Infectious Disease Billing and Coding in 2025: A Complete Guide

Changing Landscape of Infectious Disease Billing

ID specialists have been identified as being in the midst of the most complicated billing practices in healthcare. Whether it is treating common infections or caring for the most resistant organisms, HIV care, travel-related illnesses, or billing these services is not always straightforward. The difficulty is not only obtaining the time and expertise of physicians, but also facing the task of assuring compliance with CPT and ICD coding changes.

As we move into 2025, billing for infectious disease services has grown even more nuanced. Payers are tightening rules, reimbursement rates are being recalibrated, and the use of telehealth for ID care continues to influence coding. For hospitals and private practices alike, understanding how to properly document, code, and submit claims can mean the difference between clean reimbursement and repeated denials.

What are the Key CPT Codes for Infectious Disease in 2025?

Infectious disease specialists bill for a wide range of services, from outpatient consults to hospital-based care. Below is a simplified table to illustrate commonly used CPT codes:

ICD-10-CM coding for infectious disease Billing

Unlike surgical specialties, the coding of infectious diseases is heavily surrounded by a specificity of diagnosis. The infection, cause organism, and, in some cases, resistance are described with the use of ICD-10 codes. In 2025, CMS has focused on establishing a more accurate value of ICD codes in 2025, CMS has focused on increasing specificity and modification of antimicrobial resistance, as well as on the development of new infections.

Tip: Always code to the highest level of specificity. For instance, instead of A41.9 (sepsis, unspecified), use A41.01 (sepsis due to E. coli) if lab-confirmed. Insurers are now penalizing vague codes more often in 2025.

What are the biggest Reimbursement Updates in 2025?

By 2025, there will have been a significant change to infectious disease reimbursement by Medicare and other private payers:

1. Telehealth Parity—In-Office telehealth codes (99212, 99213, 99214, 99215) are allowed reimbursement rates similar to face-to-face visits. This is important for infectious diseases since follow-ups of diseases such as HIV, tuberculosis, and chronic infectious diseases are often done through telehealth.
2. Critical Care Payments – Critical care reimbursement rates (99291-99292) were raised by 3-4% in 2025, given that the need for ID specialists in the ICU area had been published as being high.
3. Prolonged Services – CMS clarified the use of codes 99417 and 99418, allowing ID physicians to capture extended counseling and antimicrobial stewardship activities.
4. New Resistance Codes – Payers now require Z16-series codes to identify drug-resistant organisms. Claims without these codes are more likely to be denied.

What Common Billing Challenges Might You Face in ID Practices?

• Consult vs. Follow-Up Confusion: ID physicians frequently get referrals. Properly distinguishing between an initial consult (99221–99223) and a subsequent visit (99231–99233) is essential.
• Bundling Issues: Procedures such as drainage (10160) may sometimes be bundled with E/M services unless documentation is clear.
• Telehealth Modifiers: Claims must include modifier 95 (for synchronous telemedicine) in 2025 to ensure full payment.
• Infection Source Coding: Missing specificity (e.g., not coding organism type) is a top denial reason.

Pro Tip for 2025: Infectious disease billing thrives on documentation clarity. Always note the infection site, causative organism, resistance pattern, and patient status (new vs. established). These details directly affect whether you get reimbursed fully — or not at all.

Documentation and Coding Strategies for Infectious Disease Billing in 2025

The idea of billing infectious disease is not merely the process of identifying a suitable code on CPT or ICD, but also involves the ability to support the decision with good documentation. In 2025, payers are embracing strictness, as denials increase every time a service level billed does not match the corresponding chart notes. In the case of infectious disease specialists, documenting something can be taxing since cases are always complicated. However, with proper planning, practices will not have to bear the expensive rejections and can increase their reimbursement success.

