If we perform an EKG on a suspected or confirmed patient with Lyme disease will we get paid from the insurance company as a legitimate procedure and, if so, how do we code?

Whether you get paid or not will depend on each payer. All you can do is code correctly. 

In this case, you’d code the EKG. You’d probably use 93000, routine ECG with at least 12 leads, with interpretation and report, but you'll want to review all the codes around this in your CPT book and report the one that reflects exactly the sort of testing you are doing. In addition, you’d report the ICD-9 for Lyme: 088.81. 
