Objectives To compare the proportions of Chlamydia trachomatis-positive specimens detected by Cobas Amplicor CT/NG (CA PCR) with C trachomatis positives in cell culture from 1999 to 2006 in order to estimate when the new variant of C trachomatis (nvCT) with a deletion in the cryptic plasmid (in the target region for CA PCR that resulted in false-negative results) emerged in Örebro County, Sweden.

Methods The annual number of specimens analysed using CA PCR in 1999–2006 ranged from 5077 to 11 622 and using cell culture (McCoy cells) from 5201 to 7425. Logistic regression was applied to evaluate the change in the proportion of C trachomatis-positive tests over the years between the two methods. The statistical interaction effect of year and method was estimated using both unadjusted and adjusted (age, gender and clinic) models.

Results From 2002, the proportion of C trachomatis-positive specimens identified using CA PCR decreased annually, whereas the proportion of culture-positive specimens increased annually. Logistic regression showed a statistically significant interaction effect between periods (1999–2006) and groups of specimens analysed using CA PCR or cell culture. A statistically significant association between the interaction of CA PCR/cell culture and period was observed in the unadjusted and adjusted models.

Conclusion This study indicates that in Örebro County, Sweden, nvCT was already present before 2002, that is, when the difference between the proportions of C trachomatis-positive specimens identified by CA PCR compared with cell culture-positive specimens began to show a statistically significant decline.