Objectives: To estimate the prevalence of new variant Chlamydia trachomatis (nvCT) in Denmark.
Methods: Initial testing of 50 consecutive CT urine samples from each of 14 regional microbiology laboratories and re-analysis with a real-time CT PCR assay targeting the 16S rRNA gene and BD ProbeTec with confirmation of positives with a plasmid PCR with the primers CTP200/CTP201 flanking the deletion.
Results: The positive rate for 691 samples was 17% by real-time CT PCR and by ProbeTec. One specimen was positive for nvCT (0.14% of all samples, 0.8% of the positives).
Conclusion: The prevalence of nvCT is very low despite very close contact between Denmark and Sweden and extensive cross-border commuting.
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