The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

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.

Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

“… 29 Most human and animal pathogens classified in the family Chlamydiaceae carry a conserved 7.5 kb plasmid with eight plasmid encoded proteins, referred to as plasmid glycoproteins Pgp1–8. 30 , 31 , 32 , 33 These low copy number plasmids 34 represent an important virulence factor in the natural host. 35 , 36 , 37 , 38 Accumulating evidence indicates coevolution of chlamydial plasmids and chromosomes within the family Chlamydiaceae.…”

Diversity in Chlamydial plasmids

“…This analysis conforms with the previously studied hypothesis that identified CDS5 (virulence associated protein) as the most polymorphic gene within C. trachomatis with a p-distance of 0.008 [30]. However, the same study identified CDS2 as the most conserved and least diverse gene on the plasmid with only 11 allelic variations within the C. trachomatis species [30], whilst a more recent study identified CDS6 as the most conserved plasmid gene in C. trachomatis across a much larger sample set (but CDS2 was the most conserved at the amino acid level) [27] Our calculations gave a p-distance of 0.254 and SE = 0.008 for CDS2, which was considerably higher compared to CDS4 with a p-distance of 0.181. One might argue that this difference could be due to two of the present species (C. avium 10DC88 and C. gallinacea 08-1274/3) possessing mutations.…”

“…Further studies established that these plasmids are present in most strains of C. trachomatis. The plasmid is highly conserved, with an intraspecific variation of around 3% [27]. Large-scale deletions or rearrangements of the plasmid are therefore rare [27,28], but in 2006 a new strain was described that evaded PCR detection due to a single large deletion in CDS1 of its plasmid [29].…”

“…The plasmid is highly conserved, with an intraspecific variation of around 3% [27]. Large-scale deletions or rearrangements of the plasmid are therefore rare [27,28], but in 2006 a new strain was described that evaded PCR detection due to a single large deletion in CDS1 of its plasmid [29]. In 2018 157 whole genome sequences of C. trachomatis (including plasmid) isolates were deposited into the pubMLST database, where 902 genes were identified.…”

Seroepidemiology of Chlamydia trachomatis Infection in the General Population of Northern China: The Jidong Community Cohort Study

“…Although our "in-house" LISA used one Pgp3 protein from serovar E of C. trachomatis, it does show comparable performance with the commercial Mikrogen ELISA, which uses multiple C. trachomatis antigens (MOMP, TARP, and CPAF). Of note, Jones et al (2020) recently reported the variation of Pgp3 protein with a genetic distance of 0.013 at the amino acid level among different C. trachomatis serovars. However, the small genetic distance of Pgp3 gene and the corresponding 98.7% sequence identity maintains a 94% probability of cross-reactivity within C. trachomatis species according to the formula "P cross = e (−9.4153 + 0.123223 × percent sequence identity) /[1 + e (−9.4153 + 0.123223 × percent sequence identity) ] reported by Rahman et al (2015Rahman et al ( , 2018b.…”