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Infection Identification: Metagenomic Next-generation Sequencing vs PCR

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In the U.S., the number of transplants is growing by approximately 4% each year. Of the 57,000 transplants that take place, roughly 30% of patients will suffer from a viral infection.

The current standard of care approach for identifying infections in post-transplant patients is quantitative PCR (qPCR). However, a new study, a joint publication of Arc Bio and Stanford University School of Medicine, demonstrates that a novel metagenomic next-generation sequencing (mNGS) platform shows comparable power in identifying the 10 most common infections in post-transplant patients when compared to qPCR.

We recently spoke with Meredith Carpenter, Director of Assay Research and Development for Arc Bio, to learn more about the capabilities of the platform. 

Molly Campbell (MC) Why is it important to have a highly sensitive method for identifying infections in post-transplant patients?

Meredith Carpenter (MCa):
Transplant patients are uniquely challenging to diagnose and manage with respect to infections because they are undergoing immunosuppressive therapy to reduce their risk of transplant rejection. However, the immunosuppressive drugs also increase their risk of infections and co-infections, while also suppressing many of the typical clinical signs and symptoms used to diagnose an infection. This means it’s crucial to have not only sensitive diagnostic tools but also ones that are highly multiplexed so you can simultaneously detect multiple potential pathogens, in this case from a single blood draw. This also allows the monitoring of viral loads, which qPCR has established as standard of care in this patient population, with the goal of customizing dosing and titration of immunosuppressive therapies and/or antivirals for each patient to maximize benefits while limiting toxicity of these drugs.

MC: Quantitative PCR is the current standard of care approach for identifying pathogens post-transplant patients. Why has it been difficult to adopt metagenomic next-generation sequencing (mNGS) in this space?

Adoption of mNGS within infectious diseases has been slower than in human genetics due to barriers related to the cost and complexity of developing and deploying these methods, as well as the small proportion of microbial genomes in a patient sample compared to the host genome, and a lack of clinical utility and outcome studies to show the value of such novel diagnostics in this setting. From a wet lab perspective, it requires that the user have expertise in preparing samples for sequencing, which can be complex. There is also a “dry lab” component, which requires a bioinformatician to analyse and interpret the sequencing data. In many cases this will need the user to build a bioinformatics pipeline in-house, which requires highly specialized expertise or the use of publicly available software; much of which is not very user friendly. Finally, the ability to quantify results requires the use of specially designed controls. Taken together, these cost and resource barriers have prevented many labs from adopting mNGS for routine use.

MC: Please can you tell us about the novel metagenomic next-generation sequencing (mNGS) test, and how it overcomes these issues?

Currently, the GalileoTM platform is for research use only and is intended to be used by researchers who are interested in the detection and quantification of DNA viruses that commonly cause infection (or reactivation of latent infections) in the transplant setting. The platform can overcome some of the barriers to deploying mNGS by including reagents and controls for sample preparation, as well as access to the GalileoTM Analytics software, which performs analysis and interpretation of the sequencing data. User-friendly reports are generated by the software that provide detection and quantification of 397 strains of 10 key DNA viruses (CMV, EBV, HHV-6A, HHV-6B, HSV-1, HSV-2, BKV, JCV, ADV, and VZV) as well as semi-quantitative detection of B19 and TTV strains. By providing a turnkey workflow, the GalileoTM platform can eliminate much of the learning curve for mNGS. This allows researchers to instead focus their time and resources on designing and conducting studies to generate the most impactful publications.

MC: What were your main findings in this study? What information can the mNGS test provide in this context that qPCR cannot?

This study was a collaborative effort between Dr. Benjamin Pinsky at the Clinical Virology Laboratory at Stanford University School of Medicine and Arc Bio to validate the GalileoTM platform using both contrived and residual clinical samples as compared to the current gold standard methods (individual qPCR assays). We report comparable performance of the GalileoTM platform and singleplex qPCR assays across a range of analytical parameters, including sensitivity, limit of detection, and viral quantitation. In addition, because GalileoTM is highly multiplexed, it identified several cases of co-infections from a single sample. While singleplex PCR could have identified these additional pathogens, they were not requested by the clinical teams at the time of ordering. This highlights one advantage of highly multiplexed technologies such as mNGS, although the clinical relevance of these additional findings must be established. Overall, the ability to detect and quantify 397 viral strains simultaneously from a single specimen could mean significantly lower time and cost burdens for researchers evaluating viral infections and reactivations.

MC: In the future, do you envision mNGS replacing qPCR as the standard of care method for identifying infections in transplant patients?

I believe many researchers and clinicians do envision mNGS eventually replacing PCR as the standard of care for diagnosing many types of complex infections, including transplant patients. However, we must begin with generating evidence of value and identifying the most cost-effective patient populations to apply this powerful technology. The GalileoTM platform is ideally positioned to help clinical researchers robustly evaluate the potential of mNGS and generate the necessary data for demonstrating value to clinicians, regulators and payers.

MC: What are your next steps in this space?

We are continuing to broaden the potential utility of the GalileoTM platform by adding key features and menu expansions aimed at extending the value of mNGS to other areas of infectious disease research.

Meredith Carpenter, Director of Assay Research and Development for Arc Bio, was speaking with Molly Campbell, Science Writer, Technology Networks.