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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.

Staudová B, Strouhal M, Zobaníková M, Cejková D, Fulton LL, Chen L, Giacani L, Centurion-Lara A, Bruisten SM, Sodergren E, Weinstock GM, Smajs D - PLoS Negl Trop Dis (2014)

Bottom Line: The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes.Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes.Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.

ABSTRACT

Background: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.

Methodology/principal findings: The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.

Conclusions/significance: The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.

No MeSH data available.


Related in: MedlinePlus

Sequence alignments of TENDBA_0133, TENDBA_0968, TENDBA_0577, TENDBA_0326 and TENDBA_0856 loci with the orthologous sequences of TPA and TPE genomes.Sequences of five TPA strains (Nichols, DAL-1, Chicago, Mexico A and SS14) and four TPE strains (CDC-2, Gauthier, Samoa D and Fribourg-Blanc) are shown. Numbers above the alignment represent gene coordinates in the re-sequenced TPA Nichols strain (CP004010.2 [14]). While the alignment of TENDBA_0133 showed locus completely identical to TPE strains, TENDBA_0968, TENDBA_0577 and TENDBA_0326 loci showed the presence of TPA sequences in the genome of Bosnia A. The TENDBA_0856 locus represent Bosnia A specific region with sporadic nucleotide positions identical to TPA sequences. The TPE-like sequence was found in most of the Bosnia A loci while the pattern found in TENDBA_0968 was also found in TENDBA_0858 (not shown) and the pattern identified in the TENDBA_0577 was found also in the TENDBA_1031 (not shown). The alignment pattern in TENDBA_0326 was previously found in TENDBA_0488 [12] and the pattern in TENDBA_0856 in TENDBA_0865.
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pntd-0003261-g003: Sequence alignments of TENDBA_0133, TENDBA_0968, TENDBA_0577, TENDBA_0326 and TENDBA_0856 loci with the orthologous sequences of TPA and TPE genomes.Sequences of five TPA strains (Nichols, DAL-1, Chicago, Mexico A and SS14) and four TPE strains (CDC-2, Gauthier, Samoa D and Fribourg-Blanc) are shown. Numbers above the alignment represent gene coordinates in the re-sequenced TPA Nichols strain (CP004010.2 [14]). While the alignment of TENDBA_0133 showed locus completely identical to TPE strains, TENDBA_0968, TENDBA_0577 and TENDBA_0326 loci showed the presence of TPA sequences in the genome of Bosnia A. The TENDBA_0856 locus represent Bosnia A specific region with sporadic nucleotide positions identical to TPA sequences. The TPE-like sequence was found in most of the Bosnia A loci while the pattern found in TENDBA_0968 was also found in TENDBA_0858 (not shown) and the pattern identified in the TENDBA_0577 was found also in the TENDBA_1031 (not shown). The alignment pattern in TENDBA_0326 was previously found in TENDBA_0488 [12] and the pattern in TENDBA_0856 in TENDBA_0865.

Mentions: Despite the overall sequence similarity of the Bosnia A genome to TPE strains, several chromosomal sequences were found to be almost identical to sequences in TPA strains. The Bosnia A sequence in the TENDBA_0577 locus was identical to four out of 5 orthologous sequences of completely sequenced TPA strains (Fig. 3). In the TENDBA_0968 locus, stretches of TPA- and TPE-like sequences were found (Fig. 3) and a similar pattern was also found in TENDBA_0858 (not shown). In addition, TENDBA_0326 (tp92, bamA) was identical to the orthologous sequence of TPA SS14 (coordinates 1593–1649, Fig. 3) and to all TPA strains (with the exception of the TPA Mexico A strain) between coordinates 2127–2494. The TPA Mexico A strain is, in this region, similar to TPE strains [12], [29]. While the latter TPA-like sequences in TENDBA_0326 were almost 0.4 kbp long, other TPA-like sequences were usually relatively short, ranging from about 50–70 bp. However, TPA-like sequences of the Bosnia A strain were clearly different from Bosnia A-specific sequences with sporadic nucleotide positions identical to TPA sequences (TENDBA_0856; Fig. 3). The previously reported 378 bp insertion almost identical to TPA strains (differing only in one nucleotide position [27]) was confirmed in TENDBA_1031 as well as the nucleotide mosaic in the TP0488 (mcp2-1) locus; revealing a sequence identical to TPA Mexico A (with the exception of 2 single nucleotide substitutions [12]). Altogether, at least seven TPA-like sequences having 5 or more nucleotide positions identical to TPA sequences and not interrupted by TPE-like nucleotide positions were found in the Bosnia A genome.


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.

