They Should Improve Slowly with Full Treatment that Leaves No
Hibernating or Biofilm Protected Forms.
A positive autoimmune marker does not necessarily establish an
autoimmune disease. Some tests are particularly important because
infections, including Borrelia, Bartonella, and Babesia, can cause
autoimmune-like abnormalities.
I. Systemic Autoimmune Diseases: Lupus, Sjögren, and Connective Tissue Disorders
# Laboratory test Main clinical significance
1 ANA Major screening test for lupus and systemic connective tissue diseases
2 Anti-dsDNA IgG Relatively specific for lupus; may correlate with
lupus nephritis
3 Anti-Smith (Sm) Highly specific for systemic lupus erythematosus
4 Anti-U1-RNP Mixed connective tissue disease and overlap syndromes
5 Anti-SSA/Ro52 and Ro60 Sjögren disease, lupus, subacute cutaneous lupus
6 Anti-SSB/La Supports selected Sjögren and lupus evaluations; limited
significance alone
7 Anti-chromatin/nucleosome antibodies Lupus, including possible renal
involvement
8 Anti-ribosomal P antibodies Relatively specific for lupus;
neuropsychiatric associations are inconsistent
9 Complement C3 Low levels can indicate immune-complex consumption
10 Complement C4 Low in lupus, cryoglobulinemia, and other
immune-complex disorders
11 CH50 Classical complement pathway function and complement deficiencies
12 Anti-C1q antibodies Associated with lupus nephritis, but not diagnostic alone
II. Rheumatoid Arthritis, Systemic Sclerosis, and Myositis
# Laboratory test Main clinical significance
13 Rheumatoid factor (RF) Rheumatoid arthritis, Sjögren disease; may
also occur in chronic infections
14 Anti-CCP / ACPA High specificity for rheumatoid arthritis
15 Anti-centromere antibodies Limited cutaneous systemic sclerosis
16 Anti-Scl-70 / topoisomerase I Systemic sclerosis, associated with
interstitial lung disease
17 Anti-RNA polymerase III Systemic sclerosis; increased renal crisis risk
18 Anti-PM/Scl-75 and PM/Scl-100 Systemic sclerosis–myositis overlap
19 Anti-Jo-1 Antisynthetase syndrome and inflammatory myopathy
20 Extended myositis antibody panel Includes Mi-2, MDA5, TIF1γ, NXP2,
SRP, HMGCR, PL-7, PL-12 and other antibodies
21 Creatine kinase (CK) Muscle injury, including inflammatory myopathies
III. Autoimmune Vasculitis, Kidney Disease, and Clotting Disorders
# Laboratory test Main clinical significance
22 MPO-ANCA Microscopic polyangiitis and some other ANCA-associated vasculitides
23 PR3-ANCA Granulomatosis with polyangiitis
24 Anti-GBM antibodies Anti-glomerular basement membrane disease
25 Cryoglobulins Cryoglobulinemic vasculitis, immune-complex disease
26 Lupus anticoagulant Antiphospholipid syndrome and thrombotic risk
27 Anticardiolipin IgG/IgM Antiphospholipid syndrome
28 Anti-β2-glycoprotein I IgG/IgM Antiphospholipid syndrome
29 Urinalysis with microscopy Hematuria, casts, proteinuria suggesting
renal involvement
30 Urine protein/creatinine ratio Quantifies proteinuria in suspected
autoimmune kidney disease
IV. Autoimmune Endocrine, Gastrointestinal, and Liver Diseases.
# Laboratory test Main clinical significance
31 Anti-thyroid peroxidase (TPO) Hashimoto thyroiditis and autoimmune
thyroid disease
32 TSH-receptor antibodies (TRAb/TSI) Graves disease
33 Anti-GAD65 antibodies Type 1 diabetes and selected autoimmune
neurological syndromes
34 Anti-tissue transglutaminase IgA plus total IgA Celiac disease
35 Anti-mitochondrial antibodies (AMA-M2) Primary biliary cholangitis
36 Anti-smooth muscle antibodies (ASMA) Autoimmune hepatitis,
particularly type 1
37 Anti-LKM-1 antibodies Autoimmune hepatitis, particularly type 2
38 Anti-intrinsic factor antibodies Autoimmune gastritis and pernicious anemia
V. Neurological, Hematological, and General Autoimmune Evaluation
# Laboratory test Main clinical significance
39 Aquaporin-4 IgG (AQP4-IgG) Neuromyelitis optica spectrum disorder
40 Myelin oligodendrocyte glycoprotein IgG (MOG-IgG) MOG
antibody-associated disease
41 Acetylcholine receptor antibodies (AChR) Myasthenia gravis
42 Direct antiglobulin test (DAT/Coombs) Autoimmune hemolytic anemia
43 ESR Nonspecific systemic inflammation
44 CRP Nonspecific acute and chronic inflammation
45 Serum IgG, IgA, and IgM Hypergammaglobulinemia, immunodeficiency,
and immune dysregulation
Most Relevant Tests for Lyme, Bartonella, and Babesia Patients
The following are particularly relevant when evaluating suspected
autoimmune complications in patients with these infections.
Suspected problem Priority tests
Lyme-associated inflammatory arthritis ESR, CRP, RF, anti-CCP, ANA
when systemic features suggest connective tissue disease
Bartonella-associated glomerulonephritis Urinalysis, urine
protein/creatinine, C3, C4, MPO-ANCA, PR3-ANCA, cryoglobulins
Babesia-associated autoimmune hemolysis DAT, CBC, reticulocytes, LDH,
bilirubin, haptoglobin
Lupus-like systemic illness ANA, anti-dsDNA, anti-Sm, C3, C4, urinalysis
Autoimmune neuropathy or myelitis SSA/Ro, AQP4-IgG, MOG-IgG when
clinically indicated
Suspected immune-complex vasculitis Cryoglobulins, RF, C3, C4,
urinalysis, inflammatory muscle disease CK, myositis-specific
antibodies.
Suspected autoimmune thrombosis Lupus anticoagulant, anticardiolipin,
anti-β2-glycoprotein I
Important distinctions
• Borrelia: Autoimmune responses have been demonstrated in
post-antibiotic Lyme arthritis, but routine autoantibody panels do not
reliably identify this mechanism.
• Bartonella: Endocarditis can produce ANCA positivity, immune-complex
glomerulonephritis, low complement, and other findings that resemble
primary autoimmune disease.
• Babesia: Autoimmune hemolytic anemia has been reported, but direct
parasitic hemolysis is more common and must be distinguished from
antibody-mediated red-cell destruction.
Additional tests worth considering: CBC with differential,
comprehensive metabolic panel, creatinine/eGFR, reticulocyte count,
LDH, haptoglobin, bilirubin, and serum protein electrophoresis. These
are not all autoimmune-specific but can be critical for evaluating
disease activity and organ injury.