Microbial detection

The increasing prevalence of infectious diseases and epidemic outbreaks underscores the need for improved detection and analysis of microbes, particularly pathogens. The combination of speed, high sensitivity, accuracy, and absolute quantification is essential for both pathogen detection and microbiome analysis in public health and epidemiology. Digital PCR, as a fast, sensitive and precise method, is highly beneficial for identifying, detecting, characterizing and monitoring changes in pathogens and microbiomes. The application areas of dPCR in microbial detection range from pathogens in food, drug resistance, microorganism research, investigating antimicrobial resistance genes and analysis of viral/bacterial-host relationships. 

Benefits of nanoplate dPCR for microbial detection

  • Precise and absolute quantification of microbial material even from complex samples or samples with high levels of inhibitors
  • Larger sample volumes (up to 28 µl) with Nanoplate 26K for boosting sensitivity and detecting targets below the detection limits of other commercial assays
  • Multiplexing up to 12 assays possible with a selection from custom-designed assays or more than 700 catalogue assays for microbial targets (bacterial, viral, virulence factors, AMG, etc.)

Wastewater monitoring with dPCR

Screening wastewater, or sewage, for pathogens, such as  SARS-CoV-2, Legionella spp. or Salmonellacan predict disease outbreaks and provide essential epidemiological data. However, wastewater is highly heterogenous and a method capable of identifying rare targets in such mixed material is required. This is where the true power of dPCR shines. Absolute quantification with dPCR detects rare events, reduces the impact of PCR inhibitors and eliminates the need for standard curves, simplifying pathogen detection in wastewater.

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Related publications

Gross M, Dunthorn M, Mauvisseau Q, Stoeck T. Using digital PCR to predict ciliate abundance from ribosomal RNA gene copy numbers. Environ Microbiol. 2024;26(4):e16619.

Rattanachak N, Weawsiangsang S, Baldock RA, Jaifoo T, Jongjitvimol T, Jongjitwimol J. A novel and quantitative detection assay (effluxR) for identifying efflux-associated resistance genes using multiplex digital PCR in clinical isolates of Pseudomonas aeruginosa. Methods Protoc. 2023;6(5):96.

Li J et al. Impact of sewer biofilms on fate of SARS-CoV-2 RNA and wastewater surveillance. Nature Water. 2023;1:272–280.

Mazumder MHH et al. Lung-gut axis of microbiome alterations following co-exposure to ultrafine carbon black and ozone. Part Fibre Toxicol. 2023;20(1):15.

Prem EM, Schwarzenberger A, Markt R, Wagner AO. Effects of phenyl acids on different degradation phases during thermophilic anaerobic digestion. Front Microbiol. 2023;14:1087043

Amman F et al. Viral Variant-Resolved Wastewater Surveillance of SARS-CoV-2 at National Scale. Nature Biotechnology. 2022;40:1814–1822.

Tiwari A et al. Application of Digital PCR for Public Health-Related Water Quality Monitoring. Science of The Total Environment. 2022;837:155663.

Thakali O et al. Pilot study on wastewater surveillance of dengue virus RNA: Lessons, challenges, and implications for future research. Environmental Challenges. 2022;9:100614.

Wurtzer S et al. First Detection of Monkeypox Virus Genome in Sewersheds in France: The Potential of Wastewater-Based Epidemiology for Monitoring Emerging Disease. Environmental Science & Technology Letters. 2022; 9(11):991–996.

Wilhelm A et al. Early Detection of SARS-CoV-2 Omicron BA.4 and BA.5 in German Wastewater. Viruses. 2022;14(9):1876.

Ahmed W et al. Comparison of RT-qPCR and RT-dPCR Platforms for the Trace Detection of SARS-CoV-2 RNA in Wastewater. ACS EST Water. 2022;2(11):1871–18.

Further resources

Kellner R et al. Accurate and sensitive detection of microbial DNA and RNA targets using nanoplate dPCR. QIAGEN, 2023.

Donohoe C et al. Wastewater-based epidemiology workflows with QIAcuity® digital PCR. QIAGEN, 2023.

Antanaviciute L et al. Vector-borne diseases identification and quantification vectored by mosquitoes using the QIAcuity® Digital PCR System and qPCR. QIAGEN, 2022.

Kross KL and Bordenstein SR. Comparison of qPCR and dPCR methods for the quantification of Wolbachia densities and arthropod gene expression. QIAGEN, 2022.