Molecular approaches to infectious disease assays

Jan. 13, 2014

The challenge in today’s diagnosis of bacterial and fungal pathogens causing severe infectious disease as well as putative antibiotic resistance is that these diagnostics are still largely microbiology-culture based. Culture often takes two to three days for pathogen identification alone and another day or so for antibiotic susceptibility testing. While awaiting a clear and comprehensive diagnosis, clinicians are empirically treating patients with broad-spectrum antibiotics. Such empiric treatment can be inadequate in as many as 40% of patients, leading to increased length of stay in intensive care units (ICUs), and it is associated with significantly higher morbidity and mortality rates. Also, the use of broad-spectrum antibiotics imposes an economic burden on the overall healthcare system as hospitals struggle to make ends meet within the respective lump-sum diagnosis-related groups for inpatients.

Today’s molecular diagnostics

The past decade has seen the advent of many molecular diagnostic (MDx) tests, including manual PCR test kits and highly integrated, easy to use, cartridge-based sample-to-answer platforms. Both types of offerings have their drawbacks. Manual test kits often leave several critical steps, such as sample preparation and DNA extraction and purification, up to the user, which can lead to a significant manual labor burden as well as variability among operators. Meanwhile, more user-friendly sample-to-answer platforms currently on the market typically offer simple tests for a small number of biomarkers. The most successful test from both a commercial viewpoint and in terms of clinical impact is the MRSA test, in which both the pathogen and its resistance status are detected. Other tests, such as those for c.difficile and TB, among others, are also low-multiplexed, relatively simple assays that deliver narrow and well-defined clinical answers.

Today’s MDx tests leave unaddressed several important unmet medical needs. First, there is the need to obtain clinically relevant and actionable answers for complex infectious disease, including respiratory tract infections, surgical site infections, prosthetic joint infections, gastrointestinal tract infections, sepsis, and many others. To obtain meaningful diagnostic answers, it can be necessary to detect several dozen—even up to 100—pathogens and their antibiotic resistance markers simultaneously. The need for sophisticated diagnostics requires solutions with high multiplexing

Second, the user of such diagnostic information is typically a clinician in an ICU who doesn’t have sophisticated laboratory resources available around the clock. Many microbiology labs are staffed only during the day and have minimal staff on weekends, leading to significant time delays in obtaining pathogen and resistance answers. In the absence of laboratory professionals during night and weekend hours, physicians or nursing staff should be able to operate these sophisticated MDx platforms outside of a traditional laboratory environment. However, requiring other medical professionals to conduct this molecular testing is often not feasible without intuitive, easy-to-use platforms that eliminate operator choices and variability and can be used in just a few minutes, with minimal hands-on time.

Third, in order to fit into routine hospital workflows, it is paramount that ICU- and hospital-based MDx cartridge solutions use native clinical sample material. However, many existing MDx solutions require either pre-culturing or are usable only with very narrowly defined clinical samples such as nasal swabs.

Finally, current MDx offerings do not combine all three requirements of an effective on-site sample-to-answer solution: highly-multiplexed assays that work with any native sample type to deliver broad, clinically actionable results in a few hours. Every hour counts in pathogen and resistance detection; mortality rates in indication areas such as sepsis tend to increase by eight percentage points per hour.

Current developments in the MDx space

Recent years have seen the development of several potential solutions to the unmet or imperfectly met needs addressed above. Technologically, the approaches are as diverse as real-time PCR, MALDI-TOF mass spec, next generation sequencing, and end-point PCR with microarray-based detection. Suffice it to say, most clinicians are agnostic when it comes to technology and view these platforms as “black-box-solutions” whose worth must be proven by addressing the shortcomings of today’s culture-based methods and MDx products.

Moreover, some of these platforms have become so easy to operate that they decentralize the laboratory, bringing MDx to the patient. A trend for ICUs running such systems has emerged with the capability for fully automated lysis of even the most complex native clinical samples available and fully closed cartri dge-based systems that allow for the detection of 100 or even more pathogens and antibiotic resistance markers within four to five hours. However, close collaboration among clinicians, microbiologists, infectiologists, and hygienists is required to interpret these new, often complex, MDx answers. With the help of modern MDx solutions, platforms are being developed that can be operated by literally anyone on a healthcare team, driving clinicians closer to a goal of improved infection management.

Another driver for adoption of novel MDx solutions is clinical validation. The higher the degree of multiplexing and the more native clinical sample types, the larger and more complex clinical trials will become to validate such MDx products. It is not uncommon to see multicenter trials enrolling several thousand patients in order to prove the clinical body of evidence to the FDA for clearance of these novel MDx solutions. Apart from the purely regulatory trials, it is also important to build the health economic case and provide data supporting the medical benefits that accompany savings to the healthcare systems.

Outlook and future trends

With a plethora of novel and innovative MDx platforms in the pipelines of small and large IVD industry players alike, it will be interesting to observe the consolidation and convergence of platforms around clinically relevant content. Having an offering that addresses truly unmet medical needs and delivers clinically actionable information “has the great potential to make treatment better for the individual and antibiotic stewardship better for the community,” in the words of David Livermore, PhD,  Professor of Medical Microbiology at the University of East Anglia.

The delivery of clinically actionable information will grow increasingly important. With the proliferation of ever-increasing resistant strains of bacteria, especially multi-drug-resistant Gram-negative bacteria, we are rapidly running out of therapeutic options. A combination of truly novel antibiotics accompanied by a more rational, MDx-based selection of antibiotic therapy regimens is urgently needed. The assays and offerings that combine detection of putative pathogens with antibiotic resistance gene detection in a broad and comprehensive manner stand to make the biggest impact on infectious disease diagnosis and treatment in the years to come. Not only will clinicians want to use such MDx solutions in their everyday treatment regimens, but pharmaceutical companies will also use these platforms in companion diagnostic settings as part of rational patient selection in clinical trials to help develop more targeted and narrow spectrum antibiotics.

Oliver Schacht, PhD, is CEO of Germany-based Curetis AG, a molecular diagnostic company developing the Unyvero™ Solution for the diagnosis of severe infectious diseases such as pneumonia and implant and tissue infection.

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