I would like to take those patients he has qualified as suffering with Lyme arthritis refractory to abx, and run some diagnostics on them, including the C6. In the actual study, I suspect he explains how he qualifies the cohort. What I want to know is why he assumes he needs to be looking for an autoimmune explanation. Occam's razor and all that.
I would also check for a a GLQP protein (for b miyamotoi), and check for garinii and afzelli. I would run as broad a group of Borrelia tests - genus level - as are available. I'm not sure there are any; but in lieu of that, I'd run as many species tests as they have, as bad as those tests may be.
I'd run Bb sensu lato WB values and stack them against other accepted protocols for two or three bands IgG to equal a positive.
Then I'd write a paper about those results.
I know there isn't any point in trying to culture Bb from the synovial fluid. I know odds are a PCR will fail. They also would likely fail in a cousin spirochete, Syphilis.
So I would preface my write-up with those salient points. If my anti-body tests suggested continued infection, I would run with that.