Staudová B, Strouhal M, Zobaníková M, Cejková D, Fulton LL, Chen L, Giacani L, Centurion-Lara A, Bruisten SM, Sodergren E, Weinstock GM, Smajs D - PLoS Negl Trop Dis (2014)

Sequence alignments of TENDBA_0133, TENDBA_0968, TENDBA_0577, TENDBA_0326 and TENDBA_0856 loci with the orthologous sequences of TPA and TPE genomes.Sequences of five TPA strains (Nichols, DAL-1, Chicago, Mexico A and SS14) and four TPE strains (CDC-2, Gauthier, Samoa D and Fribourg-Blanc) are shown. Numbers above the alignment represent gene coordinates in the re-sequenced TPA Nichols strain (CP004010.2 [14]). While the alignment of TENDBA_0133 showed locus completely identical to TPE strains, TENDBA_0968, TENDBA_0577 and TENDBA_0326 loci showed the presence of TPA sequences in the genome of Bosnia A. The TENDBA_0856 locus represent Bosnia A specific region with sporadic nucleotide positions identical to TPA sequences. The TPE-like sequence was found in most of the Bosnia A loci while the pattern found in TENDBA_0968 was also found in TENDBA_0858 (not shown) and the pattern identified in the TENDBA_0577 was found also in the TENDBA_1031 (not shown). The alignment pattern in TENDBA_0326 was previously found in TENDBA_0488 [12] and the pattern in TENDBA_0856 in TENDBA_0865.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4222731&req=5

pntd-0003261-g003: Sequence alignments of TENDBA_0133, TENDBA_0968, TENDBA_0577, TENDBA_0326 and TENDBA_0856 loci with the orthologous sequences of TPA and TPE genomes.Sequences of five TPA strains (Nichols, DAL-1, Chicago, Mexico A and SS14) and four TPE strains (CDC-2, Gauthier, Samoa D and Fribourg-Blanc) are shown. Numbers above the alignment represent gene coordinates in the re-sequenced TPA Nichols strain (CP004010.2 [14]). While the alignment of TENDBA_0133 showed locus completely identical to TPE strains, TENDBA_0968, TENDBA_0577 and TENDBA_0326 loci showed the presence of TPA sequences in the genome of Bosnia A. The TENDBA_0856 locus represent Bosnia A specific region with sporadic nucleotide positions identical to TPA sequences. The TPE-like sequence was found in most of the Bosnia A loci while the pattern found in TENDBA_0968 was also found in TENDBA_0858 (not shown) and the pattern identified in the TENDBA_0577 was found also in the TENDBA_1031 (not shown). The alignment pattern in TENDBA_0326 was previously found in TENDBA_0488 [12] and the pattern in TENDBA_0856 in TENDBA_0865.
Mentions: Despite the overall sequence similarity of the Bosnia A genome to TPE strains, several chromosomal sequences were found to be almost identical to sequences in TPA strains. The Bosnia A sequence in the TENDBA_0577 locus was identical to four out of 5 orthologous sequences of completely sequenced TPA strains (Fig. 3). In the TENDBA_0968 locus, stretches of TPA- and TPE-like sequences were found (Fig. 3) and a similar pattern was also found in TENDBA_0858 (not shown). In addition, TENDBA_0326 (tp92, bamA) was identical to the orthologous sequence of TPA SS14 (coordinates 1593–1649, Fig. 3) and to all TPA strains (with the exception of the TPA Mexico A strain) between coordinates 2127–2494. The TPA Mexico A strain is, in this region, similar to TPE strains [12], [29]. While the latter TPA-like sequences in TENDBA_0326 were almost 0.4 kbp long, other TPA-like sequences were usually relatively short, ranging from about 50–70 bp. However, TPA-like sequences of the Bosnia A strain were clearly different from Bosnia A-specific sequences with sporadic nucleotide positions identical to TPA sequences (TENDBA_0856; Fig. 3). The previously reported 378 bp insertion almost identical to TPA strains (differing only in one nucleotide position [27]) was confirmed in TENDBA_1031 as well as the nucleotide mosaic in the TP0488 (mcp2-1) locus; revealing a sequence identical to TPA Mexico A (with the exception of 2 single nucleotide substitutions [12]). Altogether, at least seven TPA-like sequences having 5 or more nucleotide positions identical to TPA sequences and not interrupted by TPE-like nucleotide positions were found in the Bosnia A genome.

Bottom Line: The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes.Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes.Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.

ABSTRACT

Background: T. pallidum subsp. endemicum (TEN) is the causative agent of bejel (also known as endemic syphilis). Clinical symptoms of syphilis and bejel are overlapping and the epidemiological context is important for correct diagnosis of both diseases. In contrast to syphilis, caused by T. pallidum subsp. pallidum (TPA), TEN infections are usually spread by direct contact or contaminated utensils rather than by sexual contact. Bejel is most often seen in western Africa and in the Middle East. The strain Bosnia A was isolated in 1950 in Bosnia, southern Europe.

Methodology/principal findings: The complete genome of the Bosnia A strain was amplified and sequenced using the pooled segment genome sequencing (PSGS) method and a combination of three next-generation sequencing techniques (SOLiD, Roche 454, and Illumina). Using this approach, a total combined average genome coverage of 513× was achieved. The size of the Bosnia A genome was found to be 1,137,653 bp, i.e. 1.6-2.8 kbp shorter than any previously published genomes of uncultivable pathogenic treponemes. Conserved gene synteny was found in the Bosnia A genome compared to other sequenced syphilis and yaws treponemes. The TEN Bosnia A genome was distinct but very similar to the genome of yaws-causing T. pallidum subsp. pertenue (TPE) strains. Interestingly, the TEN Bosnia A genome was found to contain several sequences, which so far, have been uniquely identified only in syphilis treponemes.

Conclusions/significance: The genome of TEN Bosnia A contains several sequences thought to be unique to TPA strains; these sequences very likely represent remnants of recombination events during the evolution of TEN treponemes. This finding emphasizes a possible role of repeated horizontal gene transfer between treponemal subspecies in shaping the Bosnia A genome.

No MeSH data available.


Related in: MedlinePlus