For the past decade, laboratories in Sweden have used nucleic acid amplification tests (NAAT) to diagnose C. trachomatis infections. These NAAT tests use the cryptic plasmid (a non-chromosomal genetic element with unknown function found in all C. trachomatis strains) as the target area. If the current observed decrease in infections was not a true decrease in chlamydia incidence, it could be due to a change in the target area in the cryptic plasmid or a loss of the plasmid. Such a strain would obviously behave differently epidemiologically, because it would not be diagnosed by screening and no contact tracing would be performed from symptomatic index patients. Therefore, as part of the investigations into the decrease, we tested samples with alternative target areas of the plasmid as well as with a test specific for the major outer membrane protein (MOMP) area of the chromosome. The MOMP test was a commercial assay (Artus).

From mid-September to October 2006, the county microbiology laboratory in Halmstad, Halland county, tested 1700 consecutive incoming specimens with a MOMP-specific PCR in parallel with Abbotts m2000 plasmid PCR. In 13% of all diagnosed C. trachomatis cases in Halland county during this period (24/186), we found a variant strain that was only positive in MOMP tests. Clinical data indicates no difference from infections with the wild type strains.

The strain seems to be spread throughout the country, as it has also been found in northern, eastern and southern Sweden, although prevalence in these areas is still unknown. The findings throughout the country indicate that this strain is probably not a new phenomenon.

We have sequenced part of the plasmid from the variant strainand found a deletion of 377 base pairs in the target area for the C. trachomatis NAAT tests manufactured by Abbott and Roche. Twelve variant strains have now been sequenced and found to have the same deletion. Both companies have been informed and are currently working on a solution. This deletion does not affect the target area for the BD-ProbeTec test. At the laboratory in Halmstad, we are now developing a specific PCR test for the variant C. trachomatis strain.

The finding of a C. trachomatis variant does not, however, explain the decrease of 25% in C. trachomatis infections, especially if the variant has been circulating for some years. After 10 years of almost unbroken increase in reported number of C. trachomatis infections (from 332 cases in 1996 to 1000 cases in 2005), a decrease due to natural changes in incidence would not necessarily be surprising, but a decrease of 25% is much larger than expected. The authors would like to know how long this variant strain has been circulating undiagnosed, and whether it has occurred in other countries. If readers in other countries have recently experienced unexplained decreases in C. trachomatis infections, or have identified this variant, please contact the authors by emailing torvald.ripa@lthalland.se.