The impact of molecular approaches to infectious disease diagnostics

Aug. 2, 2015

Over the past decade, molecular diagnostics have become a viable alternative to traditional diagnostic methodologies for infectious diseases and a valuable weapon in the battle against antibiotic resistance. By targeting the genomic material unique to each pathogen, molecular tests can deliver diagnostic results much quicker and, in many cases, more accurately than conventional culture-based techniques. The clinical value of rapid molecular diagnostics is underscored by the time-sensitive nature of many of the treatment decisions associated with infectious diseases.

The growing threat of antimicrobial resistance, driven by both appropriate and inappropriate antibiotic usage, represents another catalyst for the use of rapid molecular methods. Nearly 50 percent of antibiotics used are either inappropriately prescribed or misused as a result of being dosed incorrectly.1 By enabling a shorter turnaround time to optimal patient therapy, molecular diagnostic tests can lead to improved patient outcomes and infection control measures, reduced healthcare costs, and “game-changing” improvements in antimicrobial stewardship.2

Infectious disease testing: molecular approaches

There are many different approaches to the design of molecular diagnostic tests. Pathogen detection can be achieved through a number of different methods, including real-time polymerase chain reaction (PCR) detection with melt-curve analysis, fluorescent in situ hybridization (FISH)-based detection, and microarray-based detection, to name a few. Some tests provide full automation of all necessary detection steps from sample receipt to diagnostic result (sample-to-result), while others require offline steps such as nucleic acid extraction and amplification. The results of a molecular test can be qualitative or quantitative in nature.

Increasingly, molecular test manufacturers are being asked to deliver sample-to-result tests that require minimal user skill and hands-on time to perform a test and interpret results. This preference, in part, is the result of the shortage of qualified personnel entering the workforce, as there was a 67 percent reduction in graduates from medical technology programs between 1975 and 2005, and more than 80,000 clinical laboratory professionals are set to retire during the next five years.3 Molecular diagnostic tests, therefore, need to provide superior usability in addition to sensitivity, specificity, and turnaround time in order to ensure that their benefits can be realized in a broad range of healthcare settings.

Bloodstream infections

Sepsis that results from bacteremia causes nearly 500,000 hospitalizations in the United States annually and accounts for 11 percent of intensive care unit (ICU) admissions and over $20.3 billion in aggregate cost.4-5 Mortality associated with these infections is extremely high and can range anywhere from 25 percent to 80 percent.6 Time to appropriate therapy has been proven to be a critical determinant of outcomes for patients with sepsis. Kumar et al. demonstrated a 7.6 percent mean decrease in survival rates for each hour that optimal therapy is delayed following the start of sepsis-related hypotension.7 Yet, conventional culture-based diagnostics, which widely remain the standard for identification of bloodstream pathogens, provide very slow turnaround times that can reach upward of three to four days. With long time-to-identification, patients might remain on an inappropriate empiric therapy, predisposing them to a higher risk of mortality.

Molecular diagnostics have emerged as the first viable alternative to culture for the detection of bloodstream pathogens, as these tests can provide the desired rapid detection of the causative pathogens of bacteremia to enable earlier optimization of therapy. Use of rapid molecular diagnostic tests for bloodstream infections has been associated with improved patient outcomes, improved antimicrobial stewardship, improved infection control, and reduced healthcare costs.

A number of recent publications have focused on the clinical and economic impact of rapid molecular blood culture tests for the detection of specific pathogens. Following the implementation of a rapid molecular test that differentiated between MRSA and MSSA, Bauer et al. demonstrated earlier optimization of therapy by 48 hours for patients with MSSA bacteremia, a 6.2-day length of stay reduction (21.5 versus 15.3 days; p = .07), and $21,387 reduction in total hospital costs per patient ($48,350 versus $69,737; p = 0.03).8 Other studies have shown that rapidly identifying coagulase-negative staphylococci (CoNS) in positive blood cultures with molecular diagnostic tests have led to reductions in unnecessary antibiotics and length-of-stay. Forrest et al. demonstrated a cost saving of $4,005 per patient with a CoNS contaminated blood culture.9 Similarly, Wong et al. demonstrated a saving of $8,338 per patient with a CoNS contaminated blood culture.10 In this study, antibiotics were discontinued 32 hours sooner, and total antimicrobial exposure was reduced by 43.5 hours following the detection of CoNS with rapid diagnostics.

A recent study by Box et al. demonstrated the impact of implementing a 15-target multiplexed gram-positive molecular blood culture test paired with active stewardship intervention in a community-hospital setting with limited resources. Outcomes included a 25.7-hour reduction in time to targeted therapy (61.1 versus 35.4 hours; p < 0.0001), including a 26.7-hour reduction for MSSA (63.4 versus 36.7 hours; p < 0.01), 48.4-hour for E. faecalis (68.5 versus 20.1 hours; p < 0.01), 16-hour reduction for streptococci (52.4 versus 36.4 hours; p = 0.01), and a 17.8-hour reduction in time to de-escalation for CoNS contaminants (42.3 versus 24.5 hours; p = 0.03).11 The median reduction in hospital length-of-stay was 1.9 days per patient (9.1 versus 7.2 days; p = 0.03), and there was an average reduction in median hospital costs of $7,240 per patient ($17,530 versus $10,290; p = 0.04).11

Respiratory tract infections

The clinical and economic burden of respiratory tract infections can be profoundly impacted by the availability and widespread use of molecular tests for respiratory pathogens. In the U.S., five to 20 percent of the population contracts influenza each year, with epidemics costing between $71 billion and $167 billion.12-13 Other viruses such as respiratory syncytial virus, adenovirus, human metapneumovirus, and parainfluenza are also associated with significant morbidity and mortality.14-18 Rhinoviruses are the most prominent cause of the estimated one billion annual cases of the common cold and are the most common cause of respiratory tract infection in hospitalized children.19-20 Non-influenza respiratory tract infections lead to an estimated $40 billion in annual cost in the U.S.21

