Journal of the New Zealand Medical Association, 13-April-2007, Vol 120 No 1252
Chlamydia trachomatis: discovery of a new strain
A variant strain of Chlamydia trachomatis was recently detected in Sweden. The laboratory was alerted to possible false negatives due to a decrease in the positivity rate; a trend which was inconsistent with the past several years.1
The laboratory used two test methods (one commercial and one in-house) and when testing 1100 samples found 11 discrepant samples. The discrepant samples have been sequenced and a deletion of 377 base pairs was found in the target area for the C. trachomatis NAAT tests manufactured by Abbott and Roche.1
So far, this strain has been found in Sweden and two samples were found in Norway (one of the patients being Swedish). Despite efforts to locate the strain in other parts of the world, it has not been found.
In January 2007, Roche Diagnostics New Zealand initiated a local quality assurance scheme to determine if the variant strain is present in our population. Upon consultation with an epidemiologist and statistician, it was decided that a sample size of 500 patients would be sufficient to give reasonable certainty that the variant is not present in New Zealand.
The major regions of Auckland, Waikato, Bay of Plenty, Wellington, and Christchurch were chosen and DNA extracts were collected. The samples had tested negative using either the Roche Amplicor or TaqMan assay, which cannot detect the variant due to the deletion. An alternative assay on the LightCycler instrument was used to assess the prevalence of the variant C. trachomatis strain by targeting a different region of the Chlamydia genome unaffected by the deletion.
A total of 500 samples were tested for the presence of the variant strain, and the distribution is shown below (Table 1). Samples were a mixture of swabs and urines, and represented samples from both GPs and Sexual Health Clinics.
Table 1. New Zealand sample distribution and results
Current recommendations in England and Wales by the Health Protection Agency do not advocate switching assays. They state that 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”.
Alternative PCR test methods which use a different target should only be used if reasonable indications exist. Confirmatory testing with a chromosomal target like the one that was used in this study is available in New Zealand.
We have not been able to detect the variant strain in our study, however we are aware that the possibility of the variant being present in New Zealand cannot be completely excluded based on these results. This lack of variant is further confirmed by the fact that the CT prevalence rates in New Zealand continue to rise, in contrast to the Swedish situation.
Jennifer Barnes, Fabrice Merien
Roche Diagnostics NZ Ltd
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