Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Abstract Objective Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no gen...
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| Format: | Article |
| Language: | English |
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BMC
2018-01-01
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| Series: | BMC Research Notes |
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| Online Access: | http://link.springer.com/article/10.1186/s13104-017-3106-7 |
| _version_ | 1819137167554772992 |
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| author | Michal Strouhal Jan Oppelt Lenka Mikalová Natasha Arora Kay Nieselt Fernando González-Candelas David Šmajs |
| author_facet | Michal Strouhal Jan Oppelt Lenka Mikalová Natasha Arora Kay Nieselt Fernando González-Candelas David Šmajs |
| author_sort | Michal Strouhal |
| collection | DOAJ |
| description | Abstract Objective Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new “phylogenetic group” (called Lineage 2) among Chinese TPA strains. This lineage exhibited a “mosaic genomic structure” of Nichols-like and SS14-like lineages. Results We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains. |
| first_indexed | 2024-12-22T10:46:34Z |
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| institution | Directory Open Access Journal |
| issn | 1756-0500 |
| language | English |
| last_indexed | 2024-12-22T10:46:34Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Research Notes |
| spelling | doaj.art-fe070d38a74f4fc09e5cc5698569c59a2022-12-21T18:28:55ZengBMCBMC Research Notes1756-05002018-01-011111510.1186/s13104-017-3106-7Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemesMichal Strouhal0Jan Oppelt1Lenka Mikalová2Natasha Arora3Kay Nieselt4Fernando González-Candelas5David Šmajs6Department of Biology, Faculty of Medicine, Masaryk UniversityCEITEC-Central European Institute of Technology, Masaryk UniversityDepartment of Biology, Faculty of Medicine, Masaryk UniversityZurich Institute of Forensic Medicine, University of ZurichCenter for Bioinformatics, University of TübingenUnidad Mixta Infección y Salud Pública FISABIO, Universidad de ValenciaDepartment of Biology, Faculty of Medicine, Masaryk UniversityAbstract Objective Treponema pallidum subsp. pallidum (TPA) is the causative agent of syphilis. Genetic analyses of TPA reference strains and human clinical isolates have revealed two genetically distinct groups of syphilis-causing treponemes, called Nichols-like and SS14-like groups. So far, no genetic intermediates, i.e. strains containing a mixed pattern of Nichols-like and SS14-like genomic sequences, have been identified. Recently, Sun et al. (Oncotarget 2016. https://doi.org/10.18632/oncotarget.10154 ) described a new “phylogenetic group” (called Lineage 2) among Chinese TPA strains. This lineage exhibited a “mosaic genomic structure” of Nichols-like and SS14-like lineages. Results We reanalyzed the primary sequencing data (Project Number PRJNA305961) from the Sun et al. publication with respect to the molecular basis of Lineage 2. While Sun et al. based the analysis on several selected genomic single nucleotide variants (SNVs) and a subset of highly variable but phylogenetically poorly informative genes, which may confound the phylogenetic analysis, our reanalysis primarily focused on a complete set of whole genomic SNVs. Based on our reanalysis, only two separate TPA clusters were identified: one consisted of Nichols-like TPA strains, the other was formed by the SS14-like TPA strains, including all Chinese strains.http://link.springer.com/article/10.1186/s13104-017-3106-7Treponema pallidumSyphilisGenome sequencingPhylogenetic analysisSingle nucleotide variant |
| spellingShingle | Michal Strouhal Jan Oppelt Lenka Mikalová Natasha Arora Kay Nieselt Fernando González-Candelas David Šmajs Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes BMC Research Notes Treponema pallidum Syphilis Genome sequencing Phylogenetic analysis Single nucleotide variant |
| title | Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes |
| title_full | Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes |
| title_fullStr | Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes |
| title_full_unstemmed | Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes |
| title_short | Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes |
| title_sort | reanalysis of chinese treponema pallidum samples all chinese samples cluster with ss14 like group of syphilis causing treponemes |
| topic | Treponema pallidum Syphilis Genome sequencing Phylogenetic analysis Single nucleotide variant |
| url | http://link.springer.com/article/10.1186/s13104-017-3106-7 |
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