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Digital PCR in pathogen detection

Digital PCR in pathogen testing

Pathogens cause disease in humans, animals or plants, posing a substantial risk to food safety and public health. Modern pathogen detection requires methods with high specificity, reproducibility and speed. Digital PCR (dPCR) has emerged as a powerful tool for precisely identifying pathogenic microorganisms, including bacteria, viruses and fungi, in low-input samples such as wastewater, blood, FFPE, plant tissue and soil. The method is also successfully used to quantify virulence and antibiotic resistance genes, supporting rapid and accurate microbiological risk assessment.

Why use nanoplate dPCR for pathogen testing

Inhibitor resistance – thanks to its partitioning approach, dPCR is resistant to inhibitor effects and can consistently identify low-abundance pathogens in difficult samples

High reproducibility – no need for qPCR calibration curves, which reduces inter-run variability and helps obtain dependable results when monitoring pathogen loads across time, sites or labs

Multiplexing and speed – results in less than 2 hours, the ability to interrogate 12 targets at once with faster delivery than highly time-consuming culture-dependent methods; now evaluate multiplex assay compatibility with our free tool

Broad assay portfolio – select from 900+ targets in pre-designed assays (many wet-lab tested) or use unique custom assay design tool for targets outside of the catalogue

Access to genomic specialists – for custom projects, receive additional support (quick tweaking or new custom design) from our team

Use cases of digital PCR for pathogen detection

Digital PCR provides the absolute quantification needed to make informed decisions in the detection and quantification of low-abundance pathogens in difficult samples. Below is a summary of common uses of nanoplate dPCR in the testing of pathogens from human, animal plant and environmental samples.

Pathogen testing with nanoplate digital PCR

Digital PCR workflow for microbial analysis

Customer experience: QIAcuity for pathogen analysis

“We decided to use QIAcuity for several reasons. For one, hands-on time is vastly reduced. This is because the QIAcuity divides the sample into thousands of partitions in a nanoplate, and does the PCR and imaging steps all in one machine. Other systems require two to three different machines and the time to perform the same experiment is hours longer.”

Dr. Youry Kim, Post-Doctoral Research Fellow at the Peter Doherty Institute of Infection and Immunity at the University of Melbourne in Australia, who uses dPCR to measure levels of integrated HIV DNA in treated and untreated samples to determine whether the selected drugs are eliminating intact virus.

Laboratory researcher operating a QIAcuity digital PCR instrument.

Customer experience: QIAcuity for pathogen detection

Person standing in a laboratory environment.

“If PCR can find a needle in a haystack, dPCR is like laying that haystack flat across the ground so one can see it better and find the needle.”

Dr. Melissa Nolan, Assistant Professor at the Arnold School of Public Health at the University of South Carolina in Columbia, is testing if dPCR can improve the detection rate of vector-borne diseases, such as Chagas caused by the parasite Trypanosoma cruzi.

Related dPCR products for pathogen testing

* Try our new digital PCR multiplex assay compatibility checker to evaluate the performance of your dPCR assays in a multiplex analysis. Easy, quick and free.

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Related resources on dPCR for pathogen identification and quantification

Related dPCR webinars on pathogen detection

Scientific publications with QIAcuity dPCR for pathogen analysis

He M, et al. A pathogen lncRNA secreted into rice sequesters a host miRNA for virulence. Nature. 2026;655:468–477.

Barbian HJ, et al. Citywide indoor air sampling mirrors wastewater and clinical case surveillance of respiratory viruses. Nat Commun. 2026;17:6257.

Shrestha S, Malla B, Haramoto E. Evaluation of the Enterovirus serotype monitoring approach for wastewater surveillance of hand foot and mouth disease using secondary epidemiological surveillance data. Sci Total Environ. 2025;969:178896.

Kelm S, et al. Solid evidence and liquid gold: Trade-offs of processing settled solids, whole influent, or centrifuged influent for codetecting viral, bacterial, and eukaryotic pathogens in wastewater. Environ Sci Technol. 2025;59(31):16240–16249.