This is a companion article to the feature, “Respiratory Pathogen Testing.”

Guidelines on the use of traditional culture-based diagnostics for general classes of pathogens require laboratorians to perform more-specific reflex testing when necessary to identify select pathogens. Payors have long favored this protocol, and believe that it results in their paying only for medically necessary tests.

The advent of nucleic acid-based multiplex assays has made it possible for laboratories to implement large “screening” panels covering a number of infectious pathogens. Over time, the American Medical Association has established specific current procedural terminology (CPT) codes to be used in reporting the results of testing by means of such multiplex molecular pathology panels. However, it remains to be seen whether payors will continue to support such a multiplexed approach or revert back to their previously preferred use of targeted testing followed by reflex testing.

Prior to 1998, only two reimbursement codes existed for nucleic acid-based microbiology assays (87178, 87179). In 1998, these two codes were replaced with 69 organism-specific codes and a general “not otherwise specified” (NOS) code for reporting nucleic acid-based microbiology assays. It was not until 2011 that specific CPT codes for respiratory pathogens were created. At that time, three new CPT codes were established for reporting single (87501) and multiplexed (87502, 87503) influenza virus assays.

Most recently, in 2013, three new CPT codes were established for reporting respiratory pathogen panels that include three or more respiratory viruses. These codes report respiratory tests that include 3 to 5 respiratory viruses (87631), 6 to 11 respiratory viruses (87632), and 12 to 25 respiratory viruses (87633). A panel including more than 25 targets is to be reported using the unlisted microbiology code 87999, and is paid at the discretion of the Medicare contractor.

For multiplex respiratory pathogen assays that include respiratory viruses and bacteria, the appropriate influenza or respiratory virus code should be reported plus 87798, the code for an infectious agent detected by nucleic acid (DNA or RNA), not otherwise specified, amplified probe technique, for each additional bacterial pathogen tested for and reported.