Multiplex diagnostic assays for Lyme disease and other tick-borne diseases

A kit for diagnosing a tick-borne disease, the kit comprising at least two of the following:

• a. a pair of Borrelia primers for a recA gene sequence of Lyme disease-causing Borrelia, having the respective sequences of SEQ ID Nos:
• 12 and 13;
• and a Borrelia-specific molecular beacon probe capable of distinguishing among B. burgdorferi, B. afzelii, and B. garinii having the sequence of SEQ ID No:
• 5;
• b. a pair of Babesia primers for a conserved B. microti thiamine pyrophosphokinase (BmTPK) gene sequence having the respective sequences of SEQ ID Nos:
• 14 and 15 or of SEQ ID Nos:
• 24 and 25 and a Babesia-specific molecular beacon probe having the sequence of SEQ ID No:
• 16;
• and
• c. a pair of Anaplasma primers for a conserved Anaplasma phagocytophilum (APH) 1387 gene sequence of A. phagocytophilum having the respective sequences of SEQ ID Nos:
• 18 and 19, or of SEQ ID Nos:
• 26, and 27 and an Anaplasma-specific molecular beacon probe having the sequence of SEQ ID No:
• 20,
• wherein each of said primer pairs amplifies an amplicon that is 70-300 base pairs in length, wherein primer annealing is performed at a temperature below or equal to a primer-extension temperature during an amplification reaction, and wherein each molecular beacon probe is labeled with a spectrally distinguishable fluorescent or luminescent signaling moiety.