1. Documentation Essentials for ID Billing

• Payers look for specific details when reviewing ID claims. In 2025, the following documentation elements are critical:
• Site of Infection: Always specify whether it’s respiratory, urinary, bloodstream, or other. Example: “Sepsis due to Klebsiella pneumoniae” rather than just “Sepsis.”
• Causative Organism: If lab-confirmed, include the organism in your note and ICD code.
• Resistance Status: Mention resistance patterns (e.g., MRSA, VRE, carbapenem-resistant Pseudomonas).
• Patient Type: Clearly identify whether the encounter is new or established.
• Medical Decision-Making (MDM): Document the thought process — cultures reviewed, antimicrobial choices, and differential diagnoses.

Why this matters: In 2025, CMS auditors are particularly focused on upcoding (billing a higher-level E/M service without sufficient documentation). Clear MDM and organism-specific ICD codes justify higher service levels.

2. Coding Strategies for Infectious Disease

Let’s break down some practical approaches to coding in infectious disease practices.

A.Evaluation & Management (E/M) Codes

• Use 99221–99223 for inpatient consults, choosing the level based on time and complexity.
• For prolonged visits, add 99417 or 99418 when the time exceeds the threshold.
• Don’t forget telehealth — codes 99212–99215 with modifier 95 remain billable at full rates in 2025.

B.Antimicrobial Resistance Coding

The Z16-series ICD-10 codes are now indispensable in ID billing. For example:

For example:

• Resistance to penicillin 16.11
• Methicillin resistance Z16.12
• Carbapenem resistance Z16.24

Including these will allow proper claim processing and will avoid payer denials.

C.Procedural Codes

Although the various procedures performed by the ID specialists are far fewer in number than those performed by the surgeons, care should be taken to code them accurately:

• Insertion of central venous catheter 36556
• Aspirate abscess Puncture 10160
• 49083 -Abdominal paracentesis

Pro Tip: Do not leave modifier 25 out when performing a procedure and billing an E/M with that same day.

3. Payer-Specific Nuances in 2025

Different insurers apply slightly different rules when it comes to infectious disease billing. Some important updates:

Medicare

• Expanded coverage for telehealth follow-ups beyond rural areas.
• Higher reimbursement for critical care (99291–99292) by about 3.2%.
• Increased scrutiny on prolonged services (99417/99418) — requires detailed time logs.

Private Payers

• Many commercial plans now bundle certain labs with ID visits. For instance, if the provider also orders and interprets microbiology tests, reimbursement might roll into a global fee.
• Some insurers require pre-authorization for long-term IV antibiotic therapy codes.

Medicaid

• Still state-dependent, but most states have aligned with CMS telehealth parity rules.
• Documentation demands are higher, especially for resistant infections.

4. Compliance Considerations in 2025

• Compliance is not optional in ID billing — audits are increasing. Here’s what’s new in 2025:
• Modifiers for Telehealth: Modifier 95 is still required for synchronous telehealth. Claims without it risk denial.
• Time-Based Billing: When billing prolonged services, ensure time spent is clearly documented in the note. Example: “Total time spent: 65 minutes, including chart review, patient counseling, and care coordination.”
• Diagnosis Pairing: Some payers won’t reimburse if ICD codes don’t logically pair with CPT codes. For example, billing critical care (99291) with an ICD code like Z20.828 (exposure to virus) will likely be rejected, since the diagnosis doesn’t justify ICU-level care.

5. Quick Reference Table: E/M Documentation vs. ICD Codes

Pro Tip for 2025: Think of documentation as your shield against denials. If the record clearly justifies the level of care, payers have little room to reject. A well-coded and well-documented infectious disease encounter means fewer appeals and faster payment.

Reimbursement Rates, RVUs, and Denial Management in Infectious Disease Billing (2025)

One of the trickiest parts of infectious disease billing is understanding how reimbursement rates are determined. Unlike surgical specialties that rely heavily on procedural billing, ID practices lean more on evaluation and management (E/M) codes. That means revenue is tied directly to documentation quality and payer reimbursement policies. In 2025, several changes in RVUs and payer rules are reshaping how infectious disease specialists get paid.

