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Hi there and thanks for your question.
If someone has a suspect syphilis chancre, one of the best tests to do is a PCR test from the actual chancre or lesion itself. Basically, trying to get a sample from the chancre itself is the best test to do during these early stages.
One cannot always rely on the RPR test, or other syphilis blood tests to confirm a primary syphilis diagnosis. Doctors at our clinic have seen many primary syphilis cases where the RPR has been negative, as well as some of the other more specific blood tests being negative.
If you suspect a chancre, and the RPR comes back negative, best to have a repeat test a month or so later to confirm this.
Hope this answers your question.