Rapid molecular diagnostics have potential to revolutionize patient care

For infectious disease specialists, knowing the cause of an infection in a critically ill patient is vital to delivering the appropriate treatment.

When patients present with symptoms of an infection, physicians can only make educated guesses until lab results identify the pathogen, at which point they can provide more tailored treatment.

However, identifying the organism is not a simple process, and it is certainly not a quick one. With the methods currently in use by most clinical microbiology laboratories, the process can take days. In the meantime, the patient could be receiving unnecessary antibiotics, thus contributing to the major growing problem of antibiotic resistance.

“The problem we all have is that we must treat patients on an empiric basis when we don’t have all the information in front of us — we have to cover the most likely and serious potential pathogens,” Robert A. Bonomo, MD, professor of medicine, pharmacology, molecular biology and microbiology at Case Western Reserve University, and chief of medical service at Louis Stokes Cleveland VA Medical Center, told Infectious Disease News. “You don’t want to undertreat a patient, but you also don’t want to overtreat a patient. There are consequences of both. Meanwhile, we’re waiting days for the correct answer.”

The field of diagnostics has improved during the past few years, and although there are tests that can identify pathogens in less than 1 day, it still takes longer to identify the antibiotics to which the bacterial pathogens are susceptible.

There is a significant need for faster diagnostics. The interest and enthusiasm is there. Some PCR-based tests have been cleared by the FDA, and other diagnostic technologies are in development. However, there are many questions to answer before the use of any of these molecular diagnostics is implemented widely.

Infectious Disease News spoke with several experts in the field of molecular diagnostics to discuss the critical need for quicker pathogen identification, what is in the pipeline for rapid, molecular diagnostics and the challenges to their widespread use.

Outdated methods

The gold standard for identifying bacteria is culture. The process from clinical presentation to diagnosis to identifying appropriate treatment can take up to 5 days. Although it’s an accurate and reliable process, it is an extremely dated one that has changed little since it was created.

“In everyday life when we deal with infectious diseases, we still rely on culture-based methods that were developed in the 19th century,” Stephan Harbarth, MD, associate hospital epidemiologist and attending infectious disease specialist at University Hospitals of Geneva in Switzerland, told Infectious Disease News. “For many decades, everyone has agreed that we need faster diagnostics. But up until about 10 years ago, most companies invested more in therapeutics because of higher profit margins. This has changed, and there has been incredible, positive momentum surrounding novel diagnostics, and now there is healthy competition between different companies.”

Bonomo said that in addition to identifying the cause of infections more quickly, rapid diagnostics will help with development of new antibiotics by identifying whether an infection could be susceptible to a new drug available in clinical trials. Rapid diagnostics also would allow for good molecular epidemiologic information about a hospital that could help institute effective control measures.

In addition, rapid diagnostics are important in the setting of novel and emerging infectious disease threats.

“It’s important to know if enterovirus D68 is in your area, or if you have a case of MERS, SARS or a new influenza strain,” Bonomo said. “The current diagnostics are prohibitively slow at helping us identify these new pathogens that we can’t afford to not suspect.”

Eliminating guesswork

Whereas culture requires the organism to reproduce in the laboratory to be properly identified, molecular diagnostics utilize other methods, such as nucleic acid amplification, to identify a pathogen based on its DNA.

According to Paul Schreckenberger, PhD, director of the clinical microbiology laboratory at Loyola University Medical Center, one problem with current diagnostic methods is that they target only one specific organism. If a patient presents with symptoms of meningitis, for example, the physician needs to guess the potential causative agents, and order individual tests for each specific infectious agent that might be causing the meningitis.

“What’s new is that some molecular platforms can test a single specimen using a multiplex panel containing DNA probes that can target 20 or more infectious agents at the same time,” Schreckenberger told Infectious Disease News. “These new multiplex panels can identify a pathogen within an hour and allow physicians to target their therapy very specifically based on the agent identified. This is a revolution in infectious disease diagnostic testing that is changing how physicians practice medicine.”

The FDA has cleared some PCR-based multiplex test panels that are performed directly on patient samples. But these tests, while exciting, do not determine the antibiotic susceptibility of the causative bacteria.

Identifying appropriate treatment

Although identification of the organism is important, ultimately, physicians want to know what antibiotics to administer to a sick patient. That requires susceptibility testing.