1.RVUs and Infectious Disease E/M Codes in 2025

Medicare and commercial payers base reimbursement on RVUs, which reflect the physician’s work, practice expenses, and malpractice costs. Here’s an updated look at commonly used E/M codes for infectious disease in 2025 and their approximate Medicare reimbursement values:

These figures are the Medicare baseline. Commercial payers are likely to pay 20-40 percent more, and/or Medicaid may be lower.

2. Reimbursement Trends 2025

A number of changes can be of particular concern to infectious disease specialists this year:

1. Increase in Critical Care Payments – Recognizing the heavy involvement of ID specialists in ICU cases (COVID-19, sepsis, multi-drug resistant infections), CMS raised reimbursement by about 3–4% for critical care codes (99291–99292).
2. Stable Office Visit Rates – Outpatient E/M codes (99212–99215) remain stable but are now reimbursed at telehealth parity across all U.S. regions. For many ID practices, this secures steady revenue for follow-ups conducted virtually.
3. Scrutiny on Prolonged Services – Payers now require explicit time documentation for prolonged codes (99417, 99418). Simply stating “visit took longer” is no longer acceptable.

3. Common Denials in Infectious Disease Billing

Denials can be costly — both financially and administratively. Here are the top denial reasons in ID billing (2025) and how to prevent them:

Pro Tip: Always appeal denials with strong documentation. ID practices with a dedicated appeals process recover 20–25% of initially denied claims.

4. Real-World Infectious Disease Billing Examples

Sometimes, seeing how coding plays out in real life makes it easier. Here are two examples:

• Case 1: ICU Sepsis Management
• Scenario: ID physician manages a patient with septic shock due to carbapenem-resistant Klebsiella.
• CPT Codes:

• 99291 (Critical care, 60 minutes)
• 99292 (Additional 30 minutes)

• ICD-10 Codes:

• 59 (Sepsis due to other Gram-negative organisms)
• 24 (Resistance to carbapenems)

• Documentation Key: Time log (90 minutes total), cultures reviewed, and antibiotics adjusted.
• Reimbursement (Medicare 2025): ~$281 for physician time.

Case 2: Outpatient HIV Follow-Up via Telehealth

• Scenario: Patient on antiretroviral therapy, stable, virtual follow-up.
• CPT Code: 99214 with modifier 95
• ICD-10 Codes:

• B20 (HIV disease)
• 899 (Other long-term drug therapy)
• Documentation Key: Viral load reviewed, ART adherence discussed, side effects assessed.
• Reimbursement (Commercial Payer 2025): ~$120 (higher than Medicare due to commercial contract).

Maximizing Reimbursement in ID Billing

Here are practical tips ID practices can use in 2025 to improve collections:

• Leverage Telehealth: The rate of many follow-ups and management of medication services may be at the same rate as face-to-face.
• Use Resistance Codes: Always add a Z16-series code for resistant organisms. Not only does this support medical necessity, but it also protects claims from denial.
• Track Time Accurately: For prolonged or critical care services, chart exact minutes — auditors now demand this detail.
• Audit Internal Claims: Quarterly self-audits can catch underbilling and prevent payer audits from escalating.
• Negotiate with Commercial Payers: Highlight the critical role of ID specialists during outbreaks (e.g., COVID, drug-resistant TB) to argue for higher reimbursement rates.

Pro Tip for 2025: Infectious disease billing is about precision and persistence. Even if a claim is denied, most payers will reimburse upon appeal if the documentation supports medical necessity.

Advanced Billing Challenges and Co-Morbidity Coding in Infectious Disease (2025)

Infectious disease billing is already complex — but when you factor in co-morbidities, bundled payments, and payer-specific quirks, it becomes even trickier. By 2025, most insurers are moving to value-based care and bundled payments, and so, ID practices must be more conscious than ever of coding and documentation.

