Proposed Changes to the Clinical Laboratory Improvement Amendments of 1988

Rae Hintlian

Associate Editor

Loyola University Chicago School of Law, J.D. 2019

The Department of Health and Human Services Center for Medicare and Medicaid Services have proposed a ruleto update the proficiency testing (PT) regulations under the Clinical Laboratory Improvement Amendments of 1988 (CLIA).  The new rule seeks to address current analytes, substances or constituents for which the laboratory conducts testing, and newer technologies.  The rule would further make technical changes to the PT referral regulations to be more closely aligned with the CLIA statute.


In 1988, Congress enacted the Clinical Laboratory Improvement Amendments, codified at 42 U.S.C. §263(a), to ensure the accuracy and reliability of testing in all laboratories. These include those that participate in Medicare and Medicaid, that test human specimens for the purpose of diagnosis, prevention, and treatment of a disease, impairment, or as part of a health assessment. The current rules require those laboratories which conduct moderate or high-complexity testing to enroll in an approved proficiency testing program for each specialty, analyte, and subspecialty the laboratory is certified under CLIA.  PT referral was also addressed in the Taking Essential Steps for Testing Act of 2012. Testing technology is more accurate and precise than the original methods used at the time CLIA was implemented, so much so that many of the analytes which PT was not initially used for are now a part of a routine clinical work up.  The proposed rule seeks to recognize the changes in technology and advancements in treatment.

The Proposed Changes

The newly proposed rule would mainly change regulations in microbiology and non-microbiology specialties and sub-specialties.  In Microbiology, the current regulations do not specify the required analytes in determining the type of laboratory testing being performed for PT purposes at the registered laboratory.  In order to allow for flexibility, the revised regulations include broad categories of the types of PT required for each microbiology subspecialty and inclusion of new technologies.  Under Microbiology the changes would affect the laboratories which work in the areas of bacteriology, mycobacteriology, mycology, parasitology, and virology.

The regulations for microbiology labs would include a system for categorizing the types of services maintained in the regulations to help labs determine the PT they need to perform and assist in the monitoring of PT performance and patient testing.  Further, four categories of testing would be included for each microbiology subspecialty as applicable (i.e. stain(s), susceptibility and resistance testing, antigen and/or toxin detection, and microbial identification or detection). In bacteriology labs for instance, the proposed categories would include gram stains (including bacterial morphology); direct bacterial antigen detection; bacterial toxin detection; detection and identification of bacteria which includes one of the following: detection of growth or no growth in culture media or identification of bacteria to the highest level that the laboratory reports results on patient specimens; and antimicrobial susceptibility or resistance testing on select bacteria.  Another proposed change to the microbiology labs would require that the HHS regulations include a more general list of the types of organisms that are included in the PT instead of the current requirement which uses a specific list. Using a more general list would allow PT programs to be more flexible in sample selections provided to labs for PT, in particular as new organisms are discovered a broader range allows for greater clinical accuracy.

Another suggested change would instruct labs to perform all PT testing as they normally would on patient specimens, including reporting PT results for microorganism identification to the same level that would be reported for patient specimens.  Further, the PT samples must account for mixed samples.  The mixed samples must contain a mixture of a principle organism and appropriate normal flora in order to simulate the findings which could occur with an actual patient specimen.  The appropriate normal flora will be dependent upon which microbiology category the PT is designed for. Further changes are proposed for microbiology labs affects the antimicrobial susceptibility testing, which is currently only required for bacteriology.

The new regulations would require the testing for all categories of microbiology, increase the frequency and number of required susceptibility testing challenges for varying groups of organisms in order to detect potential issues with patient testing sooner. Finally, the last proposed change to microbiology labs involves direct antigen testing. Current regulations only require direct antigen testing for bacteriologyand virology, the proposed changes would require testing for all microbiology subspecialties.  Also, PT evaluation criteria would include performance and scoring based on direct antigen and toxin detection to reflect the current practice of reporting patient results when a toxin is present.

As for the non-microbiology specialties and subspecialties the new rule proposes four changes to the current PT requirements.  The rule would change the process of determining which analytes are tested for based upon the following criteria: current availability of PT materials and number of PT programs offering PT; volume of patient testing performed nationwide; impact on patient health and/or public health; and the cost and feasibility of implementation.  The new list would add 29 new analytes to the PT requirements based on the proposed process the information received from the PT programs and consultations with the Center for Disease Control (CDC) and Center for Medicaid Services (CMS).  Further, after reviewing the changes in the practice of clinical medicine, analytes which are no longer tested for frequently would be removed from the PT requirements based on the availability of the PT material and the feasibility of implementation.

To determine which tests could be removed  a threshold of 500,000 tests performed annually was used as the initial selection criteria of potential PT analytes for the addition or removal from the PT requirements, focusing on older therapeutic drugs and their current market replacements, to identify required analytics for proposed removal from the current list. Using literature reviews for alternative analytics to identify potential additions and removals from the list and to determine which diagnostic strategies have replaced earlier analytics, to evaluate the potential impact on clinical medicine and public health the additions and deletions would have on current requirements. A “target value” based on peer grouping is proposed for use in the PT programs. Under the peer grouping method, where definitive or reference values are not available or a specific method’s results indicate bias that is not observed in actual patient specimens, in a group of less than 10 participants, then the overall mean after outlier removal is used to indicate the target value for the analytic. Further, the rule proposes changing the current acceptance limits based on the improvements in sensitivity, specificity, and precision used routinely in peer grouping.  This would result in a narrowing of current accepted limits, and ideally minimize the negative consequences of the other proposed changes. The new acceptable limits would use a fixed percentage limits instead of concentration limits.   Fixed percentage limits can be directly tied to objective goals for performance, are constant in all PT events, and do not vary because of statistical randomness, masked outliers, or small sample size.  There have been some further proposed changes to the definitions of target value, acceptance limit, unacceptable score, and peer group.



Proficiency testing is a critical component of a quality management system. Since its implementation there have been many changes in the practice of laboratory medicine and improvements to the analytical accuracy of testing methods, which requires that the changes be reflected in the rules managing the system. It is important that the current clinical practices are incorporated in the criteria for compliance and acceptable performance; and that the new analytes and tests used for making clinical decisions are held to the same standard as those previously used.  The implementation of the proposed rule would result in quantifiable impacts on laboratories (currently 36, 777 laboratories are required to participate in PT under the CLIA regulations). Microbiology labs would have to replace the types and services offered, specific PT for certain tests and procedures would need to be developed, in addition to the financial costs incurred for the changes (dependent on the specialty). For non-microbiology labs, the changes would add 29 new analytes, increase the frequency and challenges of each PT event, and the cost of acquiring the new analytes PT depending on the laboratory. Overall the cost to the laboratories which participate in PT would be between $26,503,031 and $118,329,642 dollars.  Although the changes will also increase laboratory and end-user confidence, as well as the reliability and accuracy of test results.