Detecting Pathogens with Diagnostic PCR Panels

Panels of PCR-based tests have become indispensable for studying pathogens and detecting infectious diseases. These improved diagnostic tools give clinicians the ability to tailor treatments and respond faster to infections. With their high sensitivity and specificity, PCR panels allow public health officials to detect and track individual pathogen strains in epidemiological surveillance. This article looks at how PCR-based panels are improving the important processes of diagnosis, treatment, and public health monitoring.

Benefits of using PCR panels

When a clinician is faced with sepsis or a severe respiratory infection, the speed of diagnosis and initiation of treatment is crucial. But speed is only one benefit of diagnostic PCR panels, which can detect infectious diseases by amplifying pathogen DNA or RNA present in samples. Technological innovations—such as multiplexing, automation, and high-throughput methods, and better software for data analysis—have made it easier and faster to test for infectious pathogens via PCR panels, compared to previous methods that involved time-consuming pathogen culturing (which may take days or weeks and/or be difficult to culture). Furthermore, “PCR can directly analyze clinical samples without the need for extensive sample processing or enrichment steps,” says Constantine Garagounis, Product Development and Marketing Specialist at PCR Biosystems. “This direct approach speeds up the diagnostic workflow.” PCR Biosystems supplies a range of reagents for infectious pathogen testing.

Standard BioTools offers qPCR-based, customized assay panels using integrated fluidic circuits (IFCs) that give results for over 9000 reactions in about 2 hours, enabling fast turnaround times for quick answers and high testing demands. Rapid results mean that such tests can be wielded quickly and have the potential to help detect and manage disease outbreaks. “The open architecture of IFCs gives researchers flexibility to change the assay panels as needed over time,” says Bill Hunt, Director of Genomics Product Management at Standard BioTools.

PCR offers high levels of sensitivity and specificity, and the ability to differentiate between strains of pathogens. Panels undergo rigorous testing for validation, including determination of the lowest detectable concentration of each pathogen, and other important questions. “For instance, does the PCR panel detect non-target organisms that may be abundant in the chosen sample for analysis,” says Garagounis. “Does the panel detect pathogens in clinical samples as effectively as in reference samples?” Additional testing also occurs prior to approval for diagnostic use.

Ideally, PCR panels are designed to be sensitive enough to detect pathogens of interest, but specific enough to avoid false positives. “Building such panels takes time and effort, and the key here is to use authenticated [microbial] strains,” says Leka Papazisi, Principal Scientist in Microbiology R&D at ATCC. ATCC’s cultures are used as standards in developing testing guidelines for clinical labs, for example, when assessing a lab’s proficiency in testing for anti-microbial resistance.

Combating disease outbreaks

Rapid tests mean that results can be quickly wielded to help detect and manage infectious disease outbreaks. PCR panels are an important component in epidemiological surveillance. “The high specificity of PCR-based detection [offers] strain-specific information,” says Garagounis. “This helps epidemiologists track and monitor the outbreak and spread of diseases and their evolution over time.”

Standard BioTools™ panels can be customized according to purpose, including PCR panels for studying respiratory or gastrointestinal pathogens. For example, using microfluidic-based products, researchers have tested for tick-borne pathogens, and pathogens present in wastewater. “As another example using targeted NGS library prep, the CDC is piloting a program for highly multiplexed amplicon sequencing (HMAS) of Salmonella that uses our IFCs, reagents, and the Biomark™ X9 System as part of a culture-independent workflow,” says Hunt.

In formulating the content of PCR panels, Standard BioTools considers customer input, as well as scientific evidence for targeting particular pathogens. “Public health policies for conducting surveillance of outbreaks and transmission also factor into the content and need for testing,” says Hunt. “The IFCs themselves support testing several targets concurrently, so it is easy to add new targets, or change targets, to meet evolving requirements for testing.”

ATCC, a biorepository and standards organization, supports the development of infectious disease testing for public health surveillance and clinics. “Most recent examples include the SARS-CoV-2 and Zika epidemics, but there are almost no cleared medical devices detecting respiratory-, gastrointestinal-, or sexually transmitted infections that have not used ATCC cultures or their derivatives,” says Papazisi.

ATCC also supports the development of PCR panels by supplying, for example, “high-quality, quantified microbes, as well as native and synthetic nucleic acids,” says James Budnick, Senior Scientist in Microbiology (Bacteriology) R&D at ATCC. “These materials are fundamental to developing PCR panels for the development, validation, and performance monitoring of these systems.” For example, at the start of the pandemic, ATCC quickly provided multiple variants of heat-inactivated SARS-CoV-2, and other materials needed to develop PCR panels against COVID-19 variants.

Personalized medicine

Diagnostic PCR panels are already helping clinicians to treat diseases faster, earlier, and smarter. Fast turnaround times allow quicker treatment decisions, and improved diagnostic accuracy allows for targeted treatments. “A good respiratory pathogen testing panel can eliminate numerous possible pathogens in one go, even if the actual pathogen is not targeted by that panel,” says Garagounis. “This helps clinicians narrow down the possible causes and helps the diagnostic process even when results are negative.”

Diagnostic PCR panels can also help to minimize unnecessary antibiotic use—an important component of responsible antibiotic stewardship. “Some test panels also identify antibiotic resistance genes, again reducing use of antibiotics and ensuring correct treatment for drug-resistant strains is administered in a timely fashion,” says Garagounis. PCR panels are not only supporting better patient outcomes, but also arming public health officials with surveillance tools to facilitate smarter responses to events like once-in-a-lifetime pandemics.