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The global diagnostic response to antibiotic resistance is a work in progress

By Shara Rosen

The era of modern antibiotic therapy began in 1928, with Sir Alexander Fleming’s discovery of penicillin. During the 1940s, many common antibiotics became widely available, including penicillin and streptomycin. And in the decades that followed, dozens of antibiotics came to be used to cure many infectious diseases ranging from common infections such as strep throat to the plague.

Today, however, antibiotic therapy has entered a new phase—one that Fleming himself placed among the pitfalls of antibiotic usage. “I would like to sound one note of warning,” he said. “It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body.”1

In December 2014, the US Agency for Healthcare Research and Quality (AHRQ) reported significant advances against hospital-acquired conditions—including many types of infections. Compared to projections based on previous trends, the agency estimated that approximately 1.3 million fewer patients were harmed in US hospitals between 2010 and 2013.2,3

Nevertheless, the AHRQ report emphasizes that problems remain in many areas, and that there is still much to be done to ensure patient safety. In vitro diagnostic (IVD) manufacturers are challenged to find technologies and test solutions that manage the tension between achieving high sensitivity and specificity, and attaining very fast turnaround time.

In this article, CLP presents some of the pressing issues related to the worldwide increase in antibiotic-resistant organisms, including the need for antibiotic susceptibility testing in the laboratory and at the point of care, and how hospital laboratories and IVD manufacturers can address these issues in the future.

END OF THE ANTIBIOTIC ERA

Decades of antibiotic misuse have given rise to antibiotic-resistant organisms, and the development of new antibiotics has failed to offer many new solutions. Such widespread problems with antibiotic resistance led the World Health Organization to comment that “this serious threat is no longer a prediction for the future; it is happening right now in every region of the world, and has the potential to affect anyone, of any age, in any country.”4

A 2013 report by the US Centers for Disease Control and Prevention (CDC) offers a similar snapshot of the burden and threats posed by antibiotic-resistant organisms having the most impact on human health.5 The report states that each year in the United States, at least two million people become infected with bacteria that are resistant to antibiotics, and at least 23,000 people die each year as a direct result of such infections. Many more people die from other conditions that are complicated by an antibiotic-resistant infection.

President Obama has recognized that the rise of antibiotic-resistant bacteria represents a serious threat to public health and the economy. On September 18, 2014, he issued an executive order establishing a task force for combating antibiotic-resistant bacteria, to be cochaired by the secretaries of defense, agriculture, and health and human services.6 The executive order puts the development of rapid diagnostics on equal footing with the development of new antibiotics, and requires the task force to submit a 5-year plan that outlines specific actions for combating antibiotic resistance in the United States.

Martha Brumfield, PhD, Critical Path Institute

Martha Brumfield, PhD, Critical Path Institute

Martha Brumfield, PhD, president and CEO of the Critical Path Institute, Tucson, Ariz, expresses the gravity of the situation. “What’s happening with the
emergence of antibiotic resistance patterns is worrisome, and I believe that we are heading for disaster in the future. We as a society need to think about better
funding models that will encourage pharmaceutical and diagnostic companies to stay in the scheme, because they have the expertise. I am hopeful that there is going to be some incentive for or funding assistance for companies to continue doing research in this area.”

LABORATORY TOOLS

Until recently, microbiology laboratories employed a variety of techniques to perform antibiotic susceptibility testing. With the growing trend in resistant organisms, however, there is a concerted effort to discover resistance markers that can be used for therapy choices and in the development of new therapeutics.

The significant increase in the number of antibiotic-resistant organisms, such as Neisseria gonorrhea, Escherichia coli, salmonella, shigella, Candida sp, methicillin-resistant Staphylococcus aureus (MRSA), and carbapenem-resistant Klebsiella pneumonia has resulted in a growing demand for rapid and accurate antibiotic resistance tests and technologies.

