NEW YORK – A newly funded project at Brown University Health's Rhode Island Hospital aims to create a blood-based pathogen RNA test for pneumonia. Along with the recent launch of another clinical dPCR system, the work is potentially a harbinger of increased adoption of digital PCR in the clinical infectious disease testing space.
Digital PCR as a technology has sensitivity and date interpretation benefits over qPCR and cost benefits over sequencing. But, other than HIV viral load and some oncology applications, it hasn't been as widely adopted in clinical labs.
However, a clinical pivot among dPCR makers seems to be spurring more interest.
Developers have increasingly been offering dual mode dPCR instruments that run regulated in vitro diagnostics as well as laboratory-developed tests. The Bio-Rad QXDx was cleared by the US Food and Drug Administration in 2019, for example, followed by the Roche Digital LightCycler in 2022 and the Qiagen QiAcuityDx in 2024. Other dPCR systems vying for this space include the Stilla Nio+ and the Thermo Fisher Scientific Absolute Q.
Sean Monaghan, a trauma surgeon and researcher at Rhode Island Hospital and Brown University Health, said he chose RT-dPCR for his assay development work in part because it delivers quantitative results.
In fact, he and his team are hypothesizing that the absolute amount of pathogen RNA in a patient's blood correlates with the severity of their illness such that RT-dPCR results may someday be useful for triage or antimicrobial treatment response monitoring. Indeed, in prior studies of SARS-CoV-2, they suggested that deep sequencing of pathogen and host response RNA can potentially be used to predict mortality.
Monaghan and his team recently won a $1 million pilot award from CARB-X to support this work and will develop the test on Qiagen's QiAcuityDx digital PCR system.
The team chose the QiAcuityDx due to a preference for nanoplate or nanowell systems, Monaghan said, and because they were already using Qiagen sample prep systems to stabilize traces of pathogen RNA in patient blood samples and because the QiAcuityDx works hand-in-hand with those tubes and kits.
All that aside, "it was very important for me to do this work on an FDA-cleared machine," he said, since the team's ultimate goal is to license and commercialize its assays for the benefit of patients everywhere.
And a blood-based pneumonia molecular diagnostic would be a great advantage to patients and clinicians alike, Monaghan also said. At the moment, "there really isn't a great test for lower respiratory tract infections," he said, due to challenges collecting bronchoalveolar lavage samples from deep in the lungs and contamination of sputum by oral fluids.
And, BAL or sputum testing requires bacterial culture, which slows the molecular diagnostic process. While blood cultures are sometimes used for lower respiratory tract infections, they have low sensitivity for bacterial pneumonia.
All this leads to patients being given "best guess antibiotics," Monaghan said, whether they need them or not. The silver lining of pneumonia is that pathogen RNA can easily travel from the lungs to the blood, potentially giving a snapshot of the abundance and activity of the infective agent.
Indeed, depending on where they are lodged in the body, Monaghan said pathogens may express different genes. Although initial data supporting this comes from mouse experiments, he expects to see different RNA signatures in blood from patients with acute lower respiratory infections as compared to patients infected with the same pathogens but in other body sites.
They will now perform deep sequencing of pathogen RNA in pneumonia patient blood samples to find the best genomic targets within three common pneumonia-causing pathogens — specifically, Staphylococcus aureus, Pseudomonas aeruginosa, and Haemophilus influenzae bacteria — and will then develop a dPCR test using the Qiagen QiAcuityDx system.
In addition to the pneumonia test, Monaghan and his team have previously disclosed an RNA-based sepsis assay that he said they are considering porting to dPCR.
Jonathan Arnold, Qiagen's VP and head of oncology and precision diagnostics, said in an interview that the firm launched the QiAcuityDx in the US and Europe in September and quickly installed about a dozen systems.
The diagnostics instrument is built on the chassis of the QiAcuity 4, he said, and is mainly differentiated by its software architecture that allows users to pivot between IVD modes — in which the settings to run regulated assays are essentially locked — and an open-channel mode that allows for the creation and use of laboratory-developed tests.
"Precision is a differentiator for digital PCR," said Arnold. And, for applications in the oncology or infectious disease space aimed at monitoring changes in nucleic acid levels over time, "the absolute quantitation is a game change."
Qiagen has already placed more than 2,700 of its QiAcuity systems since it was launched in 2020.
The installation of the QiAcuityDx in Rhode Island marked the first US hospital to take on the dedicated diagnostics instrument, Arnold said. Though he noted it is still too early to comment on uptake of the new system, "we see the [QiAcuityDx] resonating very well."
To reach potential customers in the clinical lab, Arnold said Qiagen is focused on approaches like webinars. The firm also has a publication strategy around infectious disease, for example, supporting work on human papillomavirus quantitation and cervical cancer outcomes as well as quantitative clinical testing of fungal infections.
While oncology may be a more advanced application for dPCR at the moment, Arnold said, "the excitement around infectious diseases is beginning to really accelerate."
Arnold said Qiagen is also continuing to push dPCR in the pharmaceutical space for clinical trial screening and companion diagnostics development, particularly for hereditary and neurodegenerative diseases.
Qiagen is also working to prove the value of dPCR as a complement to next-generation sequencing, particularly in diseases requiring regular monitoring where the cost and turnaround time of NGS presents challenges.
Overall, "we're beginning to see digital PCR really find its footing now," Arnold said.