Jireh RCM Solutions
Infectious Disease Coding Portal
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Jireh RCM Solutions — Infectious Disease Coding Portal

Diagnosis search • ICD-10-CM • CPT/HCPCS reference • modifiers • documentation • infectious-disease coding workflow

Infectious Disease Quick Reference

Use the diagnosis name as a starting point. The exact ICD-10-CM selection depends on the documented condition, acuity, site, organism, laterality, complications, encounter circumstances, and applicable guidelines.
Condition / search termsCommon coding considerationsDocumentation to look for
UTI / cystitis / pyelonephritisDifferentiate site and acuity; hematuria may change code selection.Site, acuity, symptoms, hematuria, culture results, organism when documented.
PneumoniaIdentify organism and type when supported; avoid coding an organism solely from suspicion.Organism, aspiration status, lobar/interstitial/other documented type, severity.
Sepsis / severe sepsis / septic shockRequires careful application of official sepsis guidelines and documented clinical condition.Sepsis type, source/infection, organ dysfunction, shock, causal relationship.
Cellulitis / abscessSite and laterality can matter; distinguish cellulitis from abscess when documented.Anatomic site, laterality, organism if known, drainage/procedure details.
MRSA / resistant organismsOrganism/resistance coding may be additional to the infection code depending on documentation and guidelines.Culture, organism, resistance, infection site, colonization vs infection.
HIVUse the current HIV-related guideline framework and documented status/condition.HIV status, active related condition, treatment/encounter purpose.
TuberculosisSite, confirmed status, and disease manifestation are important.Confirmed disease, site, microbiology, treatment status, manifestations.
OsteomyelitisAcute/chronic, site, laterality and other documented specificity may affect code.Bone/site, laterality, acute/chronic, contiguous/hematogenous if documented.
C. difficile infectionDistinguish active infection from history/carrier/colonization documentation.Confirmed CDI, recurrence when documented, treatment and symptoms.
EndocarditisType and organism can drive specificity.Valve/site, acute/subacute/other type, organism, prosthetic status.
COVID-19 / influenza / viral infectionsUse current-year code set and applicable respiratory/infectious-disease guidance.Confirmed diagnosis, organism/test status where relevant, manifestations.
HepatitisType and acuity are key; distinguish active disease from history/status.Virus/type, acute/chronic, complications and documented manifestations.

E/M & Common ID Services Reference

Important: CPT is copyrighted by the American Medical Association. A production system must use properly licensed/current CPT data. The table below is workflow guidance, not a substitute for the official CPT code set.

Office / Outpatient E/M

Code familyUseKey point
99202–99205New patient office/outpatient E/MChoose the specific level using the current CPT rules and documentation.
99211–99215Established patient office/outpatient E/MChoose the specific level using the current CPT rules and documentation.

Common laboratory / microbiology services

CodeServiceTypical ID workflow relevance
81001Urinalysis, automated, with microscopyUTI workup when performed and documented.
81002Urinalysis, nonautomated, without microscopyPoint-of-care urinalysis workflows.
81003Urinalysis, automated, without microscopyPoint-of-care/office laboratory workflows.
87086Urine culture, quantitative colony countCulture workup when performed and reportable.
87088Culture, additional identificationUse only when the actual service and current CPT rules support it.
87186Susceptibility testingAntimicrobial susceptibility workflow when performed.
Do not automatically pair a diagnosis with a CPT service. The service must actually be performed, documented, billable for the setting/provider, and supported by payer rules.

Modifier Decision Guide

ModifierUse only when supportedQuick check
25Significant, separately identifiable E/M service on the same day as another procedure/service.Was a separately identifiable E/M service performed and documented beyond the usual work of the procedure?
59Distinct procedural service when the applicable criteria are met.Different encounter, site, organ/system, lesion, or other qualifying circumstance per current rules?
91Repeat clinical diagnostic laboratory test for a medically necessary reason.Was the same lab test repeated for clinical reasons, not error, quality control, or confirmation of the original result?
95Telemedicine services when required by the applicable payer/current CPT guidance.Confirm payer and current-year telehealth rules; modifier requirements vary.
Never add a modifier simply because a claim denied. Modifier use must describe the actual service and circumstances.

Documentation Checklist

Core Coding Rules & Workflow

  1. Identify the encounter purpose and read the provider documentation completely.
  2. Find the diagnosis in the current ICD-10-CM Alphabetic Index, then verify it in the Tabular List.
  3. Follow inclusion, exclusion, “code also,” “use additional code,” laterality, 7th-character, and other Tabular instructions.
  4. Use the highest level of specificity supported by documentation; do not invent specificity.
  5. Use signs/symptoms when a definitive diagnosis is not established and the guidelines permit symptom coding.
  6. For E/M, apply the current CPT E/M rules and document the elements required for the selected level.
  7. For labs/procedures, bill only services actually performed and supported by documentation.
  8. Check NCCI edits, bundling, modifier rules, medical necessity, frequency limits and payer policy.
  9. Verify that every code is valid for the date of service.
  10. Perform a final documentation-to-code reconciliation before claim submission.
FY2027: CMS states that FY2027 ICD-10-CM files apply to patient encounters from October 1, 2026 through September 30, 2027. The application is labeled FY2027 because that is the next effective code-set period beginning October 1, 2026.

Official Resources

Production-data note: ICD-10-CM can be sourced from official government files. CPT/HCPCS content and payer edits require appropriate licensing/current source agreements. Do not treat this static reference page as a complete licensed coding database.