0000000000243465
AUTHOR
Natasha Arora
MOESM8 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 8. The phylogenetic trees of the tp0136 and tp0548 genes. The phylogenetic trees were constructed using the Maximum Likelihood method based on the Tamura–Nei model. The bar scale represents the number of substitutions per site. The analysis involved 14 TPA nucleotide sequences including eight derived from the Chinese samples: SHC-0, SHD-R, SHE-V, SHG-I2, B3, C3, K3, and Q3. The T. pallidum subsp. pertenue Fribourg-Blanc sequence [1] was used as an outgroup. There were totals of 1547 and 1317 positions in the final dataset for tp0136 and tp0548 genes, respectively. For both genes, two separate clusters were identified: one cluster of Nichols-like TPA strains (TPA Lineage 1), …
MOESM2 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 2. Mapping statistics of input read pairs mapped to the reference genomes. Sequencing reads derived from the Chinese strain SRA data were mapped to the Treponema pallidum subsp. pallidum (TPA) SS14 and Nichols reference genomes [6] and to the rabbit genome (Statistics was calculated from post-processed mappings; repetitive and homologous sequences and PCR duplicated reads were excluded from the statistics).
MOESM6 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 6. Analysis of indels (deletions/insertions) between SS14-like and Nichols-like TPA strains. The Nichols genome (CP004010.2) [6] was used as a reference for the comparison of TPA strains.
Ancient bacterial genomes reveal a formerly unknown diversity ofTreponema pallidumstrains in early modern Europe
SummarySexually transmitted (venereal) syphilis marked European history with a devastating epidemic at the end of the 15thcentury, and is currently re-emerging globally. Together with non-venereal treponemal diseases, like bejel and yaws, found in subtropical and tropical regions, it poses a prevailing health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a previously unknown diversity ofTreponema pallidumin historical Europe. Our study demonstrates that a variety of strains related to both venereal…
Molecular characterization of Treponema pallidum subsp. pallidum in Switzerland and France with a new multilocus sequence typing scheme
Syphilis is an important public health problem and an increasing incidence has been noted in recent years. Characterization of strain diversity through molecular data plays a critical role in the epidemiological understanding of this re-emergence. We here propose a new high-resolution multilocus sequence typing (MLST) scheme for Treponema pallidum subsp. pallidum (TPA). We analyzed 30 complete and draft TPA genomes obtained directly from clinical samples or from rabbit propagated strains to identify suitable typing loci and tested the new scheme on 120 clinical samples collected in Switzerland and France. Our analyses yielded three loci with high discriminatory power: TP0136, TP0548, and TP…
Ancient bacterial genomes reveal a high diversity of Treponema pallidum Strains in early Modern Europe
Syphilis is a globally re-emerging disease, which has marked European history with a devastating epidemic at the end of the 15th century. Together with non-venereal treponemal diseases, like bejel and yaws, which are found today in subtropical and tropical regions, it currently poses a substantial health threat worldwide. The origins and spread of treponemal diseases remain unresolved, including syphilis’ potential introduction into Europe from the Americas. Here, we present the first genetic data from archaeological human remains reflecting a high diversity of Treponema pallidum in early modern Europe. Our study demonstrates that a variety of strains related to both venereal syphilis and y…
MOESM7 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 7. Alignment of tprD/tprD2 alleles. tprD and tprD2 alleles were downloaded from the NCBI GenBank database for each reference Nichols and SS14 TPA strain, CP004010.2 and CP004011.1 [6], respectively. While the Nichols reference genome harbors identical copies of tprC and tprD genes, the SS14 reference genome carries the tprD2 allele, which is not identical to the tprC gene and differs from the tprD allele by roughly 320 nucleotides. As shown in the alignment, we were able to identify the tprD2 allele (in positions 800–1791 according to the SS14 tprD2 allele) among the sequencing reads from the Chinese SRA data. The alignment was performed using SeqMan software (DNASTAR, Madis…
Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
[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 identifed. 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.