A number of tools—traditional and trendsetting—are available for the microbiology laboratory. There is a place for culture as well as molecular and other rapid methods, says Marco Schito, PhD, senior scientific officer at the Critical Path Institute. “In places that have laboratory capacity and a healthcare infrastructure, a mix of centralized traditional methods and decentralized rapid testing complement each other. They need to work together to cover most of the population,” he adds. “The services of the traditional microbiology lab are still important to validate molecular results, and also some advanced methodologies are run with a cultured colony.”

James Cottam, PhD, Alere

James Cottam, PhD, Alere

James Cottam, PhD, global product manager for antimicrobial stewardship at Alere, Waltham, Mass, supports this opinion. “Molecular technology is one of the newest technologies available. But immunoassays can have a huge impact as well. I don’t see the two approaches as mutually exclusive; there are conditions where each is more appropriate.”

As an example, Cottam describes the case of a patient who has been colonized with C. difficile, but is not really sick. In such a case, he says, “a stand-alone molecular result may not be ideal, because we may detect people that are asymptomatic. Here, a combination of tests may be more appropriate.”

Patrick R. Murray, PhD, Becton Dickinson Diagnostic Systems

Patrick R. Murray, PhD, Becton Dickinson Diagnostic Systems

Patrick R. Murray, PhD, worldwide director for scientific affairs at Becton Dickinson Diagnostic Systems, Franklin Lakes, NJ, presents the case for multiple approaches. “For rapid point-of-care immunoassays, we have not yet seen antibiotic resistance tests. But they are useful in that they allow the rapid diagnosis of infections such as sexually transmitted diseases, influenza, and other respiratory viruses. Here too, this helps guide therapy. If a patient is diagnosed with a respiratory virus, the clinician will know not to prescribe an antibiotic, and this will promote appropriate antibiotic usage. So it has an indirect effect.”

The consensus is that molecular testing is destined to make a significant impact on antibiotic resistance testing, and even though most molecular tests do not specifically detect resistance markers, they can have an important impact on patient outcome.

Photo SampathRangarajan300

Rangarajan Sampath, PhD, Abbott Ibis Biosciences

“Unfortunately, there is little margin for error when diagnosing critically ill patients, and preventable delays can be life-threatening,” says Rangarajan Sampath, PhD, senior director of R&D at Abbott Ibis Biosciences, Carlsbad, Calif. “Physicians need tools that can quickly and accurately detect the source of infection to help them administer the correct antibiotic, which has the potential to cut the patient risk of death in half. Rapid molecular diagnostics are a game-changer to help doctors start implementing treatments that can improve patient outcomes.”

“Molecular resistance testing may make a significant impact, but we have to keep in mind that when we do molecular testing for predicting antimicrobial susceptibility, we are targeting the presence of a specific gene. The organism, however, may be resistant to an antibiotic by a different mechanism that is not detected by that test,” explains Murray.

Anita Goel, MD, PhD, Nanobiosym Diagnostics

Anita Goel, MD, PhD, Nanobiosym Diagnostics

“Culture has been around for at least 100 years, and polymerase chain reaction (PCR) has been the gold standard for molecular testing for some 20 years; both offer very good sensitivity and specificity,” says Anita Goel, MD, PhD, chairman and CEO of Nanobiosym Diagnostics, Cambridge, Mass. “The problem with culture is that it is too slow. And the problem with PCR is that it is very cumbersome and needs specialized lab equipment and personnel. If PCR is a quantum leap versus culture, then our company’s Gene-Radar is a quantum leap above PCR—it can be done anywhere, is a mobile device, and can be done on a fingerstick, buccal, urine, or skin sample.”

Molecular technology continues to play a role, says Todd Keirns, microbiology group marketing manager at Roche Diagnostics, Indianapolis. “It has been recognized that the appropriate window for actionable test results is no more than 15 hours from the time the sample has been collected. With traditional microbiology culture, you would need 19 to 20 hours just to get a generic culture result. To get a more specific culture result, you would need another 24 to 48 hours. This is well beyond the actionable result window of time.”

