This client alert highlights recent regulatory developments from the Centers for Medicare & Medicaid Services (CMS) relevant to clinical laboratories. CMS is implementing or considering implementing several updates to the regulations under the Clinical Laboratory Improvement Amendments of 1988 (CLIA). This alert provides an overview of a final rule, published on July 11, 2022, which updates proficiency testing regulations (Final Rule), and a proposed rule, published, on July 26, 2022, which would impose additional fees, increase fees, and update other sanction and technical compliance provisions if finalized (Proposed Rule). CMS has extended the comment period for the Proposed Rule through September 26, 2022.

Final Rule Updates for Proficiency Testing

To maintain the quality of laboratory testing, CLIA requires that laboratories performing moderate or high-complexity testing enroll in an approved proficiency testing program for independent verification of each specialty, subspecialty and analyte (or test) for which the laboratory is certified. Given advances in technology since the proficiency testing regulations were first implemented in 1992, the Final Rule revises the proficiency testing requirements applicable to microbiology subspecialties, adds and removes various non-microbiology analytes to or from the list of those requiring proficiency testing, and updates the acceptance limits for such tests.

Changes to Microbiology Proficiency Testing

Specifically, CMS has modified the proficiency testing requirements applicable to microbiology subspecialties like bacteriology (§ 493.911), mycobacteriology (§ 439.913), mycology (§ 493.915), parasitology (§ 493.917), and virology (§ 493.919) to remove the types of services listed for each subspecialty and instead specify broad categories of tests (or categories of organisms) for which proficiency testing is required.  CMS believes this will allow flexibility for new technologies currently in use or that may be developed in the future.

Addition and Removal of Non-Microbiology Analytes

For non-microbiology specialties, CMS added 29 analytes to those already included in Subpart I of the CLIA regulations. These include various analytes in the general immunology (§ 493.927), routine chemistry (§ 493.931), endocrinology (§ 493.922), and toxicology (§ 493.937) specialties.  A table listing the new analytes can be found in the final rule in Table 1 at 87 Fed. Reg. 41,201.  CMS also deleted certain analytes from § 493.931 (LDH isoenzymes) and § 493.937 (ethosuximide, quinidine, primidone, procainamide, and N-acetyl procainamide). These revisions are largely due to changes in the types of testing that have become more or less frequently used in clinical practice. In addition to testing volume, CMS also based its revisions on the availability of proficiency testing materials, the number of proficiency testing programs that can provide the analytes, the impact on public health and patient health, and the cost and feasibility of implementation.

Revised Acceptance Limits

The Final Rule establishes acceptance limits for the newly added analytes, and recognizing that testing accuracy has improved since the regulations were first implemented, CMS is also revising the acceptance limits for currently required analytes. Even though CMS is narrowing these acceptance limits, the agency does not expect this will increase the rates of unsatisfactory or unsuccessful events due to current analytic accuracy rates.  Further, the Final Rule includes percentages with or without fixed acceptance limits for all newly added and currently required analytes.  CMS believes the combination of percentage and concentration limits will result in fairer, more realistic acceptance limits.

Technical Changes Affecting Waived Tests

Final Rule revisions at § 493.20(c) and § 493.25(d) clarify that laboratories performing moderate and high complexity testing and that also voluntarily participate in proficiency testing for waived tests are subject to the revised proficiency testing compliance requirements at § 493.801(b)(1) through (6), but that 493.801(a) (requiring enrollment in proficiency testing) and § 493.801(b)(7) (formerly § 493.801(b)(6), requiring proficiency testing for the primary method of patient testing) do not apply to waived tests. The Final Rule includes these technical revisions to better align with the CLIA statute, which does not exclude waived tests from the ban on improper proficiency testing referral.

Final Rule Effective Dates

To allow additional time for laboratories and proficiency testing programs to adopt these requirements, CMS is delaying the effective date of the revised proficiency testing requirements and acceptance limits until July 11, 2024. CMS indicated that it would consider possible ways to streamline the process for ongoing updates to proficiency testing.  Note, however, that other technical revisions included in the Final Rule, such as the above clarification regarding waived testing, were not delayed and became effective August 10, 2022.

Proposed Fee Updates and Other Technical Changes

The Proposed Rule, if finalized, would impose additional CLIA program fees and fee increases and enable CMS to impose alternative sanctions on Certificate of Waiver laboratories found to have deficiencies. Other technical changes are proposed relating to histocompatibility testing and personnel qualifications or requirements.

Additional Fees

CMS is proposing to implement fees for the following items or services for which it has not previously collected fees:

  • Follow-up surveys related to Certificate of Compliance or Certificate of Accreditation deficiencies.
  • Surveys outside the Certificate of Compliance survey cycle for the addition of specialties.
  • Substantiated complaint surveys.
  • Desk review of unsuccessful proficiency testing performance.
  • Replacement copies of lost or destroyed certificates.
  • Revised certificates for changes in laboratory director or other information found on the certificate.
Fee Increases

The Proposed Rule would impose a 20% increase on all existing fees if finalized.  Future increases would be adjusted for inflation, likely every two years unless no increase is required. In addition, CMS is proposing an increase of $25 to the biennial fee for a Certificate of Waiver to help offset program costs related to the Food and Drug Administration’s review and categorization of waived tests, but would delay this increase until the COVID-19 public health emergency expires or is terminated.

Alternative Sanctions for Certificate of Waiver Laboratories

Current regulations generally permit CMS to impose alternative sanctions for deficiencies or lack of compliance with applicable requirements for all CLIA laboratories except those holding only a Certificate of Waiver.  42 C.F.R. § 493.1804(c).  Alternative sanctions may include civil monetary penalties, a plan of correction, or on-site monitoring. CMS is proposing revisions that would allow the agency to impose alternative sanctions on Certificate of Waiver laboratories.  While laboratories conducting waived testing are not subject to routine surveys due to the lack of complexity of waived testing, they are surveyed upon any complaint. Imposing alternative sanctions should offer greater flexibility in rectifying any compliance issues found during a complaint survey rather than obligating CMS to impose principal sanctions, such as revocation, suspension, or limitation of the CLIA certificate.

Technical Changes to Histocompatibility and Personnel Requirements

CMS is proposing various technical updates to the histocompatibility testing requirements (42 C.F.R. § 493.1278) to account for technological advances and remove requirements that were made redundant by other generally applicable requirements, such as quality control requirements.  CMS is also proposing to add or expand definitions related to laboratory personnel (42 C.F.R. § 493.2) and clarify or update certain provisions related to personnel qualifications and responsibilities (42 C.F.R. Part 493, Subpart M) to offer greater flexibility and account for changes in the industry.

Please contact the authors if you are interested in submitting a comment to the Proposed Rule or if you have any questions about these recent updates or the CLIA program generally.