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Volume 10, Issue 3

Genomic insights into local-scale evolution of ocular strains within and between individuals in Gambian trachoma-endemic villages Open Access

Abstract

Trachoma, a neglected tropical disease caused by (Ct) serovars A–C, is the leading infectious cause of blindness worldwide. Africa bears the highest burden, accounting for over 86 % of global trachoma cases. We investigated Ct serovar A (SvA) and B (SvB) whole genome sequences prior to the induction of mass antibiotic drug administration in The Gambia. Here, we explore the factors contributing to Ct strain diversification and the implications for Ct evolution within the context of ocular infection. A cohort study in 2002–2003 collected ocular swabs across nine Gambian villages during a 6 month follow-up study. To explore the genetic diversity of Ct within and between individuals, we conducted whole-genome sequencing (WGS) on a limited number (=43) of Ct-positive samples with an B load ≥10 from four villages. WGS was performed using target enrichment with SureSelect and Illumina paired-end sequencing. Out of 43 WGS samples, 41 provided sufficient quality for further analysis. A analysis revealed that 11 samples had highest identity to A from strain A/HAR13 (NC_007429) and 30 had highest identity to A from strain B/Jali20 (NC_012686). While SvB genome sequences formed two distinct village-driven subclades, the heterogeneity of SvA sequences led to the formation of many individual branches within the Gambian SvA subclade. Comparing the Gambian SvA and SvB sequences with their reference strains, Ct A/HAR13 and Ct B/Jali20, indicated an single nucleotide polymorphism accumulation rate of 2.4×10 per site per year for the Gambian SvA and 1.3×10 per site per year for SvB variants (<0.0001). Variant calling resulted in a total of 1371 single nucleotide variants (SNVs) with a frequency >25 % in SvA sequences, and 438 SNVs in SvB sequences. Of note, in SvA variants, highest evolutionary pressure was recorded on genes responsible for host cell modulation and intracellular survival mechanisms, whereas in SvB variants this pressure was mainly on genes essential for DNA replication/repair mechanisms and protein synthesis. A comparison of the sequences between observed separate infection events (4–20 weeks between infections) suggested that the majority of the variations accumulated in genes responsible for host–pathogen interaction such as CTA_0166 (phospholipase D-like protein), CTA_0498 (TarP) and CTA_0948 (deubiquitinase). This comparison of Ct SvA and SvB variants within a trachoma endemic population focused on their local evolutionary adaptation. We found a different variation accumulation pattern in the Gambian SvA chromosomal genes compared with SvB, hinting at the potential of Ct serovar-specific variation in diversification and evolutionary fitness. These findings may have implications for optimizing trachoma control and prevention strategies.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Chlamydia trachomatis , evolution , trachoma and whole-genome sequencing (WGS)
Funding
This study was supported by the:
  • Horizon 2020 Framework Programme (Award 733373)
    • Principle Award Recipient: MartinJ Holland
  • Wellcome Trust (Award 079246/Z/06)
    • Principle Award Recipient: MartinJ Holland
  • Medical Research Council (Award G9826361/ ID48103)
    • Principle Award Recipient: MartinJ Holland
  • Austrian Science Fund (Award J-4608)
    • Principle Award Recipient: EhsanGhasemian
© 2024 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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Genomic insights into local-scale evolution of ocular Chlamydia trachomatis strains within and between individuals in Gambian trachoma-endemic villages
M Gen 10, 001210 (2024); https://doi.org/10.1099/mgen.0.001210
/content/journal/mgen/10.1099/mgen.0.001210
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