Another issue is how to make the laboratory efficient in that process, added Keirns. Roche Diagnostics anticipates that automation is another key to making molecular tests more efficient. “Antibiotic resistance testing programs involve a large number of samples to be tested. The best way to do that is with an automated system.” This January, Roche provided an example of such automation with the FDA clearance of an automated, sample-to-result MRSA/methicillin-sensitive S. aureus test on the Cobas 4800. (For more information, see the companion article, “Advances in Antibiotic Resistance Testing.”) 

IVD COMPANIES HAVE A ROLE

“We’ve long believed that the lab and the IVD industry are as important in the battle against resistance as are new antibiotics and the drug companies that make them. Now leading clinical organizations, such as the Infectious Diseases Society of America (IDSA) and the Society of Critical Care Medicine are urging the development of not just new antimicrobials, but faster tests to identify infections so that optimal therapy can be selected as quickly as possible,” comments Sam Bozzette, MD, PhD, vice president for medical affairs at bioMérieux Americas, Durham, NC.

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A proprietary isothermal amplification technology developed by Great Basin Scientific can amplify multiple target sequences simultaneously or in multiplex format.

A proprietary isothermal amplification technology developed by Great Basin Scientific Inc, Salt Lake City, can amplify multiple target sequences simultaneously or in multiplex format. “The real value that our system provides is the ability to multiplex our tests so that we can provide up to 64 answers per sample tested,” says Ryan Ashton, Great Basin president and CEO. “When you look at all the causes of a blood infection, what you want to get is the most accurate answer, and not just to rule out a cause but to rule in the infection-causing organism.”

“In the area of hospital-acquired blood infections, our broad panels include all of the causes of a blood infection and the appropriate antibiotic resistance markers that may be available,” Ashton adds. “This provides an answer without having to run 8 to 10 different tests—and in a much faster time frame.”

Cottam emphasizes the importance of the educational component in the use of rapid diagnostics. To this end, he says, Alere has introduced its “Test, Target, Treat” education campaign.

DECENTRALIZING MOLECULAR ANTIBIOTIC RESISTANCE TESTING

Decentralizing molecular antibiotic resistance testing is seen as a positive trend. “As the technology is being developed, it offers more flexibility for noncentralized test sites to do more testing,” says Cottam. “It is not a solution for every condition, but the tests are very easy to use and understand, which can make a big impact on treatment decisions.”

“Within a few minutes you can get an organism identification and its resistance profile—anywhere,” says Goel. “It is important to be able to decentralize with the same gold standard as lab-based testing.”

According to Schito, the advantage of molecular testing for community-based and hospital-acquired infections is that once individual practitioners, healthcare facilities, and their care teams become aware of an infection problem, they and public health agencies have the information they need to design and implement prevention strategies that protect patients and save lives. “A goal for the future is to develop small instruments that can perform sequencing—be it targeted or partial genome—on the benchtop,” says Schito. “Once those instruments come online then, I think, the treatment options will change dramatically.”

“I am very excited about the transformation that is occurring in molecular diagnostics as we move to platforms that allow virtually any laboratory to do molecular testing, and with an expanded menu, this will certainly have clinical relevance,” says Murray.

ORGANISM SEQUENCING CAN PROVIDE CLUES

A recent buzz is the use of sequencing techniques to discover gene mutations that contribute to an organism’s resistance to drugs. “Whole-genome sequencing can assist, especially when we are not 100% sure of all of the drug-resistance mutations,” explains Schito. “Testing for the whole genome of many isolates—combined with phenotypic testing that has been performed as well as some clinical outcome data—can help identify additional areas within the genome that we may want to target a little bit more and that may identify new mutations associated with resistance.”

The Critical Path Institute is working to expand that menu of diagnostic and resistance markers. “The problem is that we don’t know all of the mutations associated with a particular drug resistance,” says Schito. “We have come to the conclusion that achieving this will require a comprehensive and curated data platform with well-defined governance structures, collaborations with different stakeholders, and a process of endorsement of the markers.”

