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Billing & Coding of Infectious Disease Testing

by | Jul 4, 2023 | Essential, Lab Compliance Advisor, Reimbursement-lca

Recent developments pose reimbursement and compliance challenges for billing and coding infectious disease testing—here’s how to manage them.

Clinical laboratories routinely test for infectious pathogens that may be found in multiple body organs, tissues, and fluids. Identifying these pathogens is crucial to prevent progressive growth and tissue destruction through proper treatment. The traditional methods of infectious agent detection and treatment include various cultures, culture typings, and sensitivity testing. However, newer technologies are replacing these traditional options. Better test methods, knowledge of new pathogens, and population growth have also led to more frequent infectious disease testing.

However, these testing and technological developments pose reimbursement and compliance challenges. Here’s a general briefing and overview on the key billing and coding requirements spanning the range of infectious disease test modalities.

Polymerase Chain Reaction (PCR) Molecular Testing

As PCR testing has become more routine, the American Medical Association (AMA) has developed specific procedural codes for billing these tests (CPT 87468 – 87801). Current Procedural Terminology (CPT) provides instructions for the codes in the molecular microbiology section. Key points:1

  • These codes are intended for primary source only;
  • Infectious agents by antigen detection, immunofluorescence microscopy, or nucleic acid probe techniques should be reported as precisely as possible;
  • The molecular pathology procedures codes (81161, 81200-81408) are not to be used in combination with or instead of the procedures represented by codes 87471-87801;
  • The most specific code possible should be reported;
  • Use the general methodology code (e.g., 87299, 87499, 87797, 87798, 87799, 87899) if there’s no specific agent code;
  • When reporting separate results for different species or strains of organisms, code each result separately;
  • Use modifier -59 when reporting separate results for different species or strains described by the same code.

The Challenges of Billing & Coding Panel Testing

An Example

Panel tests that many labs are adopting can be rather extensive. For example, one lab’s sexually transmitted infections (STI) panel includes 24 bacteria, eight fungi, and two viruses. How would you code this panel for billing and reimbursement purposes? Because there is no panel code for STI testing, many laboratories would code each pathogen. With 34 agents tested, it’s likely that 13 units of CPT 87798 would be included (Medically Unlikely Edits [MUE] is 13):2

CPT Description
87798 Infectious agent detection by nucleic acid (DNA or RNA), not otherwise specified; amplified probe technique, each organism

Other questions to consider include whether the results are qualitative or quantitative and whether multiplex analysis is involved. Although other specific codes may be found, the big question labs must answer is whether medical necessity exists for the size of this panel. Note also that the AMA and the Centers for Medicare & Medicaid Services (CMS) may have different coding opinions.

Coding for Antibiotic Resistance Markers

Most of the newer panels include analysis of markers that identify antibiotic resistance. It’s common to include 20+ markers in various panels. Testing for the resistance genes isn’t testing for an infectious agent but, rather, for the nucleic acid sequences responsible for resistance. How are these resistance markers coded?

In 2007, the AMA added CPT 87640 (Staphylococcus aureus) and 87641 (Methicillin-resistant Staphylococcus aureus [MRSA]). The rationale for the additions was discussed in CPT Assistant in August 2007:3

“It was noted that prior to adding these two codes, the CPT code used to report MRSA detection by nucleic acid (DNA or RNA) amplification (87798) did not specifically identify the infectious agent being tested. This resulted in medically imprecise coding and inconsistent reimbursement.

CPT 87640 was established to report testing by amplified probe technique for the detection of Staphylococcus aureus that is not methicillin-resistant. CPT 87641 was established to report testing for the detection of MRSA by amplified probe technique.”3

Thus, by reporting CPT 87640 and 87641, only S. aureus is being evaluated for any methicillin resistance; the remaining agents are excluded.

In 2008, the AMA added CPT 87500 (Infectious agent detection by nucleic acid [DNA or RNA]; vancomycin resistance [e.g., Enterococcus species van A, van B], amplified probe technique). CPT Assistant stated in April 2008:4

“CPT 87500 was established to report the performance of a nucleic acid detection test for nucleic acid sequences specific for vancomycin resistance which is commonly found in Enterococcus species (e.g., nucleic acid sequences associated with vanA and vanB genes) by amplified probe technique. This new code is for reporting the detection of nucleic acid sequences responsible for resistance, not the organism itself.”4

By reporting CPT 87500, only enterococci are being evaluated for any vancomycin A or B resistance; the remaining agents are excluded.

Another code, CPT 87900, identifies phenotype testing:

CPT Description
87900 Infectious agent drug susceptibility phenotype prediction using regularly updated genotypic bioinformatics

Another key change is the AMA’s conversion of Category III code 0023T to Category I code 87900 in 2008:

“Code 87900 is intended to describe infectious agent drug susceptibility phenotype prediction using regularly updated genotypic bioinformatics. This testing is typically used in the management of HIV patients on antiretroviral therapy. Results provide a quantitative prediction of drug susceptibility phenotype for each antiretroviral drug. Clinicians receive a numeric measure of susceptibility or resistance on which to base the selection of multi-drug regimens.”5

However, the testing associated with CPT 87900 is antiviral and not antibacterial. Thus, many markers for bacterial infections cannot be identified. Overall, current coding options are not adequate for identifying resistance to various antibiotics.

