How to Discuss New Technologies in the Clinical Microbiology Lab

Sept. 16, 2019

There's no doubt that the development of rapid diagnostic technology is changing the way microbiology laboratories across the world think, work and provide patient results. The promise of these new platforms is both inspiring and daunting, providing quality results faster than ever. However, new tests require lab personnel to both create and change infrastructure as well as strategically address problems that didn’t previously exist.

As many microbiologists currently working in the field did, I entered the field at a time when the use of PCR was not a common practice. The understanding was that many aspects of microbiology take time (mostly due to depending on 24 hours of organism growth), and while other areas of the clinical lab (such as chemistry) were continuing to bring in automation, the microbiology lab was just different. As the lab I was working in moved from the implementation of a large, batched PCR process to truly rapid PCRs that provided results from direct specimens in an hour or less, we found ourselves faced with issues that were new and different. All clinical microbiologists agree that providing accurate results quickly is essential to providing the best care for our patients, but implementation of new technologies is a decision to carefully consider. The microbiology lab staff must discuss all aspects of implementation (not limited to cost) to ensure that the benefits outweigh the risks. 

What does this conversation potentially look like? What are the elements worth considering before bringing rapid diagnostic technology to the micro lab?

Justifying the implementation of modern technology involves several components in addition to the cost. Every lab is different and what makes technology work for one lab may not work for another. The most important items to take into account when considering the implementation of rapid diagnostics include:
  • Infrastructure: Staffing, the existence of a stewardship program, the electronic medical record system and specimen volume are all critical pillars of support for rapid diagnostic technology
  • Choosing the right test: Since cost is a major factor, picking the test that will offer the most bang for your buck is important. Consider the patient mix and what relevant stakeholders need to get from the test. 
  • Considering how the test affects other organizations: Consider if the test will allow you to continue to support public health efforts. Make a plan to implement factors that continue to support the clinical lab and public health lab relationship. 
  • Re-structuring classic methods: Figure out how to fit traditional microbiological methods, like culture, into the new molecular landscape, which will be imperative for success.

Is the Appropriate Infrastructure in Place?

This question has numerous elements that must be considered and is one of the most important questions to address before implementing a technology like multiplex PCR. The benefits of any rapid diagnostic test can be quickly outweighed by problems if the appropriate system for result management is not in place prior to implementation. The following points area critical part of any discussion among microbiologists planning to implement rapid diagnostic technology:
  1. Does the current staffing model support the technology?  The impact of a rapid test’s efficiency is diluted if the results are not released and acted on in a rapid manner as well. Tests such as the Filmarray BCID panel require staffing 24 hours a day for the utility of rapid blood culture identification to be fully realized. Additionally, if a test cannot be run and reported within a few hours, it may be difficult to justify the cost. Implementing rapid tests may require a laboratory to change from a 9-5 schedule to 24-hour operations for those rapid tests to positively affect patient outcomes.
  2. Is there a stewardship team in place? Although it is not mandatory for hospitals to have antimicrobial stewardship teams, they play a critical role in the management and interpretation of rapid microbiological test results. Studies have shown that rapid diagnostic testing combined with a stewardship intervention have an 80% chance of being cost-effective compared with a 41% chance with such testing without antimicrobial stewardship intervention. However, building an antimicrobial stewardship team when there is not one in place can also be daunting. According to the CDC, core elements of a hospital stewardship program include: leadership commitment, drug expertise, tracking, reporting, a physician leader and a pharmacy leader.
    The cycle of antimicrobial stewardship.
    The cycle of antimicrobial stewardship.
  3. Can the current electronic medical record system support the new testing? As testing technology continues to become increasingly complex, it becomes even more important for the laboratory electronic medical record (EMS) system to be able to manage and merge patient results. Purchasing a new EMS comes with a high cost, so it is important to know if the system in place can handle the results from complex medical testing.
  4. Does the lab receive enough specimens to maintain competency? We all know the saying “practice makes perfect,” a good one to remember when considering implementing complex rapid diagnostics in the micro lab. According to the Infectious Disease Society of America, “The Centers for Medicare and Medicaid should discourage facilities that do not receive enough specimens to maintain competency and accuracy from conducting highly complex diagnostic testing.” Not only will it be difficult to offset the cost of the technology if there are not enough patients to test, but it may also be difficult to ensure that staff members are competent enough to run the test and interpret results.

Deciding Between Tests: Which Test is Most Necessary?

