December 7, 1998 - CLIA Quality Control Provisions

The American Society for Microbiology (ASM) appreciates the opportunity to submit comments on the quality control provisions in the Clinical Laboratory Improvement Amendments of 1988 (CLIA '88). The ASM is a scientific and educational society dedicated to the promotion of the microbiological sciences and their applications for the common good. The Society represents 43,000 microbiologists who work in clinical, public health, industrial and research laboratories. Many of our members apply the CLIA regulations in their laboratories on a daily basis and strive to use the best microbiological practices when performing diagnostic procedures.

The ASM conducted CLIA quality control surveys and analysis in 1997 and presented findings and recommendations to the Clinical Laboratory Improvement Advisory Committee (CLIAC). As a follow-up, ASM's Public and Scientific Affairs Board (PSAB) has been working with the Subcommittee on Laboratory Regulations to determine appropriate levels and parameters of quality control for specific microbiology procedures. The following questions were developed after discussions with your staff at the Centers for Disease Control and Prevention (CDC). The ASM's Subcommittee on Laboratory Regulations of the PSAB has formulated recommendations after each question based on consultation with expert clinical microbiologists.

Question 1: For mycology, is the requirement for laboratories that use auxanographic media for nitrate assimilation to check the nitrate reagent with a peptone control relevant and necessary?

Recommendation: Most laboratories are using commercial identification systems and do not use this particular test. Therefore this requirement is not relevant and can be deleted. If the test were used, the recommendation would be to quality control each batch or lot.

Question 2: Is the following parasitology requirement appropriate: "Each month of use, the laboratory must check permanent stains using a fecal sample that will demonstrate staining characteristics?"

Recommendation: The frequency of quality control at each month of use is appropriate. However, the language "fecal sample" should be changed to "fecal sample or commercial quality control slide."

Question 3: Does the ASM membership have any data or recommendations regarding the CLIA mandated frequency or necessity of QC testing in the microbiology subsections (e.g. mycology, mycobacteriology)?

Recommendation: Although there was insufficient time to collect the quality control data for the tests performed in the other microbiology subsections, the ASM recommends that the frequency of quality control testing should be standardized for all areas of microbiology (e.g. bacteriology, mycobacteriology, mycology, parasitology, virology). The general experience of the ASM membership is that the reagents used for tests performed in the other microbiology subsections perform as well as the reagents used in bacteriology.

Also, we would recommend that the decontamination process for specimens submitted for mycobacteriology culture be quality controlled by processing a specimen containing M. fortuitum with each new lot or batch of reagent (i.e. NaOH).

Question 4: What is the ASM's recommendation regarding the QC of the new technology (e.g. amplification tests, sequencing, etc) used in clinical microbiology laboratories?



  1. Amplification tests: This is a difficult area to define necessary quality control requirements because it is constantly evolving. Generally, the recommendation is to adhere to the standards outlined in the NCCLS document "Molecular Diagnostic Methods for Infectious Diseases, MM3-A, 1995" and the accreditation standards suggested by the College of American Pathologists. As a minimum, the quality control should validate cell lysis, absence of inhibitors, absence of contamination, and adequate amplification. As a minimum the following controls should be included with each run: a) positive control (low range of assay sensitivity), b) negative control (one to 5), and c) an internal control. Quantitative assays should include 2 to 3 standards of known copy number.
  2. Genotyping: include at least two isolates of the same species being tested. One isolate with same phenotype as the unknown and one isolate with a different phenotype.

The ASM appreciates the opportunity to assist the CDC in it's efforts to publish a final regulation for the CLIA program and to streamline the quality control requirements.