New variant of Chlamydia trachomatis reported in Sweden

A new variant Chlamydia trachomatis strain has been isolated in Sweden [1,2]. Certain commercial diagnostic platforms generate false negative results when screening specimens from patients who are infected with the new variant strain.

The Chlamydia trachomatis cryptic plasmid (a non-chromosomal genetic element with unknown function found in all C. trachomatis strains) is high copy number and as such, is a popular target for commercial diagnostic platforms. This new strain has a 377bp deletion in a portion of the plasmid that is the target area for the C. trachomatis NAAT tests manufactured by Abbott and Roche.

Consequently these Platforms, which remain unaffected by this deletion, are the Aptima Combo 2 (AC2: Genprobe), RealArt CT Kit (Artus), and the Strand Displacement Assay (SDA) (Probetec, Becton Dickinson), as they target rRNA, the omp gene and a different region of the cryptic plasmid, respectively. In Sweden, the majority of laboratories were using a Roche platform whereas information obtained from the National External Quality Assessment Scheme (NEQAS) programme showed 39% of laboratories reporting to the scheme in the United Kingdom (UK) are currently using the Roche/Abbott platforms for the detection of C. trachomatis.

The length of time that this new variant has been circulating undiagnosed in the Swedish community is, as yet undetermined, although recent decreases in C. trachomatis infections have been observed and consequently concerns are that the strain is widely distributed throughout the country. There is currently no evidence that the new C. trachomatis variant is present within the UK. Indeed a recent large-scale study: the C. trachomatis NAAT evaluation programme screened 2375 urine specimens (of which 595 were positive and 131 were discordant), collected from patients attending at one of three geographically diverse sites in the UK, using four commercial platforms in a direct head-to-head comparison. Of the discordant specimens, only three urine specimens where found to be reproducibly negative on the Roche Cobas platform and positive on both the SDA and AC2 platforms. Differences in specimen status could also, however, be explained by differences in analytic sensitivity for the three platforms rather than a missing target region.

Current Recommendations to Diagnostic Laboratories in England and Wales

Laboratories performing testing on two platforms, including either the Roche or Abbott tests, should consider using the Roche or Abbott tests for confirmation rather than primary testing;
Laboratories who are using Roche or Abbott platforms as their only method of C. trachomatis detection should carry on using this approach but be vigilant for obvious decreases in the number of positives cases;
All laboratories should look for new alerts containing updated information.

The Sexually Transmitted Bacteria Reference Laboratory (STBRL) is happy to assist with any local problems or discuss potential discrepant results that may be due to the variant strain: email

Future studies
STBRL, in collaboration with the European Surveillance of Sexually Transmitted Infections (ESSTI, collaborative group, is currently investigating this new variant strain. The following strategies will be employed to determine the whether the new variant is present within the UK/Europe and if it is, ascertain its prevalence.

Investigation of the presence of this variant in samples from different geographical locations across Europe.

Perform trend analyses to identify unexpected decreases in the number of positive cases of C. trachomatis.

All findings will be made available as soon as possible.


New variant of Chlamydia trachomatis reported in Sweden
by ( Author at Spirit India )
Posted on at 1:16 pm.
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