The Lyme testing can be confusing and I think often misleading, especially if you child has been on antibiotics prior to the testing.
I don't know if I want to advise you one way or the other. Mommy gut is huge in my book, too. But I will share my story in case it help you consider things in another light. I've stated it before, so sorry if it's redundant.
When we originally saw Dr. B. almost three years ago, he ran a regular Western Blot on my dd. Bands 41 and 39 came up. He interpreted the test as negative. At that point, she had been on Zithromax for perhaps 2 months. She had some positive strep titers in previous months, so he diagnosed her with PANDAS and upped her Zithromax dose. She did really well for about 6 months, then took a nose dive. Her brother had strep, so we attributed it to that. But even after we treated him and gave her a steroid burst, she continued to decline. So he suspected another infection and retested for Lyme and co-infections, but this time through IgeneX. By now she had been on antibiotics for close to one year. Her IgeneX Lyme results only showed IND on 41. No other bands. So, negative for Lyme, right? She did test positive for Bartonella, though, so he referred us to Dr. J. and added bactrim.
Dr. J. confirmed Bartonella but still suspected Lyme. He tested her through IgeneX again, but it came out the same.
Fast forward to November 2011. She was doing really well...probably 90%, but had plateaued. He theorized Lyme may be in cyst form and prescribed a cyst buster (Tindamax) to be given every weekend. This past spring, he ran IgeneX Lyme again and she finally showed positive again on band 41 and IND on the Lyme specific band of 34 and 39 (the one she originally showed something for).
What this says to me is that as the Tindamax does it's work and breaks up the cysts, her body is finally making antibodies.
Maybe I'm wrong. Maybe the IgeneX tests are just inconsistent and unreliable. But to LLMs point, the treatment we have been using is working. She is 100% 95% of the time. We get hiccoughs, but their pretty small and she recovers from them very quickly.
On a different note, my son, who was often sick with strep, was also tested for Lyme. Initially nothing (after being on abx). Then, after not being on them for several months (but getting strep again and myco P), he tested positive for Lyme by IgeneX standards (and very close to positive by CDCs standards).
I think strep and Lyme are often found together. If you read Cure Unknown, there is actually a sentence in their where Pamela Weintraub recounts one of her interviews with Dr. Jones. When Lyme was first identified, but the cause not yet know, he suspected it was bacterial (whereas many others thought it might be viral). He thought this because many of his patients that came in with Lyme symptoms also had strep. When they did, he would put them on abx and their LYme symptoms would improve. If you haven't already, I suggest reading that book.
Kara