“Knowing that answer, you can go from broad and empiric treatment to a more focused treatment,” Colleen S. Kraft, MD, assistant professor of pathology and laboratory medicine at Emory University School of Medicine, told Infectious Disease News. “For example, 50% of the Staphylococcus aureus isolates at our hospital are susceptible to penicillin, which is the better drug for those patients compared to vancomycin. But if you give penicillin to all patients with S. aureus infections, you wouldn’t cover the other half of the patients with MRSA. You can’t take that gamble, so we start with vancomycin to cover all S. aureus.”

Harbarth said this is one of the major errors that some of the diagnostic companies have made in the last 10 years: developing rapid molecular systems that can identify an organism but not determine its antibiotic susceptibility.

That is not to say that quickly knowing the organism isn’t helpful, he said. Experienced ID physicians are familiar with the epidemiology of resistance in their institutions, which can help streamline treatment. But in the end, clinicians have to rely on results of antibiotic susceptibility tests.

“Identifying the bacteria and the antibiotic susceptibility results is an essential combination,” Harbarth said. “The ultimate wish of many physicians is to have rapid identification of the organism plus the antibiogram to guide therapeutic decision-making.”

This would have positive ramifications for antibiotic stewardship, allowing for prompt, targeted therapy. It also would help avoid complications of unnecessary therapy, particularly selection of antibiotic-resistant pathogens and emergence of Clostridium difficile infections.

MALDI-TOF mass spectometry

A step in the direction of rapid diagnostics is the introduction of matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectometry, which is used on positive blood cultures to expedite the identification of an organism. It can identify pathogens causing bloodstream infections, usually within 1 day.

MALDI-TOF is cost-effective and has been exciting for physicians, but it does not provide susceptibility results, although some people are evaluating its potential for that purpose. Additionally, its results may not be as fast as ID specialists would like.

“If you can cut 48 hours off the typical growth and susceptibility testing, that would be amazing,” Kraft said. “To get to the point of identifying organisms and appropriate treatment in 1 day would be considered rapid.”

According to data published in the Archives of Pathology and Laboratory Medicine, the implementation of MALDI-TOF at a Houston hospital reduced the time to pathogen identification and antimicrobial susceptibility results by almost 1 day: from 47.1 ± 13.7 hours to 24.4 ± 11.4 hours (P<.001).

MALDI-TOF has been a revolution, Harbarth said, and extremely beneficial, cutting time to correct therapy down to just 1 day for several clinically important infections, compared with up to 4 days.

“There’s no question that MALDI-TOF is extremely helpful and certainly a major breakthrough,” Harbarth said. “In everyday life, here in a major teaching hospital, MALDI-TOF really helps with the management of our patients. But the real breakthrough will be routine use of molecular diagnostic methods done directly on whole blood.”

Cost and patient outcomes

At the hospital level, molecular diagnostic tests will need to demonstrate more than just the quick identification of organisms and antibiotic susceptibility; they also will need to demonstrate cost-effectiveness and improved patient outcomes, including length of hospital stay, Schreckenberger said.

The initial costs, including the necessary equipment and training for laboratory technicians, are high.

“Hospitals have been slow to adopt these because they don’t have the resources to do so,” Schreckenberger said. “Most look at the individual costs: laboratory costs, pharmacy costs, clinic costs, etc. They don’t look at the total cost of care and the fact that if we can identify the cause of an illness more quickly, we might be able to avoid an admission and unnecessary antibiotic use, or discharge the patient faster.”

In the Houston hospital study, the use of MALDI-TOF decreased the mean length of stay for survivors from 11.9 days to 9.3 days (P=.01). It also decreased the cost per survivor from $45,709 to $26,162 (P=.009).

Under the Affordable Care Act, the federal government requires hospitals to report patient-centered outcomes. In terms of cost outcomes, it will be necessary for hospitals to identify and analyze costs such as unnecessary isolation room days (ie, when patients with possible infections are isolated to prevent spread, but it turns out that they do not have the concerning infection).

“This is the type of scenario where rapid diagnostics will come into play for reducing hospital costs and increasing patient satisfaction,” Schreckenberger said. “This is becoming a new standard of health care. Rapid diagnostics are right in line with the changes in health care delivery. You can’t treat a patient effectively if you’re guessing what is wrong.”

Barriers to research

The barriers to developing molecular diagnostics are the same that exist with clinical drug trials, Bonomo said. First, you need the proper infrastructure and second, the trials need to be designed correctly. The systems to support these trials need to be designed for easy use.

