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The nature and extent of plasmid variation in Chlamydia trachomatis

The nature and extent of plasmid variation in Chlamydia trachomatis
The nature and extent of plasmid variation in Chlamydia trachomatis
Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.
Chlamydia trachomatis, Diagnostics, Evolution, Genetic variation, Plasmid, Sequencing
Jones, Charlotte
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Hadfield, James
4badecc0-e49b-468f-9412-89e7bcf1f84b
Thomson, Nicholas R.
5497a110-069d-4156-bccb-c77db572b1c2
Cleary, David
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Marsh, Peter
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Clarke, Ian
ff6c9324-3547-4039-bb2c-10c0b3327a8b
O'neill, Colette
3de0c221-6578-4a1a-96bd-2a3fba2b6193
Jones, Charlotte
e5a1e661-cab8-4105-acef-25221d08ecd2
Hadfield, James
4badecc0-e49b-468f-9412-89e7bcf1f84b
Thomson, Nicholas R.
5497a110-069d-4156-bccb-c77db572b1c2
Cleary, David
f4079c6d-d54b-4108-b346-b0069035bec0
Marsh, Peter
18f63c35-264b-4ec9-8505-9c57bf707ad2
Clarke, Ian
ff6c9324-3547-4039-bb2c-10c0b3327a8b
O'neill, Colette
3de0c221-6578-4a1a-96bd-2a3fba2b6193

Jones, Charlotte, Hadfield, James, Thomson, Nicholas R., Cleary, David, Marsh, Peter, Clarke, Ian and O'neill, Colette (2020) The nature and extent of plasmid variation in Chlamydia trachomatis. Microorganisms, 8 (3), [373]. (doi:10.3390/microorganisms8030373).

Record type: Article

Abstract

Chlamydia trachomatis is an obligate intracellular pathogen of humans, causing both the sexually transmitted infection, chlamydia, and the most common cause of infectious blindness, trachoma. The majority of sequenced C. trachomatis clinical isolates carry a 7.5-Kb plasmid, and it is becoming increasingly evident that this is a key determinant of pathogenicity. The discovery of the Swedish New Variant and the more recent Finnish variant highlight the importance of understanding the natural extent of variation in the plasmid. In this study we analysed 524 plasmid sequences from publicly available whole-genome sequence data. Single nucleotide polymorphisms (SNP) in each of the eight coding sequences (CDS) were identified and analysed. There were 224 base positions out of a total 7550 bp that carried a SNP, which equates to a SNP rate of 2.97%, nearly three times what was previously calculated. After normalising for CDS size, CDS8 had the highest SNP rate at 3.97% (i.e., number of SNPs per total number of nucleotides), whilst CDS6 had the lowest at 1.94%. CDS5 had the highest total number of SNPs across the 524 sequences analysed (2267 SNPs), whereas CDS6 had the least SNPs with only 85 SNPs. Calculation of the genetic distances identified CDS6 as the least variable gene at the nucleotide level (d = 0.001), and CDS5 as the most variable (d = 0.007); however, at the amino acid level CDS2 was the least variable (d = 0.001), whilst CDS5 remained the most variable (d = 0.013). This study describes the largest in-depth analysis of the C. trachomatis plasmid to date, through the analysis of plasmid sequence data mined from whole genome sequences spanning 50 years and from a worldwide distribution, providing insights into the nature and extent of existing variation within the plasmid as well as guidance for the design of future diagnostic assays. This is crucial at a time when single-target diagnostic assays are failing to detect natural mutants, putting those infected at risk of a serious long-term and life-changing illness.

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Accepted/In Press date: 3 March 2020
e-pub ahead of print date: 6 March 2020
Keywords: Chlamydia trachomatis, Diagnostics, Evolution, Genetic variation, Plasmid, Sequencing

Identifiers

Local EPrints ID: 445212
URI: http://eprints.soton.ac.uk/id/eprint/445212
PURE UUID: 4e91e3da-b043-4fc9-851a-adab11d5f8f4
ORCID for David Cleary: ORCID iD orcid.org/0000-0003-4533-0700
ORCID for Ian Clarke: ORCID iD orcid.org/0000-0002-4938-1620

Catalogue record

Date deposited: 25 Nov 2020 17:32
Last modified: 18 Feb 2021 17:24

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