MOESM3 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 3. Genome coverage statistics for individual Chinese strains. Sequencing reads derived from the Chinese strains SRA data were mapped to the TPA SS14 and Nichols reference genomes [6]. The number of bases with a coverage depth of 1 or more, number of bases with more than 10× coverage depth and average/median coverage depth are shown. Statistics were calculated from previously post-processed mappings; repetitive and homologous regions and PCR duplicated reads were excluded from statistical analysis.
MOESM5 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 5. Number of SNVs from whole genome alignments produced by NUCmer. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Chinese strains are shown in bold.
Origin of modern syphilis and emergence of a contemporary pandemic cluster
AbstractSyphilis swept across the world in the 16th century as one of most prominent documented pandemics and is re-emerging worldwide despite the availability of effective antibiotics. Little is known about the genetic patterns in current infections or the evolutionary origins of the disease due to the non-cultivable and clonal nature of the causative bacterium Treponema pallidum subsp. pallidum. In this study, we used DNA capture and next generation sequencing to obtain whole genome data from syphilis patient specimens and from treponemes propagated in laboratory settings. Phylogenetic analyses indicate that the syphilis strains examined here share a common ancestor after the 15th century…
Origin of modern syphilis and emergence of a pandemic Treponema pallidum cluster
The abrupt onslaught of the syphilis pandemic that started in the late fifteenth century established this devastating infectious disease as one of the most feared in human history1 . Surprisingly, despite the availability of effective antibiotic treatment since the mid-twentieth century, this bacterial infection, which is caused by Treponema pallidum subsp. pallidum (TPA), has been re-emerging globally in the last few decades with an estimated 10.6 million cases in 2008 (ref. 2). Although resistance to penicillin has not yet been identified, an increasing number of strains fail to respond to the secondline antibiotic azithromycin3. Little is known about the genetic patterns in current infec…
Evolutionary processes in the emergence and recent spread of the syphilis agent, Treponema pallidum
Abstract The incidence of syphilis has risen worldwide in the last decade in spite of being an easily treated infection. The causative agent of this sexually transmitted disease is the bacterium Treponema pallidum subspecies pallidum (TPA), very closely related to subsp. pertenue (TPE) and endemicum (TEN), responsible for the human treponematoses yaws and bejel, respectively. Although much focus has been placed on the question of the spatial and temporary origins of TPA, the processes driving the evolution and epidemiological spread of TPA since its divergence from TPE and TEN are not well understood. Here, we investigate the effects of recombination and selection as forces of genetic diver…
MOESM1 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 1. Data analysis and methods used in the reanalysis of Chinese Treponema pallidum samples.
MOESM4 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 4. A Genome coverage statistics—number of non-covered bases for individual Chinese strains. SS14 genome (CP004011.1) [6] was used as a reference for mapping; coordinates according to the CP004011.1. The list includes all positions without any coverage by mapped reads. B Genome covearge statistics—number of zero covered bases for individual Chinese strains. Nichols genome (CP004010.2) [6] was used as a reference for mapping; coordinates according to the CP004010.2. The list includes all positions without any coverage by mapped reads.
MOESM9 of Reanalysis of Chinese Treponema pallidum samples: all Chinese samples cluster with SS14-like group of syphilis-causing treponemes
Additional file 9. Genomic SNVs used for phylogenetic analysis. List of SNVs used for construction of phylogenetic trees. Only SNVs detected in all analyzed genomes (i.e., positions with the “N” base in any of the compared genomes were not considered) were used in the analysis. Genes tp0433 (arp), tp0470, and tp0897 (tprK) were excluded from analyses. Altogether, 2444 unique SNV positions were identified when the TPE Fribourg-Blanc genome sequence was used as an outgroup. Coordinates (positions) and gene annotations according to the SS14 genome (CP04011.1); “NA” = not annotated (IGR, intergenic region); “.” = deletion.