“I’ve seen some systems that have incredible sensitivity and specificity, but they are so complicated that they can only be used in a small number of hospitals because they have the personnel to do it,” Bonomo said. “For rapid molecular diagnostics to be successful, the technologies need to be usable for a broad base of people at any hospital in the United States.”

Another problem applies to all areas of research: funding. What may help is an executive order and national strategy released last September by President Barack Obama to combat the threat of antibiotic resistance.

The national strategy outlines a 5-year plan to enhance domestic and international capacity to prevent and contain outbreaks of resistant infections, maintain efficacy of current and new antibiotics and develop next-generation diagnostics, antibiotics, vaccines and other therapeutics. It includes a $20 million prize, co-sponsored by the NIH and the Biomedical Advanced Research and Development Authority, to develop a rapid, point-of-care diagnostic test for clinicians to use to identify resistant infections.

Bonomo said the challenge for companies will be to make the right decisions to fund or not fund particular research projects, and to pick the projects that will yield the biggest benefit for society.

“The basic scientists and clinicians are just part of the equation,” he said. “We need to work together so that those at the highest levels will pick the best projects that will have the most yield. That is a very difficult decision.”

Tests in the pipeline

Molecular testing platforms that are available now include the Iridica Platform (Abbott) and the GeneXpert system (Cepheid). Each has unique characteristics, Bonomo said, but both can be used to identify multiple organisms. Also available is the FilmArray series (Biofire Diagnostics), which has three panels that can test for multiple pathogens: a respiratory panel, a gastrointestinal panel and a blood culture identification panel. The company also has a meningitis/encephalitis panel in development.

In response to the need for quicker susceptibility testing, a new test by Accelerate Diagnostics is in the pipeline to identify pathogens and perform susceptibility testing on positive blood cultures within 5 hours, Schreckenberger said. This test uses fluorescent in situ hybridization (FISH) probes to identify the bacteria.

Bonomo highlighted a new platform that uses T2 nuclear magnetic resonance and can detect fungi down to a few pathogens per milliliter. He also said there are platforms using molecular beacons to identify pathogens.

There are many potential methods being investigated, and all are competing for the same space.

“My feeling is that most of them are going to give adequate information to make reasonably good clinical decisions,” Bonomo said. “One platform may offer something another one doesn’t, but they are subtle nuances. The hardest decision will still be how to best treat the patient.”

Kraft also said it is important that these new rapid tests do not overlook good specificity and sensitivity for the sake of a rapid diagnosis. For example, there are rapid influenza tests that can be conducted quickly in the office, but they lack good sensitivity and specificity.

“The definition of rapid is going to be very infection-specific and patient-specific,” Kraft said. “We want to make sure we’re doing the right test, for the right patient, for the right infection. Rapid diagnostics is where we want to go, but we need to make sure that we don’t sacrifice a highly sensitive and specific test.”

The ideal rapid diagnostic test

Opinions on the ultimate rapid diagnostic were unanimous: a point-of-care test completed at the patient’s bedside that identifies the organism and its antibiotic susceptibility within 1 hour. The test also must be inexpensive, sensitive and specific.

Culture testing will never go away, Bonomo said. Even if the ultimate molecular diagnostic test is developed and used widely, cultures will always be part of the process: the “fail-safe.”

He said the role of molecular diagnostics will be to guide empiric therapy, with definitive therapy waiting until culture confirmation.

“As rapid diagnostics get introduced into the therapeutic arena, the balance of what culture-based methods really mean also needs to be evaluated,” Bonomo said. “For many years, we believed that culture was the gold standard. It may really be silver, or brass or maybe even tin.”

Harbarth is optimistic that within the next 10 years, there will be more and more rapid molecular diagnostic systems developed.

He is also hopeful that the “Holy Grail” — powerful point-of-care tests installed in ICUs — will be available in that time.

“This maybe a little wishful thinking,” Harbarth said, “but you don’t have to be a true visionary to see that over the next 5 to 10 years, this field will evolve. There is a lot of momentum and it’s really good for our patients.” – by Emily Shafer

References:

Perez KK. Arch Pathol Lab Med. 2013;137:1247-1254.

For more information:

Robert A. Bonomo, MD, can be reached at: robert.bonomo@va.gov.
Colleen S. Kraft, MD, can be reached at: colleen.kraft@emory.edu.
Stephan Harbarth, MD, can be reached at: stephan.harbarth@hcuge.ch.
Paul Schreckenberger, PhD, can be reached at: pschrecken@lumc.edu.