With the wide variety of known respiratory pathogens, it can be difficult for a physician to determine optimal patient management based upon clinical symptoms alone. Physicians must consider whether the causative agent is likely to be bacterial, viral, or non-pathogenic, decide whether it is appropriate to prescribe antimicrobials empirically, decide which diagnostic test(s) should be ordered, and determine whether the necessary diagnostic results will be available in time to make the best management decisions for the patient. Molecular diagnostics are quickly replacing the previous gold-standard diagnostics for respiratory pathogen testing, as they have been able to provide the necessary sensitivity, specificity, and turnaround time to support the decision-making process of the physician to enable better patient management.

The clinical value of rapid molecular diagnostics is underscored by the time-sensitive nature of many of these treatment decisions. In the case of influenza, the most commonly prescribed antiviral medications are most effective when administered within 48 hours of the onset of symptoms.22 When considering both influenza and non-influenza respiratory pathogens, Rogers et al. found that implementing a broad molecular respiratory pathogens test led to a reduction in time to identification by 12.27 hours (383 versus 1,119 minutes; p < 0.001), a 0.4-day reduction in the duration of antibiotic use (2.8 versus 3.2 days; p = 0.003), a 0.2-day reduction in inpatient length of stay (3.2 versus 3.4 days; p = 0.16), and a three-hour reduction in time in isolation (70 versus 73 hours; p = 0.27).23

In addition to the numerous clinical benefits associated with the earlier optimization of patient treatment and avoidance of unnecessary therapy, the accuracy and turnaround time offered by molecular diagnostic tests for respiratory tract infections have been associated with significant reductions in healthcare costs. In one study, Mahony et al. described how converting all pediatric respiratory virus testing to a more expensive FDA-cleared multiplex molecular method from a protocol of DFA and viral culture led to an annual cost savings of more than $500,000 per year, or $291 per case.24

Gastrointestinal tract infections

Infectious enteritis and foodborne illness are responsible for more than 300,000 emergency department visits and 225,000 inpatient stays each year in the U.S. and are associated with healthcare costs of about $1.8 billion.25 This burden is further complicated by the fact that only 20 percent of acute diarrheal episodes are caused by known pathogens and chemicals.26 The remainder of acute diarrheal episodes are attributed to unspecified agents or substances with unproven ability to cause illnesses. While norovirus causes a majority (58 percent) of foodborne illness in the U.S., it is not on the national notifiable disease list because clinical laboratories are not equipped to routinely test for norovirus along with other viral causes of infectious enteritis.26,27 Because of this, viral enteritis not otherwise specific remains the most common diagnosis code for infectious enteritis.25

Treatment for community-acquired diarrheal illness will vary depending on the identity of the stool pathogen, so rapid and accurate identification of pathogenic bacteria and viruses from a stool specimen is critical. However, conventional stool culture, with turnaround times of three to five days and low sensitivity, limits physicians’ abilities to stratify those patients with particularly virulent infections, those with mild self-limiting infections, and those with no infection. This leads to defensive medical practices, longer hospital stays, overuse of antibiotics, and higher costs of patient care. Molecular diagnostic tests have been well suited to fill this diagnostic need, as these tests can target a majority of bacterial, viral, and parasitic stool pathogens in one test and with minimal hands-on time required. These tests not only address a clinical need by providing rapid and accurate detection of true infections, but also a stewardship need through rapid identification of negative specimens. If antibiotics can be avoided or discontinued based on a negative rapid molecular screen, antimicrobial stewardship can be improved and the cost of patient care decreased.

Clinically, molecular stool tests provide improved sensitivity when compared to culture-based methods and have led to improved patient management, antimicrobial stewardship, and infection control.28 Molecular testing for shiga-toxin producing Escherichia coli has been demonstrated to be twice as sensitive as enrichment broth EIA testing, allowing for earlier optimization of patient management for severe infections that have the potential to escalate to hemolytic uremic syndrome if not managed properly.29 Antibiotic treatment is recommended for all cases of Shigella, while antibiotics should only be used for Campylobacter spp. or Salmonella spp. to treat severe or invasive infections.30,31 Rapid detection of these pathogens allows physicians to optimize antibiotic therapy earlier. Moreover, faster disposition of patients out of isolation or discharge from the hospital altogether is made possible by the rapid results and broader pathogen coverage enabled by multiplex molecular panels. Halligan et al. demonstrated a 154-day reduction in unnecessary patient isolation days over an eight-month period and an associated $52,360 cost savings following implementation of a multiplexed molecular stool pathogens test.32

Future trends

As the emergence and spread of antimicrobial resistance continues globally and the supply of available antibiotics continues to dwindle, it is imperative that healthcare providers practice good antimicrobial stewardship to preserve the remaining efficacious antibiotics. Rapid molecular diagnostics have proven to be a vital tool for stewardship efforts. These tests have also had a substantial impact on clinical and economic outcomes for a number of different infectious diseases. In order to enable more widespread use of these diagnostics, manufacturers will need to be responsive to the needs of a changing clinical laboratory environment. Molecular tests will need to become even faster, more affordable, easier to use, and more accurate, and will need to provide broader coverage of infectious diseases. This will help ensure that these tests can be used not only in large academic medical centers and reference labs, but also in smaller community-based hospitals and other near-patient settings—where the majority of patients receive their healthcare. 


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