Diagnostic Microbiology

The past two decades have been the first era during which parts of diagnostic pathology and laboratory medicine began the transition from traditional to molecular diagnostic methods. We are now entering the next era, during which this transition will accelerate and occur throughout all disciplines. This acceleration is due to the emergence of better analytic methods, the fact that many test results now directly guide therapy, and wider acceptance in the medical community from better understanding of the role of molecular diagnostics. Perhaps the fastest change in diagnostic testing has occurred in clinical microbiology and infectious disease testing, where molecular testing is rapidly replacing much of conventional culture-based testing. There are many reasons for this, not the least of which is that much of molecular biology was first studied and defined in microorganisms. Additionally, microorganisms are easy to work with and inexpensive to study, and many phenotypic changes can be readily identified. Although the number of commercially available molecular microbiology tests remained low for many years, the past few years have seen a rapid increase in the number of test platforms, assays, and test menus. Initial tests were typically limited to detection of one or a few pathogens, some of the earlier examples being nucleic acid identification tests designed to detect Mycobacterium tuberculosis. Ongoing improvements in technology have not only improved the quality of assays but also made the assays faster (now many assays take only about an hour), eliminated the need for extensive specimen preparation, improved automation, and facilitated development of multiplex platforms able to detect multiple pathogens simultaneously. Today, molecular microbiology assays are used throughout the world. Examples include the BioFire FilmArray (BioFire Diagnostics, Salt Lake City, UT), Verigene (Nanosphere, Northbrook, IL), and GeneXpert (Cepheid, Sunnyvale, CA), and many others. Different assays play different roles: many microbiology laboratories now use a suite of platforms that allow them to tailor specific testing requirements. The introduction of newer molecular diagnostic platforms and assays has taught microbiologists a number of lessons. The most important of these is that molecular assays in some cases replace conventional methods, whereas in others they augment conventional methods. As an example, detection of some common viruses can be done more quickly and easily using nucleic acid amplification assays, and because most of the time there is no medical indication to look for mutations conferring drug resistance, molecular assays can replace conventional viral cultures. The same is true for a few bacterial pathogens, but only a few. For most bacterial pathogens, molecular methods only augment cultures, because recovery of live bacteria is still needed to perform antimicrobial susceptibility testing (AST). At this time, only a few assays are available to detect specific antimicrobial resistance genes (most commonly mecA and VanA). Although the number of molecular diagnostic tests to detect antimicrobial resistance likely will increase through time, the complexity of bacterial resistance determinants, and the need to verify phenotypic expression, means that traditional cultures and AST will need to continue for the foreseeable future. Another challenge for microbiology laboratories is reporting results. Many information systems were not designed with the ability to handle results from multiplex platforms, although new integrated electronic health records have this ability. Perhaps the greatest challenge is integrating the results of molecular assays with those of conventional testing performed on the same specimen. The results of many molecular assays, which are automated, can be sent immediately to information systems via an interface. In contrast, results of cultures and AST on the same specimen only become available 1 to 3 days later. Designing integrated reporting systems requires careful thought, particularly for multiplex assays. Introduction of these platforms and assays has also taught providers a number of clinical lessons. First, use of multiplex platforms means that clinicians may be surprised when their differential diagnosis included one pathogen but another is detected. In some cases this does not present any problem, but sometimes the detected pathogen may not be related to the patient’s clinical signs and symptoms. With laboratory tests available that can detect pathogens carried by asymptomatic hosts, clinicians will need better diagnostic tools to determine the clinical relevance, if any, of pathogens. Second, in some cases differential diagnoses will need to change as new patterns of infection are defined. Third, in some cases new assays allow for detection of pathogens that just a short time ago could only be detected at highly specialized reference laboratories. Clinicians are not used to having access to routine testing that is this robust; as a result, they may need to rethink their approach to testing. Last, there may well be different performance characteristics for individual analytes on multiplex platforms, which complicates how providers interpret test results and act on the information. Because many molecular microbiology tests do not replace but only augment conventional culture-based methods, cost becomes a concern. As a general rule, molecular diagnostic tests are an order of magnitude more expensive compared with their conventional counterparts. Moreover, because only limited assays are available for AST, cultures are still needed to recover microorganisms so that susceptibility testing can be performed. The fact that most susceptibility test results are not available any faster compared with conventional methods may also lessen some of the positive impact on patient care. Although there are data showing that use of rapid molecular assays can have a positive impact on antimicrobial stewardship programs, there are fewer data regarding an impact on patient outcomes or overall cost savings. The transition from culture-based to molecular-based testing represents the biggest change in testing in many years. Changes such as this are difficult, often meet resistance if not outright skepticism, and require a great deal of work to be implemented successfully. The advantages to this transition, however, far outweigh any disadvantages. It bears remembering that we are still relatively early in the era of clinical molecular testing, and that future technologies will bring even more impressive and useful assays. It has been the goal of physicians throughout history to have readily available, objective, and reproducible tests that guide specific treatment of patients. With careful and thoughtful introduction of these assays, and careful integration with clinical services, this goal will finally become reality.