Digital PCR assays for microbial targets
The digital PCR microbial assays on GeneGlobe are as varied as the targets themselves. The rich portfolio captures bacterial, fungal, parasitic and viral targets, as well as antibiotic resistance and virulence factor genes.
Multiplexing capabilities, the option to combine microbial DNA and viral RNA targets in one reaction and the possibility to design custom assays can personalize your dPCR microbial detection to perfectly suit your needs. Start exploring below.
Available Product Categories
dPCR Microbial DNA Detection Assays
Cat. No.: Varies
For digital PCR detection of microbial targets, including bacterial, fungal, parasitic, viral, antibiotic resistance or virulence factor genes
How to use dPCR to detect bacterial vs parasitic vs fungal vs viral targets
Digital PCR enables sensitive, absolute quantification of low-abundance microbial targets even in complex matrices. Compared to qPCR, dPCR offers improved precision and tolerance to inhibitors, supporting reliable detection of subtle changes in microbial abundance.
Compare dPCR assay considerations for bacterial vs parasitic vs fungal vs viral targets and get tips for each in the table below.
Key factors | Bacterial targets | Parasitic targets | Fungal targets | Viral targets |
|---|---|---|---|---|
| Typical target | Genomic DNA; occasionally rRNA genes | Genomic DNA; occasionally multicopy mitochondrial genes or rRNA | Genomic DNA; multicopy rDNA (ITS, 18S/28S) | DNA or cDNA; gene choice depends on genome organization (segmented vs non‑segmented, integrated vs episomal). |
| Copy number expectations | Single or few copies per cell; 16S/rRNA multicopy if chosen. | Often low per parasite cell in sample | Variable: some multicopy rDNA clusters; ploidy and multinucleate hyphae complicate copies per CFU | Highly variable: viremic loads can span >6 logs; integration or latency can yield very low copies per host cell |
| Target sequence selection | Species‑/strain‑specific genes; avoid conserved housekeeping regions that cross‑react with commensals | Species/complex‑specific markers with minimal homology to host; consider life‑stage conservation (cyst vs trophozoite, egg vs adult) | Genus‑/species‑specific ITS or unique gene loci; account for intra‑species ITS variability in primer placement | Conserved but type‑specific regions (e.g., polymerase, capsid, envelope genes); avoid hypervariable regions unless genotyping. |
| Amplicon length | 60–150 bp, moderate GC; avoid strong secondary structures in GC‑rich bacteria. | Short (70–120 bp) for degraded DNA from stool, blood, or tissues | 70–150 bp; avoid problematic GC or repetitive motifs in fungal genomes | 60–120 bp given frequent fragmentation in clinical samples |
| Need for reverse transcription | Only if targeting RNA (rRNA, mRNA); otherwise DNA targets | Occasionally RNA targets | Sometimes mRNA/viability markers | RT essential for RNA viruses; validate RT separately |
| Controls | Internal amplification control (16S or housekeeping gene) | Host gene control (e.g., human single-copy gene) | Pan-fungal or species-specific controls | RT control, host gene control |
| Common inhibitors | Hemoglobin, bile salts, humic acids. | Inhibitors from bile, complex polysaccharides, hemoglobin. | Mucins, polysaccharides | Host proteins and extraction reagents |
| Multiplexing considerations | Often multiplex species/serotype and internal control; ensure separation of amplitude clusters | Panel assays targeting multiple parasites or combined parasite–bacteria–virus panels; balance sensitivity across targets with very different abundance | Syndromic respiratory or invasive fungal panels; consider wide dynamic range and variable genome sizes | High‑plex viral panels common; careful dye/channel planning and compensation is crucial |
“Within our microbial assay portfolio, you can find more than 900 predesigned assays for bacterial, fungal, parasitic, viral, antibiotic resistance or virulence factor genes. If your assay of interest is missing, you can find a custom dPCR assay tool on GeneGlobe to design your own using our microbial pipeline.”
Dr. Ronny Kellner, Associate Director R&D, QIAGEN
Additional microbial resources
Need more than just dPCR assays for your research? Find more information or contact our specialists to improve every step of your microbial research.
