CLIA-waived molecular diagnostic tests are poised to transform clinical Microbiology

June 18, 2015

Since the discoveries of Louis Pasteur and Robert Koch, the field of clinical microbiology has primarily relied on conventional lab culture methods for pathogen detection and identification. These culture methods, widely recognized as the best practice in modern-day pathogen diagnostics, are time- and labor-intensive because they rely on the organism's natural replication cycles and visual identification of the organism grown in culture over a period of several days by clinical microbiologists. Using these methods, patient results can be communicated to a treating physician within three to four days in the best case, or several weeks in the cases of slow-growing or difficult-to-culture pathogens.

With the advent of polymerase chain reaction (PCR) and other nucleic acid amplification methods, it became possible to detect many viral and bacterial organisms directly from a patient specimen. These newer molecular methods rely on complex in vitro enzymatic reactions performed in central laboratories using extracted and purified nucleic acids from clinical specimens as starting material. Using this technology, test results can be to the clinician in two-to-10 days, depending on the proximity of the testing lab and its frequency of performing such tests.

In an effort to deliver better molecular diagnostic products, in vitro diagnostic manufacturers have focused their efforts on simplifying and automating both the specimen extraction and the nucleic acid detection steps. More recently, manufacturers have begun developing more automated platforms that allow for diagnostic testing but require minimal hands-on time by trained laboratorians. These innovations, in part, have enabled the shift of testing from centralized laboratories to settings closer to the patient, such as hospital labs. The next transformation in molecular testing, allowing for pathogen detection and identification at the point of care (POC), would require attainment of a challenging United States regulatory goal: a Clinical Laboratory Improvement Amendments (CLIA) waiver.

Point-of-care molecular testing

Point-of-care diagnostic testing provides rapid diagnostic information that enables immediate clinical management decisions to be made.1 In many settings, rapid decisions related to patient management improve patient safety, clinical outcomes, and patient satisfaction. In aggregate, this lowers the cost of healthcare.

Since the mid-1980s, routine clinical laboratory testing has gradually been moving to POC format, starting with tests for glucose and blood gases. Today, more than 110 laboratory tests are available to be performed at the point of care.2 The key to adoption of POC tests is clinical utility, as well as sensitivity and specificity similar to those of current lab-based methods.

For infectious disease tests, the main obstacle with the acceptability of POC tests has been their (relatively) poor performance.3 The sensitivity and specificity achieved with the lateral flow technologies available at the point of care was inferior to those achievable in central labs routinely utilizing nucleic acid methods. While these POC tests provided quick, on-site test results, definitive diagnosis was necessarily deferred to confirmatory testing done by nucleic acid amplification tests (NAATs) in the central lab setting. This drove up the total cost of patient diagnosis while providing some diagnostic information earlier in the treatment cycle than previously possible.

Recent technological innovations have enabled nucleic acid testing improvements that make POC molecular diagnostic testing possible. One such innovation was the advent of isothermal amplification methods,4 which allowed for rapid detection of DNA/RNA without the requirement for thermal cycling. This technology permits more rapid generation of results; however, it is hampered by its minimal ability to multiplex, long time-to-result (for POC), and by the requirement to refrigerate consumables containing enzymes. A second, more promising, technological advance was the development of an enzyme-free, electrochemical amplification method for the detection of nucleic acids, known as amplified redox assay. This technology can produce a highly multiplexed, 20-minute, nucleic acid test result using room temperature-stable consumables.

Next step: CLIA waivers

Technological advances such as those described above, along with strategic investments in complementary or enabling technologies by United States government agencies and increasing clinical demand for more rapid, accurate diagnostic testing solutions, have been key drivers for POC molecular diagnostic solutions.5 Some healthcare reforms under the Affordable Care Act provide further, and timely, incentives to deliver products that helped to find efficiencies in the delivery of healthcare, as the overall system moves toward a preventative model of healthcare delivery while empowering patients.

On January 6, 2015, the FDA granted the first waiver under CLIA for a nucleic acid-based test—an influenza A and B product. This major milestone in clinical diagnostics allowed, for the first time, high quality molecular testing to be performed at the point of care. The significance of this was highlighted at the time in comments by Alberto Gutierrez, director of the Office of In Vitro Diagnostics and Radiological Health in the FDA's Center for Devices and Radiological Health: “We expect many other simple and accurate tests using nucleic acid-based technology to be developed in the near future. Once cleared by FDA, such on-site tests can allow healthcare professionals to receive test results more quickly to inform further diagnostic and treatment decisions.”

An eye toward the future

While CLIA waiver of a flu A and B test is a good first step toward enabling broader POC molecular testing, widespread adoption of POC molecular diagnostics will be driven by tests that have the greatest clinical utility and that provide demonstrable efficiencies to the healthcare system that are unattainable through traditional central laboratory methods.

As such, obvious diagnostic products for development in this area may include those that can:

  • Screen discrete patient populations for asymptomatic infectious diseases—for example, chlamydia and gonorrhea;
  • Provide a definitive diagnosis for a multitude of pathogens with similar clinical presentation—for example, respiratory pathogen panels;
  • Produce a rapid and definitive test result in critically ill patients—for example, patients with sepsis;
  • Determine quickly whether a hospitalized patient needs to be isolated due to a nosocomial infection; and
  • Drive good antibiotic stewardship practices by conferring resistance and/or susceptibility information.

For each of these applications, there are clear patient management benefits to having a definitive diagnosis while the patient is being seen by the clinician. Also providing each of these solutions at the point of care drives easily understandable, and quantifiable, benefits to the healthcare system.

Clinical microbiology has evolved since Pasteur and Koch, transforming once with the advent of lab-based molecular methods, and more recently with the availability of automated molecular testing platforms. Recent technological advances, as well as the first CLIA waiver for a molecular platform, are paving the way for molecular tests at the point of care. The most successful tests will be those with greatest clinical utility at the point of care, which are also able to demonstrate healthcare delivery efficiencies.


  1. Point of Care Testing Toolkit. Accessed May 11,2015.
  2. DuBois JA. The role of POCT and rapid testing. MLO. 2013;45(9):18-22.
  3. Glorikian, H. POCT key to widespread access to healthcare. MLO. 2011;44(1):38.
  4. Zanoli LM, Spoto G. Isothermal amplification methods for the detection of nucleic acids in microfluidic devices. Biosensors. 2013; 3(1):18-43.
  5. Paxton A. How POC testing is pushing the envelope. CAP Today. April 18, 2014.