Method of diagnosing persistent, chronic synovitis and progressive joint degradation in the joint of a mammal. The method including providing a test sample comprising synovial fluid, cell or tissue from the joint of a mammal; detecting the presence of bacterial DNA, measuring the concentration of one or more biomarkers being cathepsin K, MMP-2 and -9, cathepsin S, tartrate-resistant acid phosphatase, invariant chain, CD4+ T-lymphocytes, CD8+ T-lymphocytes, CD44+ mononuclear cells, Toll-like receptor-2, Toll-like receptor-9, or a combination thereof; and, comparing the concentration of the biomarker from the test sample to a corresponding biomarker concentration in a control sample from healthy dogs, or an internal PBMC control sample, wherein a statistically significant elevated concentration of the biomarker in the test sample indicates that the mammal's joint is diseased.