Whole genome sequence of the Treponema pallidum subsp. endemicum strain Iraq B: A subpopulation of bejel treponemes contains full-length tprF and tprG genes similar to those present in T. p. subsp. pertenue strains

• Type of Material: Article
• Authors: Lenka Mikalová, Masaryk University; Klára Janečková, Masaryk University; Markéta Nováková, Masaryk University; Michal Strouhal, Masaryk University; Darina Čejková, Veterinary Research Institute, Brno, Czech Republic; Kristin N Harper, Emory University; David Šmajs, Masaryk University
• Language: English
• Date: 2020-04-01
• Publisher: Public Library of Science (PLoS)
• Publication Version: Final Published Version
• Copyright Statement: © 2020 Mikalová et al
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1371/journal.pone.0230926
• Title of Journal or Parent Work: PLoS One
• Volume: 15
• Issue: 4
• Grant/Funding Information: This work was supported by the Grant Agency of the Czech Republic (GA17-25455S; GC18-23521J; gacr.cz) to DS and (GJ17-25589Y; gacr.cz) to MS. DČ was supported by the grant RVO0518 of the Czech Ministry of Agriculture (eagri.cz).; The commercial company Harper Health & Science Communications provided support in the form of salaries for author KNH, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section.; This work was also supported by funds from the Faculty of Medicine, Masaryk University (med.muni.cz), provided to junior researchers LM and MN. These funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
• Keywords: Genetic heterogeneity
• Research Categories: Biology, Ecology; Health Sciences, Immunology

Abstract

Treponema pallidum subsp. endemicum (TEN) is the causative agent of endemic syphilis (bejel). Until now, only a single TEN strain, Bosnia A, has been completely sequenced. The only other laboratory TEN strain available, Iraq B, was isolated in Iraq in 1951 by researchers from the US Centers for Disease Control and Prevention. In this study, the complete genome of the Iraq B strain was amplified as overlapping PCR products and sequenced using the pooled segment genome sequencing method and Illumina sequencing. Total average genome sequencing coverage reached 3469×, with a total genome size of 1,137,653 bp. Compared to the genome sequence of Bosnia A, a set of 37 single nucleotide differences, 4 indels, 2 differences in the number of tandem repetitions, and 18 differences in the length of homopolymeric regions were found in the Iraq B genome. Moreover, the tprF and tprG genes that were previously found deleted in the genome of the TEN Bosnia A strain (spanning 2.3 kb in length) were present in a subpopulation of TEN Iraq B and Bosnia A microbes, and their sequence was highly similar to those found in T. p. subsp. pertenue strains, which cause the disease yaws. The genome sequence of TEN Iraq B revealed close genetic relatedness between both available bejel-causing laboratory strains (i.e., Iraq B and Bosnia A) and also genetic variability within the bejel treponemes comparable to that found within yaws- or syphilis-causing strains. In addition, genetic relatedness to TPE strains was demonstrated by the sequence of the tprF and tprG genes found in subpopulations of both TEN Iraq B and Bosnia A. The loss of the tprF and tprG genes in most TEN microbes suggest that TEN genomes have been evolving via the loss of genomic regions, a phenomenon previously found among the treponemes causing both syphilis and rabbit syphilis.