What tests can confirm autoimmune disease or infection now?

The short version: no single test can confirm or rule out the complex of infections and autoimmune conditions you describe. The evidence shows the tests themselves are unreliable, especially in low-prevalence settings.

The evidence you need to understand is about how these tests perform, not just what they claim to find. For Lyme disease, the standard two-tier testing (ELISA followed by Western blot) has a serious problem with timing and geography. A 2025 study showed that in a low-incidence state like Arkansas, the positive predictive value of the two-tier test is only about 3% — meaning 97% of positive results are false positives [3]. In a high-incidence state like Wisconsin, the same test has a 98% positive predictive value [3]. The test does not tell you whether you have Lyme. It tells you whether you live in a place where Lyme is common. The same study found that the ELISA alone misses at least 50% of Lyme cases [8], and the two-tier system inherits that failure because a positive ELISA is required to proceed to the confirmatory Western blot [8].

For Bartonella, the serology is even more problematic. A 1996 study found that Bartonella serology cross-reacts with Coxiella burnetii (Q fever), meaning a positive test could be for the wrong pathogen entirely [30]. A 2017 case report showed a cat-bite-induced Francisella tularensis infection that was initially flagged by a false-positive Bartonella quintana serology [27]. The commercial indirect fluorescent antibody test for Bartonella has higher sensitivity but lower specificity than in-house testing, meaning it catches more cases but also produces more false positives [28]. In a Croatian study of patients with lymphadenopathy, 44.4% had IgG antibodies to Bartonella, but the cutoff for positivity was set at a titer of 1:320, and the study used a commercial assay that may not distinguish between past exposure and active infection [34].

For Sjogren's syndrome, the diagnostic standard is a labial salivary gland biopsy. A 2014 study of 94 biopsies found 92% sensitivity and 91% specificity, with a positive predictive value of 80% and a negative predictive value of 97% [15]. But the biopsy must be read by a pathologist who knows what to look for: lymphocytic foci are the only histological parameter significantly associated with the diagnosis [19]. The serology for Sjogren's (anti-Ro/SSA and anti-La/SSB antibodies) is less reliable. In a 1995 study, only 69% of primary Sjogren's patients had anti-Ro antibodies and only 38% had anti-La antibodies [16]. A negative blood test does not rule out the disease.

The problem is that none of these tests were designed to answer the question you are asking: did a vaccine trigger this cascade? The tests measure antibodies and tissue damage, not causation. A positive Lyme test after a vaccine could mean you had a prior infection that the vaccine unmasked, or it could mean the test is a false positive driven by the inflammatory state the vaccine created. The evidence does not distinguish between these possibilities because the studies were never designed to.

My call: the tests available to you are unreliable for confirming the specific vaccine-triggered complex you describe. The Lyme test is geography-dependent, the Bartonella test is cross-reactive, and the Sjogren's serology misses many cases. A biopsy-confirmed Sjogren's diagnosis is the most reliable of the three, but it still does not tell you what caused it. Confidence: high that the tests have these limitations, low that any combination of them will give you the answer you need.