A., Heidelberg J. F., Dodson R. J., Davidsen T. M., DeBoy R. T., Fouts D. E. & other authors (2004). Comparison of the genome of the oral pathogen Treponema denticola with other spirochete genomes. Proc Natl Acad Sci U S A 101, 5646–5651 10.1073/pnas.0307639101 PubMed DOI PMC

Šmajs D., Mikalová L., Čejková D., Strouhal M., Zobaníková M., Pospisilova P., Norris S. J., Weinstock G. M. (2011a). Whole genome analyses of treponemes: new targets for strain- and subspecies-specific molecular diagnostics. In Syphilis – Recognition, Description and Diagnosis, pp. 19–34 Edited by Sato N. S. Rijeka, Croatia: InTech; 10.5772/21496 DOI

Šmajs D., Zobaníková M., Strouhal M., Čejková D., Dugan-Rocha S., Pospís˜ilová P., Norris S. J., Albert T., Qin X. & other authors (2011b). Complete genome sequence of Treponema paraluiscuniculi, strain Cuniculi A: the loss of infectivity to humans is associated with genome decay. PLoS ONE 6, e20415 10.1371/journal.pone.0020415 PubMed DOI PMC

Smith J. M. (1992). Analyzing the mosaic structure of genes. J Mol Evol 34, 126–129 10.1007/BF00182389 PubMed DOI

Stamm L. V., Bergen H. L. (2000). A point mutation associated with bacterial macrolide resistance is present in both 23S rRNA genes of an erythromycin-resistant Treponema pallidum clinical isolate. Antimicrob Agents Chemother 44, 806–807 10.1128/AAC.44.3.806-807.2000 PubMed DOI PMC

Stamm L. V., Kerner T. C., Jr, Bankaitis V. A., Bassford P. J., Jr (1983). Identification and preliminary characterization of Treponema pallidum protein antigens expressed in Escherichia coli. Infect Immun 41, 709–721 PubMed PMC

Stamm L. V., Bergen H. L., Walker R. L. (2002). Molecular typing of papillomatous digital dermatitis-associated Treponema isolates based on analysis of 16S–23S ribosomal DNA intergenic spacer regions. J Clin Microbiol 40, 3463–3469 10.1128/JCM.40.9.3463-3469.2002 PubMed DOI PMC

Stewart F. J., Cavanaugh C. M. (2007). Intragenomic variation and evolution of the internal transcribed spacer of the rRNA operon in bacteria. J Mol Evol 65, 44–67 10.1007/s00239-006-0235-3 PubMed DOI

Strouhal M., Šmajs D., Matějková P., Sodergren E., Amin A. G., Howell J. K., Norris S. J., Weinstock G. M. (2007). Genome differences between Treponema pallidum subsp. pallidum strain Nichols and T. paraluiscuniculi strain Cuniculi A. Infect Immun 75, 5859–5866 10.1128/IAI.00709-07 PubMed DOI PMC

Takahashi N. K., Yamamoto K., Kitamura Y., Luo S.-Q., Yoshikura H., Kobayashi I. (1992). Nonconservative recombination in Escherichia coli. Proc Natl Acad Sci U S A 89, 5912–5916 10.1073/pnas.89.13.5912 PubMed DOI PMC

Tamura K., Dudley J., Nei M., Kumar S. (2007). mega4: Molecular Evolutionary Genetics Analysis (mega) software version 4.0. Mol Biol Evol 24, 1596–1599 10.1093/molbev/msm092 PubMed DOI

Turner T. B., Hollander D. H. (1957). 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 35, 3–266 PubMed

Wendel G. D., Jr, Sánchez P. J., Peters M. T., Harstad T. W., Potter L. L., Norgard M. V. (1991). Identification of Treponema pallidum in amniotic fluid and fetal blood from pregnancies complicated by congenital syphilis. Obstet Gynecol 78, 890–895 PubMed

Wormser G. P., Brisson D., Liveris D., Hanincová K., Sandigursky S., Nowakowski J., Nadelman R. B., Ludin S., Schwartz I. (2008). Borrelia burgdorferi genotype predicts the capacity for hematogenous dissemination during early Lyme disease. J Infect Dis 198, 1358–1364 10.1086/592279 PubMed DOI PMC

Woznicová V., Šmajs D., Wechsler D., Matějková P., Flasarová M. (2007). Detection of Treponema pallidum subsp. pallidum from skin lesions, serum, and cerebrospinal fluid in an infant with congenital syphilis after clindamycin treatment of the mother during pregnancy. J Clin Microbiol 45, 659–661 10.1128/JCM.02209-06 PubMed DOI PMC

Whole-genome sequencing reveals evidence for inter-species transmission of the yaws bacterium among nonhuman primates in Tanzania

The hare syphilis agent is related to, but distinct from, the treponeme causing rabbit syphilis

Low genetic diversity of Treponema pallidum ssp. pertenue (TPE) isolated from patients' ulcers in Namatanai District of Papua New Guinea: Local human population is infected by three TPE genotypes

The genomes of the yaws bacterium, Treponema pallidum subsp. pertenue, of nonhuman primate and human origin are not genomically distinct

Evolutionary Processes in the Emergence and Recent Spread of the Syphilis Agent, Treponema pallidum

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains

Directly Sequenced Genomes of Contemporary Strains of Syphilis Reveal Recombination-Driven Diversity in Genes Encoding Predicted Surface-Exposed Antigens

Identification of positively selected genes in human pathogenic treponemes: Syphilis-, yaws-, and bejel-causing strains differ in sets of genes showing adaptive evolution

MLST typing of Treponema pallidum subsp. pallidum in the Czech Republic during 2004-2017: Clinical isolates belonged to 25 allelic profiles and harbored 8 novel allelic variants

Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Indonesia: Modular structure of several treponemal genes

Sequencing of Treponema pallidum subsp. pallidum from isolate UZ1974 using Anti-Treponemal Antibodies Enrichment: First complete whole genome sequence obtained directly from human clinical material

Complete genome sequences of two strains of Treponema pallidum subsp. pertenue from Ghana, Africa: Identical genome sequences in samples isolated more than 7 years apart

Human Treponema pallidum 11q/j isolate belongs to subsp. endemicum but contains two loci with a sequence in TP0548 and TP0488 similar to subsp. pertenue and subsp. pallidum, respectively

Macrolide Resistance in the Syphilis Spirochete, Treponema pallidum ssp. pallidum: Can We Also Expect Macrolide-Resistant Yaws Strains?

Whole genome sequence of the Treponema pallidum subsp. endemicum strain Bosnia A: the genome is related to yaws treponemes but contains few loci similar to syphilis treponemes

Resequencing of Treponema pallidum ssp. pallidum strains Nichols and SS14: correction of sequencing errors resulted in increased separation of syphilis treponeme subclusters

Whole genome sequence of the Treponema Fribourg-Blanc: unspecified simian isolate is highly similar to the yaws subspecies

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