Twelve years ago, I had a large boil or pimple on my penis. I was too young and stupid to do anything about it and it went away. It did not look terribly like many of the syphilis chancres that you can see online. Less that a year later, I met my wife. She has never had any signs of syphilis, nor did I ever have any signs of secondary syphilis like the rashes etc. I was and am in much better than average health since this incident. My wife also tested negative for syphilis a few years ago when her doctor gave her a pre-natal battery (we ended up not having kids). Recently, I became worried and took a RPR test that came back non-reactive.
I assume that I am all in the clear, but have read some places that the RPR can give off false negatives after people have been latent for a long time.
As you found by looking at pictures of syphilitic lesions, a boil or pimple doesn't sound like a chancre. Although it is true that the RPR and related syphilis blood tests can become negative with chronic infection, your negative result is proof you do not have active syphilis and cannot transmit the infection, and it is almost 100% insurance against ever having been infected. Assuming you are in the United States and not a gay or bisexual man, for you to have syphilis at least 3 very unlikely scenarios would all have to turn up the wrong way: heterosexual acquisition, atypical clinical presentation, and false negative blood test in you. The odds of all three going the wrong way are astronomically low. If you remain concerned--for example, if in fact you were at high risk (gay/bi, sex with a person known to have syphilis, immigrant from areas where syphilis is more common), you could ask your provider to do a more specific test, such as TPPA (Treponema pallidum particle agglutination) test. However, unless you have such risk factors, I really don't recommend it, because false positive results sometimes occur.
Tertiary syphilis almost never occurs in people with negative RPR. To my knowledge, I have never seen a case of false negative RPR "in a case like yours". No, you definitely don't need treatment.
You seem overly focused on syphilis. You never had symptoms that sound like syphilis, you say you don't have the typical risk factors, and you have a negative test. What more evidence do you need? If you're concerned about asymptomatic STDs going back to your premarital sex life, why are you worrying about the least common one of all, and not HSV, HPV, or hepatitis B? I suggest you follow your own notion ("I assume that I am all in the clear") and move on.
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