NEW YORK (GenomeWeb) – A team of researchers in Belgium and the UK have shown that a customized respiratory panel increased their ability to identify respiratory infections in immunocompromised patients when compared to traditional methods.
In a study published late last month in the Journal of Clinical Virology, the group compared a panel developed in house using the real-time PCR-based TaqMan array card from Thermo Fisher Scientific to the conventional methods of direct fluorescence antibody assays, enzyme immunoassays, and culture.
The TaqMan card was designed to detect 24 different viruses, eight bacteria, and two fungi, and the group used this array to test 143 respiratory samples from 120 immunocompromised patients.
Rather than choosing one of these, the group instead chose the "completely open" system from Thermo, Deborah Steensels, corresponding author on the JCV study and a clinical microbiology researcher at Erasme Hospital and Université Libre de Bruxelles, told GenomeWeb in an email.
"We think it is important to know your assays, to have a Ct-value, [and] to be able to choose and change the targets instead of having a 'black box' that gives you a result of [either] positive or negative," Steensels said.
The TaqMan array card's flexibility meant the researchers could tailor it to include the targets most relevant to immunocompromised patients. The study noted that the spatial segregation of the 48 reaction wells also allowed the assay to be adjusted without the need for extensive re-validation that would be required for a typical highly multiplexed assay.
Quantitative results can also help to interpret co-infections, and the group found the workflow to be simple and the cost per test lower compared to commercial panels, with the TaqMan card costing about €50 ($56) compared to €100 ($112) for commercial panels, Steensels said.
Time-to-result was approximately one hour, excluding sample extraction, which was faster than the three-hour DFA assays or the culture methods, but would be slower than "all-in-one systems" like those offered by Biofire or GenMark, Steensels noted.
In the study, conventional testing indentified 27 samples with one pathogen each, while the TaqMan array identified 77 samples with one or more viral respiratory pathogens.
The group used Qiagen's QiaSymphony for extraction and the Thermo Fisher QuantStudio 7 thermal cycler for PCR. That thermal cycler can function in an "open" research-use-only mode as well as an in vitro diagnostic mode. In IVD mode, parameters are set and locked for particular assays.
Steensels said her group used RUO mode, and will continue in that path to develop another panel, as the card used in the study is the IP of the affiliated institutions of two other co-authors — AZ Sint-Jan Brugge-Oostende Hospital and Cambridge University Hospital. Future studies will compare this new assay with different PCR-based methods, she said. The patented technology cited in the study is referred to as a pre-market version from Cambridge-Brugge.
"We do not plan to develop this as an IVD assay at this stage, but we are open for collaboration with an interested industry partner," Steensels said.
The group is also working on a one-year, multi-center epidemiological study of respiratory infections in immunocompromised patients, and Steensels noted that in the future the team might develop the TaqMan array card-based panels for other infectious syndromes.
The need for careful target selection in panels was recently reiterated by a discovery that homology between picornaviruses allowed the GenMark panel to detect an EV-D68 outbreak even though the panel was not explicitly designed for that purpose. BioFire's panel, meanwhile, was shown to have a specificity edge because target choice enabled it to not over-diagnose pertussis. Meanwhile, clinical end users continue to discuss the best way to handle multiplex panel design and data.
A spokesperson for Thermo Fisher highlighted the importance of international connections like those embodied by the JCV study for infectious disease research.
"As infectious diseases continue to be a growing global concern, stronger multi-country collaboration will be needed to help identify and essentially address these diseases," Poupak Farahani, TaqMan Arrays product manager for Thermo Fisher Scientific said in an email to GenomeWeb.
Farahani also emphasized the easy setup and reproducible results of TaqMan array cards, noting that the cards can "serve as a valuable tool to accurately and reliably identify various diseases, making a significant impact and progress in pathogen identification studies across multiple international laboratories."