Most bumps are normal parts or your anatomy or irritation not related to STDs. Unfortunately, the only way to be sure is to have the bumps examined by a doctor or STD specialist. Your description sounds more like a rash than warts, but that is just a guess.
HPV is a very common infection, and most people with several sexual partners over their lifetime will acquire at least one HPV infection. While symptoms of these infections usually become apparent in the months following exposure, they sometimes show up years, even decades later. It is important for your wife to continue to get her PAPs done, as they will indicate if there are any changes, caused by HPV that may be precancerous. This test is not a HPV test though, and most people with HPV infections will have normal PAPs.
Have a doctor take a look to be sure. Expect the bumps to be unrelated to HPV, but if they turn out to be warts, simply have them treated.
Also I would like to add that my wife and I have been together for 8 years and she has always had normal paps. With her last one being 5 months ago.
Could my antibiotics being causing this?