Syndrome-based Testing in Infectious Disease


Vol. 24 • Issue 5 • Page 24

Infectious Disease

Diagnostic testing is critical to the management of patients with infectious disease (ID). Accurate diagnosis, provided in a timely fashion, allows appropriate triage and medical therapy for both serious infections as well as less severe illness. We are in a golden age of diagnostics, with increasingly sophisticated technologies available and a heightened appreciation of how accurate diagnosis improves patient outcomes and antibiotic stewardship while reducing healthcare costs.1

A decade ago it was not clear that syndromic panels – multiplexed tests for the detection of a number of pathogens causing a specific clinical syndrome – would be successful. Would they have the necessary sensitivity and specificity, would they be approved by regulatory agencies and would they be accepted for routine use by clinical laboratories and physicians? The answer today is a definite yes, even if some uncertainties about implementation remain.2 Multiplexed assays for the detection of pathogens causing respiratory disease, bloodstream infection and gastrointestinal illness have all received FDA clearance or CE-IVD marking.3,4 Additional panels for the identification of pathogens responsible for meningitis, pneumonia, viral hepatitis and sexually transmitted infections are nearing commercial readiness. While outcomes data are urgently needed to show the impact of syndromic panels on both the cost and the quality of patient care, there has been growing use of this testing modality throughout the healthcare system.

Novel diagnostic development continues at a rapid pace; however, syndrome based technologies are at a crossroads. Where will the next big improvements occur? And what is the best use of unbiased strategies such as next-generation sequencing (NGS)?5 Can NGS or even newer technologies disrupt the syndromic panel pipeline to solve some of the most pressing diagnostic needs of today? The marketplace and further research will sort this out; at the moment it is difficult to predict what the best uses of this technological bounty will be.

Diagnostic Questions, Current Technology

Direct Detection of Sepsis: Now that molecular identification of bacteria from blood culture is an established procedure, with validated, specific, pathogen panels, manufacturers can move on to the development of tests that directly detect pathogens from whole blood. The key technical issues (exquisite sensitivity in the presence of a large excess of human cells and reagents with the lowest levels of contaminating bacteria) can be solved with current technology and will benefit from automated manufacturing. The first multiplex test system to successfully jump this hurdle has been recently cleared by the FDA.6 Widespread adoption of such technology will be game changing for clinical medicine.

Rapid Determination of Antibiotic Resistance: Antibiotic resistant organisms are a high priority emerging threat.1 Rapid identification of these organisms improves patient care and decreases spread. Several resistance genes of greatest concern, e.g., mecA, KPC and vanA/B, have already been added to syndromic panels.7 To further expand resistance testing with current methods, at least two technical problems need to be solved. First, the genetic information required to predict an antibiotic resistance phenotype from the bacterial genotype must be determined; second, this information must be used to construct multiplex panels that detect all of the relevant genetic markers. The first problem may be more trackable than some commentators have assumed: Geneticists are developing the tools to correlate subtle human disease phenotypes with genetic markers present in genomes that are 1,000 times larger than the typical bacterial genome. Applying these algorithms to well characterized pathogen isolates will define the genetic markers of antibiotic resistance, even if the mechanism of resistance is not initially understood. Solving the second problem will require developing multiplex panels that can detect hundreds of polymorphisms, a difficult but not insurmountable task for the current technologies.

Host Response to Infection: Protein biomarkers of infection are well established and used frequently to guide clinical care. Studies using microarrays and NGS have begun to further characterize the host (human) transcriptional response to infection, including differences in response to viral versus bacterial pathogens. This transcriptional response is amenable to detection using quantitative amplification technologies and may provide the basis for a new type of syndromic panel. As with the development of pathogen-based syndromic panels, it will take actual deployment into the clinical laboratory to determine the value of this new panel.

How Will NGS Disrupt ID Diagnostics?