1. Advanced Billing Problems in Infectious Disease

This can present a challenge to ID experts when aging the services because billing often does not fall quite into a single CPT, ICD code. Some more advanced challenges include

• Multi-System Infections: HIV + sepsis + pneumonia. Patients may need to have multiple ICD codes. Selecting the principal diagnosis may affect reimbursement
• Long-Term IV Antibiotic Therapy: Insurers often require pre-authorization for outpatient parenteral antimicrobial therapy (OPAT). Billing delays happen if the paperwork isn’t complete.
• Concurrent Procedures and E/M Services: If you drain an abscess (10160) and also provide a detailed E/M visit (99233), you must use modifier 25 to ensure both are reimbursed.
• Bundling with Hospital Services: Hospitals sometimes bill globally for infection management, making it harder for ID specialists to bill separately. Proper documentation and negotiation with the facility are essential.

2. Billing and ID Co-Morbidities Coding

Among the key changes in 2025, the focus on coding co-morbidities would have to be listed. CMS has been speaking loud and clear in that failing to perform complete diagnosis coding = lower reimbursement. In the case of ID specialists, this entails more than just capturing the infection, but it also involves the capture of the possible underlying risks.

Examples of Common ID Co-Morbidities:

Pro Tip: Always code for secondary diagnoses when they impact patient management. In 2025, insurers are increasingly using HCC (Hierarchical Condition Category) coding for risk adjustment — missing co-morbidities can lower your practice’s reimbursement profile.

3. Single/Bundled Services Infectious Disease

Another trend toward 2025 is the increase in bundled payments. This implies that payers pay one international rate only a rate of services rather than by visit. In the case of infectious disease, it is common that bundles are applied to:

• Sepsis care (hospital-based)
• Post-operative infection management
• HIV chronic care management
• OPAT programs

Example: Sepsis Bundle (2025)

A patient admitted with severe sepsis may generate:

• Initial consult (99223)
• Daily follow-up visits (99232/99233)
• Critical care time (99291/99292)
• Lab interpretations (87040 – blood culture, if applicable)

Instead of paying for each service separately, insurers might roll these into a flat bundled rate (e.g., $1,500 for 7 days of sepsis management).

ID specialists: Deliveries that are bundled can unjustly cheapen the time-consuming nature of ID care. To assuage this, many practices can carve out extended services or telehealth follow-ups of the bundle through contract negotiations.

4. Staying Ahead of Reimbursement Changes in 2025

Here are practical strategies for ID specialists to keep revenue healthy this year:

• Stay Updated on ICD-10 Changes: New codes for antimicrobial resistance (Z16-series) must be used — ignoring them risks denials.
• Negotiate Carve-Outs in Bundled Payments: If your practice regularly provides prolonged services, negotiate with payers to exclude codes like 99417/99418 from bundles.
• Adopt Telehealth Efficiently: Virtual follow-ups (99212–99215 with modifier 95) are reimbursed at parity in 2025 — a huge revenue booster for HIV and TB follow-ups.
• Invest in Coding Audits: Quarterly internal audits help catch missed charges and prevent compliance penalties.
• Leverage Technology: Use EHR alerts to flag missing co-morbidity codes. Many practices lose money simply by under-documenting secondary conditions.

5. Quick Reference: Bundled vs. Non-Bundled Services (2025)

Pro Tip for 2025: Treat coding like storytelling. Each diagnosis and CPT entry should tell payers why the patient needed your expertise and why it required higher complexity. The more complete the story, the stronger your case for full reimbursement.

Practical Tips, FAQs, and Final Thoughts on Infectious Disease Billing (2025)

At this point, it has been made evident that the whole practice of infectious disease (ID) billing is an art and science. It demands accuracy, sensitivity to the payer trends, and foolproof documentation. As reimbursement rates, bundled payment, and antimicrobial resistance coding may be changing in 2025, ID specialists need to be more vigilant than ever to prevent revenue leakage.

To bring everything together, let’s go over practical tips, answer common questions, and then close with a big-picture view of how ID billing can thrive in 2025.

