IQCP for Microbiology: Media, Identification Systems and AST
In microbiology, IQCP lets a lab reduce end-user QC for commercially prepared media, ID systems and AST below the default CLIA requirements, if its risk assessment and in-house data support it. Without an IQCP, labs must follow 42 CFR 493.1256(e) and 493.1261 QC as written.
Microbiology was the area most affected when CMS removed the CLSI-based QC exceptions from its guidelines. This page maps each common use to the rule it modifies.
Last reviewed Oct 2026 · By Sound Lab Consultants CLIA team · General information, not legal advice.
Why microbiology labs use IQCP
A CDC-authored review, "The Individualized Quality Control Plan – Coming Soon to Clinical Microbiology Laboratories Everywhere!" by Nancy Anderson in Clinical Microbiology Newsletter (2015), describes IQCP as a voluntary, risk-based option available to microbiology labs from January 1, 2016, built on three steps: risk assessment, a QC plan, and monitoring through quality assessment. CMS says labs now have two choices: follow all applicable CLIA QC rules, or implement IQCP (CMS IQCP Frequently Asked Questions (Aug 2016)).
Media
Default CLIA QC (42 CFR 493.1256(e)(4)): before or with first use, check each batch for sterility when required and for its ability to support growth and select, inhibit or react as appropriate, and document compromised physical characteristics. CMS allows a single master media IQCP or separate ones. The CAP says a combined IQCP must list every media type it covers, and media checked per default QC doesn't need an IQCP (the CAP's public IQCP FAQ (updated Nov 2024)). Visual checks and manufacturer quality certificates can be part of the data, per CMS.
Identification systems
Systems using two or more substrates or reagents fall under §493.1256(e)(1): check each batch, lot and shipment for positive and negative reactivity of each substrate. Doing less requires an IQCP, per CMS.
Antimicrobial susceptibility testing
42 CFR 493.1261(b) requires checking each batch of media and each lot and shipment of antimicrobial agents before or with first use, running control organisms each day of testing, and confirming zone sizes or MICs are in limits before reporting. Reduced frequency requires an IQCP.
What IQCP doesn't change (CAP)
The CAP says no IQCP is needed for reagents with defined checklist QC, such as weekly Gram stain QC. It also says blood culture instruments have no CLIA daily QC requirement, though an IQCP can support accepting the manufacturer's media QC.
Free templates
ASM's IQCP protocol templates for microbiology and molecular testing include media, streamlined ID, MIC and disk diffusion AST examples, plus AST Q&A. Treat them as starting points for your own data.
IQCP for Microbiology checklist
☐ List each media type, ID system and AST method in scope
☐ Note the default CLIA rule for each
☐ Collect historical QC, visual checks and manufacturer certificates
☐ Risk assessment includes specimen-source risks
☐ QC plan states what end-user QC remains
☐ Director approval; QA monitors for QC failures and complaints
CDC resources on CLIA
CDC's overview of the CLIA program: CDC explains that CLIA applies to every U.S. site that tests human specimens to assess health or to diagnose, prevent, or treat disease. It also explains that CDC supports the program alongside CMS and FDA.
CDC on CLIA test complexity categories: CDC explains how FDA scores tests as moderate or high complexity using seven criteria. It also notes that lab-developed or modified tests default to high complexity, and that moderate and high complexity standards differ only in personnel requirements.
CDC's free CLIA educational materials: CDC offers brochures and booklets on waived testing, PPM, and IQCP.
Frequently asked questions
Do microbiology labs need an IQCP?
Only to perform less QC than the default CLIA rules. CMS says labs can follow CLIA QC as written or implement IQCP.
Can one IQCP cover all culture media?
CMS allows a single media IQCP or separate ones. The CAP says a combined plan must list every media type covered.
Is an IQCP needed for AST?
Only if you run less QC than §493.1261(b) requires, such as fewer than daily control organisms.
Can CLSI guidelines replace an IQCP?
No. The CAP says CLSI documents can't be the sole basis for reduced QC; data gathered under CLSI guidance can support an IQCP.
Does a blood culture instrument need an IQCP?
The CAP says there's no CLIA daily QC requirement for blood culture instruments. An IQCP is an option for accepting the manufacturer's media QC.
Where can I find microbiology IQCP templates?
ASM publishes media, ID and AST IQCP examples developed with CLSI and CAP.
Official sources and further reading
ASM's IQCP protocol templates for microbiology and molecular testing
Developing an IQCP - A Step-By-Step Guide (CDC/CMS workbook)
Related IQCP guides
IQCP for Molecular Testing: Cartridge PCR, LDTs and Exclusions
IQCP Risk Assessment: Five Components and How to Document Them
Talk to an IQCP consultant
Sound Lab Consultants helps labs nationwide build, review and maintain IQCPs from their own data and the official CMS and CDC guidance.
Sound Lab Consultants, PO Box 2135, Chandler, AZ 85244