Abstract
BackgroundTreponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multistage disease endemic in tropical regions in Africa, Asia, Oceania, and South America. To date, seven TPE strains have been completely sequenced and analyzed including five TPE strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) and two TPE strains isolated from the baboons (Fribourg-Blanc and LMNP-1). This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes.Methodology/principal findingsThe genomes were determined using the pooled segment genome sequencing method combined with the Illumina sequencing platform resulting in an average coverage depth of 1,021x and 644x for the TPE Kampung Dalan K363 and TPE Sei Geringging K403 genomes, respectively. Both Indonesian TPE strains were genetically related to each other and were more distantly related to other, previously characterized TPE strains. The modular character of several genes, including TP0136 and TP0858 gene orthologs, was identified by analysis of the corresponding sequences. To systematically detect genes potentially having a modular genetic structure, we performed a whole genome analysis-of-occurrence of direct or inverted repeats of 17 or more nucleotides in length. Besides in tpr genes, a frequent presence of repeats was found in the genetic regions spanning TP0126–TP0136, TP0856–TP0858, and TP0896 genes.Conclusions/significanceComparisons of genome sequences of TPE Kampung Dalan K363 and Sei Geringging K403 with other TPE strains revealed a modular structure of several genomic loci including the TP0136, TP0856, and TP0858 genes. Diversification of TPE genomes appears to be facilitated by intra-strain genome recombination events.
Highlights
The infectious agent of yaws, Treponema pallidum subsp. pertenue (TPE), causes chronic infections in children and young adults, which is characterized by skin lesions including nodules and ulcerations of the skin, which is later accompanied by joint, soft tissue, and bone manifestations
Treponema pallidum subsp. pertenue (TPE) is the causative agent of yaws, a multi-stage disease that is endemic in tropical regions of Africa, Asia, Oceania, and South America
Whole genome sequences of two TPE strains isolated from patients in Indonesia were determined in this study
Summary
The infectious agent of yaws, Treponema pallidum subsp. pertenue (TPE), causes chronic infections in children and young adults, which is characterized by skin lesions including nodules and ulcerations of the skin, which is later accompanied by joint, soft tissue, and bone manifestations (reviewed in [1]). The recent study by Edmonson et al [5] showed a successful long-time in vitro cultivation of syphilis treponemes that could be potentially applied to TPE strains. This could result in an increase in the number of characterized TPE strains. Seven TPE strains have been completely sequenced, including five strains of human origin (CDC-2, CDC 2575, Gauthier, Ghana-051, and Samoa D) [6,7] and two TPE strains (Fribourg-Blanc and LMNP-1) isolated from a Guinea baboon (Papio papio) in West Africa [8] and an olive baboon (Papio anubis) from Tanzania [9], respectively. This study revealed the complete genome sequences of two TPE strains, Kampung Dalan K363 and Sei Geringging K403, isolated in 1990 from villages in the Pariaman region of Sumatra, Indonesia and compared these genome sequences with other known TPE genomes
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