One fateful Friday afternoon several years ago, we ran out of respiratory pathogen PCR panels in the middle of respiratory season. We had to quickly devise a plan to hold us over the weekend until we could get more kits. After involving all appropriate parties, it was decided that we would only test patients that were highly suspicious for Influenza and Respiratory Syncytial Virus (RSV)  using individual Influenza and RSV PCRs. Interestingly, the number of requests for this testing over the next several days was minimal. This made me wonder: what makes an institution choose one PCR over another? While the respiratory panel offers identification of 21 respiratory pathogens, only a few of those can be treated, so why test for the ones that can’t be treated? Are we over-using this technology? When is it better to implement a multiplex PCR when a major pathogen (that can be treated) can be detected using a single PCR? We considered the following, which I recommend you and your colleagues discuss too:
  • Hospital volume: if the testing volume is low, a multiplex panel may not be appropriate and may offer little clinical value. Choosing a PCR that targets a disease with the most clinical impact (influenza) may be the best choice.
  • Patient population: if the patient mix includes complex cases and patients with immunosuppression, testing for pathogens other than the ones that can be treated can still be beneficial. It is important to remember the role infection control plays, as patients may need to be isolated based on certain test results. 
  • Laboratory setup: based on staffing and space, it is important to consider if it would make more sense to batch specimens and run them all at once, or run them one at a time as they are received.

Is the Lab Prepared to Implement Molecular Testing AND Maintain Culture?

Often, the implementation of molecular technology does not mean that the older microbiological methods go away. Even though the use of molecular technology provides an accurate organism identification within a few hours, bacterial culture is still required to obtain complete antimicrobial susceptibility information. At this time, growth of an organism on media is required to determine a susceptibility result, which plays an important role dosing of some antibiotics. Additionally, antimicrobial susceptibilities are key to building antibiograms, which aid clinicians in assessing local susceptibility rates. The lab should be prepared to consider the cost and staffing needs of continuing to perform culture when implementing rapid methods.

How Will the Implementation of Rapid Diagnostics Affect Public Health Processes and Relationships?

Although the benefits of diagnostics in the clinical setting are clear, the impact on public health laboratories should be taken into consideration before implementation. Several common molecular platforms have the potential to put the public health laboratory process at risk of falling behind. Which public health elements should we be thinking about during rapid diagnostic implementation?
  • Stool culture, pathogen tracking and food supply safety: The convenience of a molecular stool test is that testing can be done directly from stool without having to grow organisms on specialized media. This can be problematic for public health laboratories because their current testing methods rely on the recovery of isolates from clinical labs. The submission of isolates from culture have long been the backbone of public health enteric pathogen surveillance and outbreak investigation. Even if a rapid diagnostic method is implemented, a modified stool culture procedure will still be necessary in order to provide isolates of organisms like Salmonella, Shigella and shiga-toxin producing E. coli to the state public health laboratory. Maintaining the powerful and cost-effective program Pulsenet, the National Molecular Subtyping Network for Foodborne Disease Surveillance, is imperative to maintaining food supply safety and is heavily reliant on bacterial isolates submitted from clinical laboratories.
A graphical representation of annual savings from PulseNet.
Annual savings from PulseNet.
  • Coming up with a public health plan: Before implementing new testing, discuss plans with public health laboratory stakeholders. Understanding what the public health lab needs in order to continue important surveillance and sequencing can shed light on the procedures and supplies necessary to add to the new testing process. Consider issues like frequency of testing (if the lab only tests for Influenza during respiratory season, could a new strain or outbreak during non-seasonal months be missed?), and which organisms will always need to be grown in culture and submitted to the public health laboratory.

How Can the Cost Be Justified?

Although the cost of a rapid diagnostic platform cannot be the only factor to consider, it might be the one that prevents you from bringing the instrument in-house entirely. One of the biggest barriers to rapid diagnostic test implementation is cost. Although companies like BioFire claim that cost-savings from the use of their technologies are enough to cover capital expenditure and reagent cost, you will likely have to justify these savings within your institution in order to obtain the equipment. It is important to also consider the cost associated with strengthening of the infrastructure when justifying the implementation of new rapid diagnostic technology.

Bringing it All Together:

Think of the above considerations like you would with the purchase of an expensive vehicle. If there were no roads for you to drive the car on, and no gas stations available for fueling the vehicle, the car would never serve its intended purpose and its expenses would never be recovered. Cars are great for short commutes, but traveling between Hawaii and California requires a different technology. Similarly, rapid diagnostics are only effective if implemented in a setting with appropriate infrastructure and used as intended. Implementing expensive technology without working through these considerations may leave the lab like a car without gas: running on empty.

The above represent the views of the author and does not necessarily reflect the opinion of the American Society for Microbiology.

Read more about the importance of implementing new tests in our interview about clinical utility with Melissa Miller, Ph.D., D(ABMM), F(AAM).

Author: Andrea Prinzi, Ph.D., MPH, SM(ASCP)

Andrea Prinzi, Ph.D., MPH, SM(ASCP)
Andrea Prinzi, Ph.D., MPH, SM(ASCP) is a field medical director of U.S. medical affairs and works to bridge the gap between clinical diagnostics and clinical practice.