The World Health Organization has agreed to help in that endeavor and will participate in a collaboration between the Critical Path Institute, the National Institutes of Health, CDC, the Foundation for Innovative New Diagnostics, and the new diagnostics working group that is part of the Stop TB Partnership, Geneva, Switzerland. The collaboration has received a grant from the Bill and Melinda Gates Foundation to help coordinate and host the database.

It is not a slam-dunk, according to Murray. “Whole-genome sequencing can detect resistance markers, but you don’t know if they are expressed, and you can only detect those markers that you know. If we find a mutation that has not been previously described, we cannot automatically predict if this would result in true resistance. We have to do viral load studies to demonstrate a resistance action. So, I do not think that we can be comprehensive in predicting susceptibility by genomic techniques.”

[reference id=”41288″]Sidebar: WHO Takes a Global View[/reference]

THE WAY FORWARD

In a recent policy statement, IDSA has issued a call for collaboration among clinicians, IVD companies, pharmaceutical companies, and professional associations to develop improved diagnostics for infectious diseases.

Despite dramatic advances in diagnostic technologies, many patients with suspected infections receive empiric antimicrobial therapy rather than appropriate therapy dictated by the rapid identification of the infectious agent. The result is overuse of our small inventory of effective antimicrobials whose numbers continue to dwindle due to increasing levels of antimicrobial resistance. New tests are needed that can identify a specific pathogen or at a minimum, distinguish between bacterial and viral infections, and also provide information on susceptibility to antimicrobial agents.7

“I think we have to move away from culture-based testing—it is an old methodology that is clearly accepted in hospital laboratories around the world, but we also know that it is fraught with problems. It is not terribly efficient,” says Goel.

“The science is there to lead to more molecular-based test methods, and I believe that is the direction that the infectious disease community needs to move. But we need the technology to make molecular tests more efficient, cheaper, and usable at the bedside,” she adds. “This will take a combination of investment by diagnostic companies as well as by pharmaceutical companies. Ideally, as drug companies are developing antibiotics, they will marry them to diagnostic tests that complete the antibiotic package they are developing.”

Shara Rosen is a contributing writer for CLP. For more information, contact CLP chief editor Steve Halasey via [email protected].

 

REFERENCES

  1. Fleming A. Nobel Lecture: Penicillin. Stockholm: The Nobel Foundation, 1945. Available at: http://www.nobelprize.org/nobel_prizes/medicine/laureates/1945/fleming-lecture.html. Accessed February 24, 2015.
  1. Efforts to improve patient safety result in 1.3 million fewer patient harms: interim update on 2013 annual hospital-acquired condition rate and estimates of cost savings and deaths averted from 2010 to 2013. Rockville, Md: Agency for Healthcare Research and Quality, 2014. Available at: www.ahrq.gov/professionals/quality-patient-safety/pfp/interimhacrate2013.html. Accessed February 24, 2015.
  1. National and state healthcare-associated infections progress report. Atlanta: Centers for Disease Control and Prevention, 2015. Available at: www.cdc.gov/HAI/pdfs/progress-report/hai-progress-report.pdf. Accessed February 24, 2015.
  1. Antimicrobial resistance: global report on surveillance, 2014 summary. Geneva: World Health Organization, 2014. Available at: http://www.who.int/drugresistance/documents/surveillancereport/en. Accessed February 24, 2015.
  1. Antibiotic resistance threats in the United States, 2013. Atlanta: Centers for Disease Control and Prevention, 2013. Available at: http://www.cdc.gov/drugresistance/threat-report-2013/index.html. Accessed February 24, 2015.
  1. Executive order: combating antibiotic-resistant bacteria. Washington, DC: The White House, 2014. Available at: http://www.whitehouse.gov/the-press-office/2014/09/18/executive-order-combating-antibiotic-resistant-bacteria. Accessed February 24, 2015.
  1. Better tests, better care: improved diagnostics for infectious diseases [policy statement]. Arlington, Va: Infectious Diseases Society of America, 2013. Available at: www.idsociety.org/2013_IDSA_Diagnostics. Accessed February 24, 2015.