Practical Tips for ID Billing Success in 2025

Here are strategies that every ID practice — whether hospital-based or outpatient — should keep top of mind:

1. Code to the Highest Specificity

• Use detailed ICD-10 codes (e.g., A41.01 – E. coli sepsis instead of A41.9 – unspecified sepsis).
• Add resistance codes (Z16-series) when applicable.

2. Track Time Meticulously

• For critical care (99291–99292) and prolonged services (99417/99418), write exact minutes and activities in your notes.
• Payers won’t accept “spent a long time” — they want “65 minutes reviewing labs, counseling, coordinating care.”

3. Use Telehealth to Your Advantage

• Telehealth follow-ups (99212–99215 with modifier 95) are paid at full parity in 2025.
• Great for HIV care, chronic infections, and travel-related follow-ups.

4. Document Co-Morbidities

• Don’t stop at the infection code — add diabetes, HIV, CKD, or immunosuppression if relevant.
• This boosts reimbursement under HCC (Hierarchical Condition Category) coding.

5. Stay Ahead of Bundled Payments

• Review payer contracts carefully. If you provide high volumes of prolonged services, negotiate carve-outs.
• Don’t accept one-size-fits-all bundles that undervalue ID care.

6. Audit and Appeal

• Perform quarterly audits to spot missed codes or underbilling.
• Appeal denials aggressively — many payers approve claims on second submission if documentation is solid.

FAQs: Infectious Disease Billing in 2025

Q1: What are the most commonly used CPT codes for infectious disease billing?

• 99221–99223 (initial inpatient visits),
• 99231–99233 (follow-up inpatient visits),
• 99291–99292 (critical care),
• 99212–99215 (outpatient visits, including telehealth),
• 99417/99418 (prolonged services),
• 10160 (abscess drainage), 36556 (central line placement).

Q2: Which ICD-10 codes are most important for ID billing in 2025?

• A41-series (sepsis),
• B20 (HIV disease),
• J15-series (bacterial pneumonia),
• U07.1 (COVID-19),
• Z16-series (antimicrobial resistance),
• Z20.828 (exposure to communicable disease).

Q3: What’s new in 2025 reimbursement?

• Critical care codes increased by ~3–4%.
• Telehealth parity continues (office visits reimbursed at the same rate virtually).
• Prolonged service codes require strict time documentation.
• New antimicrobial resistance codes (Z16-series) must be used for accurate payment.

Q4: How can ID specialists avoid denials?

• Document infection site, organism, and resistance.
• Always use modifier 95 for telehealth.
• Pair CPT and ICD codes logically (e.g., don’t bill critical care with only an “exposure” code).
• Attach modifier 25 when performing procedures and E/M visits on the same day.

Q5: Do private payers reimburse more than Medicare?

Generally, yes. Commercial payers often reimburse 20–40% higher than Medicare rates, though Medicaid tends to pay less.

Final Thoughts: Infectious Disease Billing in 2025

Infectious disease specialists are some of the unsung heroes of medicine. Whether fighting hospital-acquired infections, managing HIV patients long-term, or coordinating care for septic patients in the ICU, their work is vital — but billing for it isn’t always easy.

2025 has brought both opportunities and challenges:

• Telehealth parity has leveled the playing field for outpatient care.
• Resistance coding has made claims more precise — but also more demanding.
• Bundled payments are becoming more common, requiring negotiation and vigilance.

At the end of the day, infectious disease billing success comes down to three pillars:

1. Accuracy — Every code must reflect the full story of the patient encounter.
2. Documentation — If it isn’t written down, it didn’t happen (as far as payers are concerned).
3. Adaptability — Billing rules change every year, and 2025 is no exception.

Think of your billing system as your life raft in the stormy sea of healthcare finance. If you keep it watertight — detailed notes, correct codes, and payer-savvy strategies — you’ll stay afloat no matter how choppy the reimbursement waters get.