READ ME File For 'Characterisation of Genetic Diversity within Chlamydia trachomatis in High-Risk Sexual Networks'

Dataset DOI: 10.5258/SOTON/D2505

ReadMe Author: Chloe Manning, ORCID ID: 0000-0003-2428-7731

This dataset supports the thesis entitled Characterisation of Genetic Diversity within Chlamydia trachomatis in High-Risk Sexual Networks
AWARDED BY: University of Southampton
DATE OF AWARD: 2023

DESCRIPTION OF THE DATA
This dataset contains three folders, each given a different thesis chapter number. Details are provided for each folder below.

Chapter 3
The ompA gene is a mutational hotspot within the Chlamydia trachomatis genome, and extensive sequence variation within ompA has been reported amongst C. trachomatis strains. In Chapter 3, ompA genotyping was applied to C. trachomatis DNA extracted from a conjunctival swab collected from a 10 year old female that had migrated to the UK from Afghanistan, to ascertain whether the child was infected with a trachoma-causing strain, or a strain associated with sexually transmitted urogenital tract infections. The consensus ompA nucelotide sequence for this sample has been deposited in the folder. The nucleotide sequence can be accessed using MEGA, BioEDIT.

Chapter 5
In Chapter 5, the MLVA-ompA genotyping system was applied to genotype LGV-positive clinical specimens from London, to assess genotypic diversity within LGV C. trachomatis strains within this population. The study detected several distinct LGV MLVA-ompA genotypes, in addition to a hybrid L2b/D ompA genotype that had previously been reported in Portugal. This folder contains a spreadsheet of MLVA-ompA genotypes obtained for every sample included in the genotyping survey. This spreadsheet can be accessed using Excel or Access.  Example ompA nucleotide sequence traces have also been deposited in the folder. These can be accessed using MEGA, BioEDIT. 

Chapter 6
In Chapter 6, three LGV isolates collected from asymptomatic and symptomatic MSM in Brighton were whole genome sequenced, to identify any genomic loci or key sequences that may account for the differences in symptomology between the three patients. The study identified several mutations within the genomes of the three isolates. These mutations are detailed within the thesis. The raw trimmed reads for the three isolates have been deposited in the Chapter 6 folder. These can be accessed using Artemis, Artemis Comparison Tool (ACT), SnapGene.

Date of data collection: Chapter 3 (2017-2018), Chapter 5 (2019-2021), Chapter 6 (2021).

Information about geographic location of data collection: United Kingdom

Related projects/Funders:
UK Health Security Agency
Faculty of Medicine Vice-Chancellor's Scholarship (FACVC17A/Clarke/TBC/201718/264)

Related publications:
High Resolution genotyping of Lymphogranuloma venereum (LGV) strains of Chlamydia trachomatis in London using multi-locus VNTR analysis-ompA genotyping (MLVA-ompA). Doi: 10.1371/journal.pone.0254233

Reducing Suspicion of sexual abuse in paediatric chlamydial conjunctivitis using ompA genotyping. Doi: 10.1136/bcr-2020-238871

Licence: CC-BY

Date that the file was created: January, 2023