Metagenomic Next-Generation Sequencing (mNGS)

The National Institutes of Health’s National Center for Biotechnology Information defines metagenomics as “the functional and sequence-based analysis of the collective microbial genomes that are contained in an environmental sample.”6 Few laboratories have adopted this methodology to date but metagenomics is gaining favorable attention.

For example, the University of California San Francisco (UCSF) Center for Next-Gen Precision Diagnostics writes on its website that metagenomic next-generation sequencing (mNGS) can potentially diagnose all infectious agents—viruses, bacteria, fungi, and parasites—in a single test. According to the center, “metagenomic next-generation sequencing (mNGS) is a shotgun sequencing approach in which all of the nucleic acid (DNA and RNA) in a clinical sample is sequenced at a very high depth, 10-20 million sequences per sample. mNGS can be performed for any type of clinical sample, including cerebrospinal fluid, plasma, respiratory secretions, urine, stool, or tissue.”7

Most labs believe that the PCR codes in the microbiology section of CPT are appropriate. In my experience, none of the 87XXX codes reflect NGS testing and are not likely to specifically relate to actual test findings. The limiting factor is that the current codes only identify germline or somatic conditions—not acquired diseases or disorders. Tier 1 and 2 codes identify actual genes, meaning the only coding option left for labs is an unlisted code, CPT 81479, but this doesn’t allow for payment. Were a lab under the MolDx Program, it could report CPT 81479 with a “Z” code that would identify the testing and allow adjudication.8

Coverage Policies and Medical Necessity

When a payer creates a policy regarding coverage of a particular procedure, it’s usually accompanied by an article that explains coding and billing of that same procedure. Commercial payer policies may mimic policies established by CMS administrative contractors. Palmetto, the home of the MolDx Program, has created a policy for infectious disease pathogen testing:9

Molecular Syndromic Panels for Infectious Disease Pathogen Identification Testing

A “syndromic panel” is defined as one that simultaneously detects multiple different pathogens associated with similar and overlapping clinical symptomatology. This policy relates to:

  • Limited coverage of outpatient testing
  • Definition of a panel as more than one pathogen
  • Testing for multiple types of pathogens
  • The distinction between small, targeted panels (up to five pathogens) and larger, expanded panels (six or more pathogens)
  • Which specific CPT, Proprietary Laboratory Analyses (PLA), and International Classification of Diseases (ICD) codes are acceptable

It should be noted that the policy does not pertain to metagenomic NGS.

The accompanying article for the policy includes the following requirements for coding panel tests:10

  • ICD-10-CM diagnosis codes supporting medical necessity must be submitted with each claim. Claims submitted without such evidence will be denied as not medically necessary
  • Any diagnosis submitted must have documentation in the patient’s record to support coverage and medical necessity
  • The submitted medical record must support the use of the selected ICD-10-CM code(s). The submitted CPT/ Healthcare Common Procedure Coding System (HCPCS) code must describe the service performed
  • The test panel is a single test with multiple components and is characterized by a single unit of service (UOS =1). A panel cannot be unbundled and billed as individual components even though the test reports multiple individual pathogens and/or targets

Other Palmetto policies address gastrointestinal and respiratory panel testing. Labs may also want to examine commercial policies.

Infectious Disease Pathogen Panel Billing & Coding Outlook

The above discussion shows the challenges that exist for coding and billing infectious disease panels. The AMA seems willing to accept a certain level of stacked codes for PCR testing and the CMS appears to limit PCR panels to three to five pathogens/codes. In addition, although limited coverage policies exist, some CPT and PLA codes are covered, while others are not. Commercial payer requirements may further vary coding formats.

Current coding also doesn’t provide an adequate way to identify resistance to various antibiotics. Coding for mNGS doesn’t appear to exist, and an unlisted code would not provide reimbursement unless there are individual payer arrangements. FDA approvals for infectious disease pathogen panel tests are still infrequent.

Laboratories are increasingly requesting PLA or multianalyte assays with algorithmic analyses (MAAA) codes for these infectious disease panels. Twenty-two new PLA codes were approved for use in April, with six relating to infectious pathogen testing.11 These codes make billing and coding for infectious pathogen testing more transparent—one code is approved and reported, which identifies the panel procedure performed. The PLA code can also include antibiotic resistance testing, allowing for reimbursement.


  1. https://www.ama-assn.org/system/files/2020-10/cpt-assistant-guide-coronavirus-october-2020.pdf
  2. https://www.cms.gov/medicare-coverage-database/view/article.aspx?articleId=58761
  3. American Medical Association, CPT Assistant. August 2007
  4. American Medical Association, CPT Assistant. April 2008
  5. American Medical Association. 2008. https://www.ama-assn.org/
  6. https://www.ncbi.nlm.nih.gov/books/NBK6858/
  7. https://nextgendiagnostics.ucsf.edu/technology/
  8. https://www.palmettogba.com/MolDx
  9. https://www.cms.gov/medicare-coverage-database/view/lcd.aspx?lcdid=39044
  10. https://www.cms.gov/medicare-coverage-database/view/article.aspx?articleId=58761
  11. https://www.g2intelligence.com/medicare-to-pay-for-22-additional-pla-codes-starting-april-1/


Diana W. Voorhees, MA, CLS, MT, SH, CLCP, CPCO, is the principal of DV & Associates, Inc., Salt Lake City, UT. DV & Associates makes no representation, guarantee, or warranty, expressed or implied, that the information provided is free of error, and bears no responsibility or liability for results or consequences of its use.

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