Evidence map›Paper›PMID 25375929›Full record

ArticlePLoS neglected tropical diseases2014

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.

Barbora Staudová, Michal Strouhal, Marie Zobaníková, Darina Cejková, Lucinda L Fulton, Lei Chen, Lorenzo Giacani, Arturo Centurion-Lara, Sylvia M Bruisten, Erica Sodergren and 2 more

Open access · goldAbstract readComparative Study
In one paragraph

Article in PLoS neglected tropical diseases, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.

0numbers the graph read from it
0cells of the map it votes in
37citing papers in PubMed
2.1field-weighted citation impact, top 14% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

37 citing papers in PubMed, 59 citations in OpenAlex.

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  13. Current Methods for Recombination Detection in Bacteria.International journal of molecular sciences · 2022
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  16. High-throughput nanopore sequencing ofFrontiers in microbiology · 2022
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

12 authors at 4 institutions in 3 countries.

Barbora StaudováDepartment of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
Michal StrouhalDepartment of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Marie ZobaníkováDepartment of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
Darina CejkováDepartment of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic; The Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Lucinda L FultonThe Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Lei ChenThe Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
Lorenzo GiacaniDepartment of Medicine, University of Washington, Seattle, Washington, United States of America.
Arturo Centurion-LaraDepartment of Medicine, University of Washington, Seattle, Washington, United States of America.
Sylvia M BruistenPublic Health Service GGD Amsterdam, Amsterdam, The Netherlands.
Erica SodergrenThe Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
George M WeinstockThe Genome Institute, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, United States of America.
David SmajsDepartment of Biology, Faculty of Medicine, Masaryk University, Brno, Czech Republic.
Washington University in St. Louis · USMasaryk University · CZUniversity of Washington · USGGD Amsterdam · NL

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundT. 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

findingsThe 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.

Indexed as

Base SequenceBosnia and HerzegovinaCluster AnalysisGene Transfer, HorizontalGenome, BacterialHumansMolecular Sequence DataSequence AlignmentSequence Analysis, DNASpecies SpecificitySyntenySyphilisTreponema pallidumYaws

Identifiers

PMID25375929
PMCPMC4222731
OpenAlexW1969715015

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.