A new variant of Chlamydia trachomatis was discovered in Sweden in 2006. This variant contains a mutant sequence that cannot be detected with either the Abbott m2000 (Abbott Diagnostics, Chicago, IL, USA) or Cobas Amplicor/TaqMan48 (Roche Diagnostics, Basel, Switzerland) systems.¹ The first description reported that the new variant constituted 13% of all detected chlamydia infections (from mid-September to October 2006) in the county of Halland (south west of Sweden). It soon became apparent that the proportion was higher and that the new variant had spread widely in Sweden.^2–4 We now know that in the counties that have used the Abbott or Roche test systems during the past year or so the new variant accounts for 20% to 65% of all detected chlamydia cases. In local areas, as many as 78% of all cases have been found to have the mutation (Britta Loré, personal communication).

How great is the national impact of this emerging variant of C trachomatis? As in many other countries chlamydia rates have increased in Sweden during the past 10 years. However, for 2006 the national figures showed a reversal of this trend.⁵ The 2% decrease in reported cases was because of the inability of some diagnostic systems to detect the new variant. Counties using the Abbott or Roche test systems reported fewer chlamydia cases in 2006 compared to 2005, while counties using methods that detected the strain, mainly the BectonDickinson ProbeTec, reported an increase. In a preliminary analysis, if we assume …