Medical billing for infectious disease specialists is complex, with a vast array of CPT codes covering office visits, hospital care, lab tests, procedures, and infusion therapy. If coded incorrectly, healthcare providers risk delayed reimbursements, denied claims, and revenue losses. Understanding infectious disease CPT codes is essential for accurate billing, compliance, and maximizing reimbursements.
Whether you’re a medical coder, billing specialist, or healthcare provider, this guide will help you navigate evaluation & management (E/M) services, diagnostic tests, treatment procedures, and telehealth consultations with ease.
Evaluation & Management (E/M) CPT Codes for Infectious Disease
Medical billing for infectious disease specialists begins with Evaluation & Management (E/M) CPT codes, which cover new patient consultations, hospital visits, and follow-ups. Proper documentation is key to ensuring accurate claim reimbursement and avoiding billing errors.
New & Established Patient Office Visits
When an infectious disease specialist sees a patient in an outpatient setting, these CPT codes are used:
- 99202-99205: New patient office visits (based on time and complexity)
- 99211-99215: Established patient follow-ups
Hospital & Inpatient Visits
Patients with severe infections like sepsis, pneumonia, or tuberculosis (TB) often require hospitalization. These CPT codes apply:
- 99221-99223: Initial hospital care (new patient admission)
- 99231-99233: Subsequent hospital visits (follow-ups)
- 99238-99239: Hospital discharge services (based on time spent)
Consultations & Critical Care
Some cases require specialist consultations or intensive care management, particularly for severe bacterial or viral infections.
- 99241-99245: Outpatient consultations
- 99251-99255: Inpatient consultations (higher complexity evaluations)
- 99291-99292: Critical care services (for patients with sepsis, meningitis, or severe COVID-19)
Laboratory & Diagnostic CPT Codes for Infectious Disease
Accurate diagnosis of infectious diseases relies on laboratory tests such as blood cultures, PCR tests, and rapid antigen tests. Below are the most commonly used CPT codes for infectious disease diagnostics:
Blood & Bacterial Testing
Blood tests help detect bacterial infections, fungal infections, and sepsis. These are the standard CPT codes:
- 87040: Blood culture (bacterial infections)
- 87205: Smear, primary source interpretation
- 87186: Antimicrobial susceptibility testing (to check antibiotic resistance)
- 87486-87488: PCR tests for bacterial & viral infections
COVID-19 & Respiratory Infection Testing
Patients presenting with flu-like symptoms often need respiratory pathogen testing:
- 87635: SARS-CoV-2 (COVID-19) testing (PCR)
- 87641: RSV (Respiratory Syncytial Virus) testing
- 87804: Rapid flu test (Influenza A & B)
HIV & STI Testing
Infectious disease specialists frequently screen, diagnose, and manage patients with HIV, AIDS, and sexually transmitted infections (STIs):
- 86703: HIV-1 & HIV-2 antibody test
- 87389: HIV antigen/antibody screening
- 87535: HIV-1 quantitative PCR test
- 87806: Rapid HIV test
Infectious Disease Treatment & Procedure CPT Codes
After a diagnosis, patients often require specific treatments and minor procedures for infections, abscesses, or wound care.
Common Procedures for Infectious Disease Management
- 10060-10061: Incision & drainage of abscess (for MRSA, cellulitis, or deep skin infections)
- 10120: Foreign body removal (for infected wounds)
- 11042-11047: Debridement of infected wounds (used for diabetic ulcers, gangrene, or necrotizing fasciitis)
- 12001-12018: Wound repair & closure (suturing after infections are treated)
Immunizations & Preventive Care
Prevention is crucial in infectious disease management, requiring vaccinations for high-risk patients.
- 90471-90474: Vaccine administration (single/multiple injections)
- 90658: Influenza vaccine
- 90732: Pneumococcal vaccine (for pneumonia prevention)
- 90670: Prevnar 13 (pneumococcal vaccine)
- 86580: Tuberculosis (TB) skin test
Infusion Therapy & Injection CPT Codes for Infectious Disease
Many patients with severe bacterial or viral infections require intravenous (IV) antibiotics, antifungals, or hydration therapy. Here are the CPT codes used for infusion therapy:
Intravenous Infusion Therapy
- 96365: Initial IV infusion, first hour
- 96366: Each additional hour of IV infusion
- 96374: IV push, single or initial drug
- 96375: IV push, additional sequential drug
Therapeutic & Prophylactic Injections
- 96372: Subcutaneous or intramuscular injection (for antibiotics or prophylaxis)
- 99070: Supplies for treatment procedures (medications, syringes, IV kits)
Telehealth & Virtual Consultation CPT Codes for Infectious Disease
The rise of telemedicine has revolutionized infectious disease management, allowing specialists to consult patients remotely. Telehealth visits reduce hospital visits and provide quicker access to care for conditions like COVID-19, HIV, or chronic infections. Here are the CPT codes for telehealth and virtual consultations:
Telehealth & Virtual Visits
- 99441-99443: Telephone E/M services (5-30 minutes)
- 99421-99423: Online digital E/M services (secure patient messaging or portal consultations)
- G2010, G2012: Medicare virtual check-in (brief 5-10 minute consultations)
These telehealth CPT codes ensure infectious disease specialists can provide ongoing care while maintaining reimbursement eligibility for remote services.
Best Practices for Infectious Disease Billing & CPT Code Compliance
Correct use of infectious disease CPT codes ensures accurate billing, avoids claim denials, and maximizes reimbursements. Here are some essential best practices for billing compliance:
Use the Most Specific CPT Codes
- Always match CPT codes to the exact procedures performed.
- For example, 99291 (critical care for sepsis) is different from 99223 (hospital admission for an infection).
Ensure Proper Documentation
- Include medical necessity details for lab tests, procedures, and treatments.
- Document infection severity, diagnostic findings, and treatment protocols to justify CPT code usage.
Verify Insurance Policies & Reimbursement Guidelines
- Some insurance carriers have specific billing rules for infectious disease procedures.
- Medicare, Medicaid, and private insurers may require prior authorization for certain tests or IV infusions.
Stay Updated with CPT Code Changes
- The AMA (American Medical Association) regularly updates CPT codes.
- Always check current guidelines for COVID-19 testing, telehealth services, and infusion therapies to avoid denied claims.
Summary
Proper coding is the foundation of successful infectious disease billing. Whether you’re coding for E/M visits, lab tests, infusion therapy, or telehealth consultations, using the correct CPT codes ensures that healthcare providers receive accurate reimbursement and avoid claim denials.
By following best practices, staying updated on billing regulations, and ensuring detailed documentation, medical coders and billing specialists can optimize revenue cycle management (RCM) and improve efficiency in infectious disease practices.
