Resequencing of Treponema pallidum ssp. pallidum Strains
Nichols and SS14: Correction of Sequencing Errors Resulted in
Increased Separation of Syphilis Treponeme Subclusters

J 2013

Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters

PĚTROŠOVÁ, Helena, Petra POSPÍŠILOVÁ, Michal STROUHAL, Darina ČEJKOVÁ, Marie ZOBANÍKOVÁ et. al.

Basic information

Original name

Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters

Authors

PĚTROŠOVÁ, Helena (203 Czech Republic, belonging to the institution), Petra POSPÍŠILOVÁ (203 Czech Republic, belonging to the institution), Michal STROUHAL (203 Czech Republic, belonging to the institution), Darina ČEJKOVÁ (203 Czech Republic, belonging to the institution), Marie ZOBANÍKOVÁ (203 Czech Republic, belonging to the institution), Lenka MIKALOVÁ (203 Czech Republic, belonging to the institution), Erica SODERGREN (840 United States of America), George M. WEINSTOCK (840 United States of America) and David ŠMAJS (203 Czech Republic, guarantor, belonging to the institution)

Edition

PloS ONE, San Francisco, Public Library of Science, 2013, 1932-6203

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10600 1.6 Biological sciences

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Impact factor

Impact factor: 3.534

RIV identification code

RIV/00216224:14110/13:00065631

Organization unit

Faculty of Medicine

DOI

http://dx.doi.org/10.1371/journal.pone.0074319

UT WoS

000327538600088

Keywords in English

Treponema pallidum ssp. pallidum; Syphilis; Whole genome sequencing; Genetic clusters

Abstract

V originále

Background:Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques.Methodology/Principal Findings:The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related.Conclusion/Significance:We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.

Links

EE2.3.30.0009, research and development project

Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GAP302/12/0574, research and development project

Name: Celogenomové sekvencování v analýze genomů a transkriptomů patogenních bakterií rodu Treponema

Investor: Czech Science Foundation

NT11159, research and development project

Name: Mapování výskytu makrolidové rezistence původce syfilis v ČR a molekulární typizace jednotlivých syfilitických kmenů

Investor: Ministry of Health of the CR

Files attached

resequencing_of_Treponema.pdf

Request the author's version of the file

Citovat

PĚTROŠOVÁ, Helena, Petra POSPÍŠILOVÁ, Michal STROUHAL, Darina ČEJKOVÁ, Marie ZOBANÍKOVÁ, Lenka MIKALOVÁ, Erica SODERGREN, George M. WEINSTOCK and David ŠMAJS. Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters. PloS ONE. San Francisco: Public Library of Science, 2013, vol. 8, No 9, p. e74319, 8 pp. ISSN 1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0074319.

@article{1126319,
   author = {Pětrošová, Helena and Pospíšilová, Petra and Strouhal, Michal and Čejková, Darina and Zobaníková, Marie and Mikalová, Lenka and Sodergren, Erica and Weinstock, George M. and Šmajs, David},
   article_location = {San Francisco},
   article_number = {9},
   doi = {http://dx.doi.org/10.1371/journal.pone.0074319},
   keywords = {Treponema pallidum ssp. pallidum; Syphilis; Whole genome sequencing; Genetic clusters},
   language = {eng},
   issn = {1932-6203},
   journal = {PloS ONE},
   title = {Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters},
   volume = {8},
   year = {2013}
}

TY  - JOUR
ID  - 1126319
AU  - Pětrošová, Helena - Pospíšilová, Petra - Strouhal, Michal - Čejková, Darina - Zobaníková, Marie - Mikalová, Lenka - Sodergren, Erica - Weinstock, George M. - Šmajs, David
PY  - 2013
TI  - Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters
JF  - PloS ONE
VL  - 8
IS  - 9
SP  - e74319
EP  - e74319
PB  - Public Library of Science
SN  - 19326203
KW  - Treponema pallidum ssp. pallidum
KW  - Syphilis
KW  - Whole genome sequencing
KW  - Genetic clusters
N2  - Background:Treponema pallidum ssp. pallidum (TPA), the causative agent of syphilis, is a highly clonal bacterium showing minimal genetic variability in the genome sequence of individual strains. Nevertheless, genetically characterized syphilis strains can be clearly divided into two groups, Nichols-like strains and SS14-like strains. TPA Nichols and SS14 strains were completely sequenced in 1998 and 2008, respectively. Since publication of their complete genome sequences, a number of sequencing errors in each genome have been reported. Therefore, we have resequenced TPA Nichols and SS14 strains using next-generation sequencing techniques.Methodology/Principal Findings:The genomes of TPA strains Nichols and SS14 were resequenced using the 454 and Illumina sequencing methods that have a combined average coverage higher than 90x. In the TPA strain Nichols genome, 134 errors were identified (25 substitutions and 109 indels), and 102 of them affected protein sequences. In the TPA SS14 genome, a total of 191 errors were identified (85 substitutions and 106 indels) and 136 of them affected protein sequences. A set of new intrastrain heterogenic regions in the TPA SS14 genome were identified including the tprD gene, where both tprD and tprD2 alleles were found. The resequenced genomes of both TPA Nichols and SS14 strains clustered more closely with related strains (i.e. strains belonging to same syphilis treponeme subcluster). At the same time, groups of Nichols-like and SS14-like strains were found to be more distantly related.Conclusion/Significance:We identified errors in 11.5% of all annotated genes and, after correction, we found a significant impact on the predicted proteomes of both Nichols and SS14 strains. Corrections of these errors resulted in protein elongations, truncations, fusions and indels in more than 11% of all annotated proteins. Moreover, it became more evident that syphilis is caused by treponemes belonging to two separate genetic subclusters.
ER  -

PĚTROŠOVÁ, Helena, Petra POSPÍŠILOVÁ, Michal STROUHAL, Darina ČEJKOVÁ, Marie ZOBANÍKOVÁ, Lenka MIKALOVÁ, Erica SODERGREN, George M. WEINSTOCK and David ŠMAJS. Resequencing of Treponema pallidum ssp. pallidum Strains Nichols and SS14: Correction of Sequencing Errors Resulted in Increased Separation of Syphilis Treponeme Subclusters. \textit{PloS ONE}. San Francisco: Public Library of Science, 2013, vol.~8, No~9, p.~e74319, 8 pp. ISSN~1932-6203. Available from: https://dx.doi.org/10.1371/journal.pone.0074319.

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