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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

Unrooted tree based on the alignment of the Bosnia A genome with additional treponemal genomes.An unrooted tree was constructed from the complete genome sequences of TPA strains (Nichols, Chicago, DAL-1, SS14, and Mexico A), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strain (Bosnia A) using the Maximum Parsimony method and MEGA5 software [25]. The bar scale corresponds to a difference of 200 nucleotides. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There were a total of 1,128,391 nucleotide positions aligned in the final dataset.
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pntd-0003261-g001: Unrooted tree based on the alignment of the Bosnia A genome with additional treponemal genomes.An unrooted tree was constructed from the complete genome sequences of TPA strains (Nichols, Chicago, DAL-1, SS14, and Mexico A), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strain (Bosnia A) using the Maximum Parsimony method and MEGA5 software [25]. The bar scale corresponds to a difference of 200 nucleotides. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There were a total of 1,128,391 nucleotide positions aligned in the final dataset.

Mentions: Sequence relatedness of the Bosnia A genome to other Treponema pallidum genomes is shown in Fig. 1. This unrooted tree was constructed using several available whole genome sequences of uncultivable pathogenic treponemes. The image clearly showed clustering of the Bosnia A strain with the TPE strains. The Bosnia A genome was found to be 99.91–99.94% and 99.79–99.82% identical to the TPE and TPA genomes, respectively (Table 3). The nucleotide diversity between TPE strains and the Bosnia A strain (0.00063±0.00032 to 0.00086±0.00043) was about three times lower than the nucleotide diversity between TPA strains and the Bosnia A strain (0.00181±0.00090 to 0.00212±0.00106). For comparison, calculated π values between the Bosnia A strain and individual TPA strains were of the same order of magnitude as π values between TPA and TPE strains (Table 4).


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)

Unrooted tree based on the alignment of the Bosnia A genome with additional treponemal genomes.An unrooted tree was constructed from the complete genome sequences of TPA strains (Nichols, Chicago, DAL-1, SS14, and Mexico A), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strain (Bosnia A) using the Maximum Parsimony method and MEGA5 software [25]. The bar scale corresponds to a difference of 200 nucleotides. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There were a total of 1,128,391 nucleotide positions aligned in the final dataset.
© Copyright Policy
Related In: Results  -  Collection

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

pntd-0003261-g001: Unrooted tree based on the alignment of the Bosnia A genome with additional treponemal genomes.An unrooted tree was constructed from the complete genome sequences of TPA strains (Nichols, Chicago, DAL-1, SS14, and Mexico A), TPE strains (CDC-2, Gauthier, Samoa D, and Fribourg-Blanc), and the TEN strain (Bosnia A) using the Maximum Parsimony method and MEGA5 software [25]. The bar scale corresponds to a difference of 200 nucleotides. Bootstrap values based on 1,000 replications are shown next to the branches. All positions containing indels in at least one genome sequence were omitted from the analysis. There were a total of 1,128,391 nucleotide positions aligned in the final dataset.
Mentions: Sequence relatedness of the Bosnia A genome to other Treponema pallidum genomes is shown in Fig. 1. This unrooted tree was constructed using several available whole genome sequences of uncultivable pathogenic treponemes. The image clearly showed clustering of the Bosnia A strain with the TPE strains. The Bosnia A genome was found to be 99.91–99.94% and 99.79–99.82% identical to the TPE and TPA genomes, respectively (Table 3). The nucleotide diversity between TPE strains and the Bosnia A strain (0.00063±0.00032 to 0.00086±0.00043) was about three times lower than the nucleotide diversity between TPA strains and the Bosnia A strain (0.00181±0.00090 to 0.00212±0.00106). For comparison, calculated π values between the Bosnia A strain and individual TPA strains were of the same order of magnitude as π values between TPA and TPE strains (Table 4).

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