The cost of DNA sequencing has dropped by four orders of magnitude since 2008.8 Reports demonstrating the application of NGS and metagenomic analysis to the detection of bacterial and viral pathogens in human clinical samples have exploded in the literature.9,10 NGS represents a looming challenge to “classical” nucleic-acid amplification based syndromic panels, but NGS technologies and their associated bioinformatics tools are not, at present, fast enough or simple enough to be used in the clinical laboratory for the rapid diagnosis of infection.5 The race is on to streamline these technologies for routine clinical use. Once optimized for the clinical laboratory, the unbiased nature of NGS testing may prove superior to the targeted panels of multiplex tests.

Syndromic Panels, NGS and the Innovators Dilemma

NGS lacks many of the features of a “disruptive” technology for ID diagnostics as defined by Christensen;11 notably, it is not faster or cheaper than the existing molecular methods. Nonetheless, syndromic panel manufacturers recognize the risks posed by this technology and are responding by reducing the time to result,12 moving their platforms into CLIA-waived settings and increasing the number of analytes per panel. Costs will come down as production of test cartridges is automated and economies of scale are achieved. One can anticipate the day when the cost and time to test for a respiratory or ðgastrointestinal ðpathogen are low enough to have little impact on overall healthcare costs.

Should clinical labs and diagnostics developers focus on establishing new panels or optimizing workflows for NGS? There will likely be room for both approaches – rapid, panel-based testing for common pathogens with the potential for follow up with an unbiased NGS-type diagnostic if targeted testing does not provide an answer.

Mark Poritz is vice president of chemistry, BioFire Defense, Salt Lake City, UT. Anne Blaschke is associate professor of pediatrics and pediatric infectious diseases, University of Utah School of Medicine, Salt Lake City, UT.

References

1. Caliendo AM, et al., Better tests, better care: improved diagnostics for infectious diseases. Clin Infect Dis, 2013; 57 Suppl 3: p. S139-70.

2. Schreckenberger P and A. McAdam, Large multiplex PCR panels should be first line tests for detection of respiratory and intestinal pathogens. Journal of Clinical Microbiology, 2015. in press.

3. FDA. U.S. Food and Drug Administration, In Vitro Diagnostics > Nucleic Acid Based Tests. [cited March 31, 2015]; Available from: http://www.fda.gov/MedicalDevices/ProductsandMedicalProcedures/InVitroDiagnostics/ucm330711.htm.

4. Tuite N, et al. Rapid nucleic acid diagnostics for the detection of antimicrobial resistance in Gram-negative bacteria: is it time for a paradigm shift? J Antimicrob Chemother, 2014; 69(7): p. 1729-33.

5. Schrijver I., et al. Opportunities and challenges associated with clinical diagnostic genome sequencing: a report of the Association for Molecular Pathology. J Mol Diagn, 2012; 14(6): p. 525-40.

6. Mylonakis E, et al. T2 magnetic resonance assay for the rapid diagnosis of candidemia in whole blood: a clinical trial. Clin Infect Dis, 2015; 60(6): p. 892-9.

7. Bhatti MM, et al. Evaluation of FilmArray and Verigene systems for rapid identification of positive blood cultures. J Clin Microbiol, 2014; 52(9): p. 3433-6.

8. Wetterstrand KA. National Institutes of Health, DNA Sequencing Costs: Data from the NHGRI Genome Sequencing Program (GSP). 2015 October 31, 2014 [cited March 29, 2015]; Available from: http://www.genome.gov/sequencingcosts/.

9. Long SW, et al. A genomic day in the life of a clinical microbiology laboratory. J Clin Microbiol, 2013; 51(4): p. 1272-7.

10. Neill JD, Bayles DO, and Ridpath JF. Simultaneous rapid sequencing of multiple RNA virus genomes. J Virol Methods, 2014; 201: p. 68-72.

11. Christensen CM. The innovator’s dilemma : when new technologies cause great firms to fail. 2013, Boston, Massachusetts: Harvard Business Review Press. pages cm.

12. Farrar JS and Wittwer CT. Extreme PCR: efficient and specific DNA amplification in 15-60 seconds. Clin Chem, 2015; 61(1): p. 145-53.

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