Development of PMAxx-droplet digital PCR method for the absolute quantification of viable Shigella flexneri and Shigella sonnei strains in water

TL;DR

A new PCR method was developed to detect and quantify live Shigella bacteria in water, improving water safety monitoring.

Contribution

A PMAxx-ddPCR method was developed for simultaneous, viability-discriminative quantification of Shigella flexneri and Shigella sonnei in water.

Findings

The PMAxx-ddPCR assay detected viable Shigella with a detection limit of ≤10 CFU/reaction in fecal-spiked water.

Duplex amplification showed amplification efficiencies comparable to singleplex assays for all targets.

PMAxx treatment effectively suppressed signals from dead cells, ensuring specificity for viable bacteria.

Abstract

Shigella spp. are waterborne pathogens responsible for global diarrheal disease outbreaks via contaminated groundwater, drinking water, and recreational water systems. Their extremely low infectious dose necessitates the development of highly sensitive detection methods capable of distinguishing viable pathogens.

In this study, we developed and optimized a viability-discriminative droplet digital PCR (ddPCR) assay incorporating propidium monoazide (PMAxx) treatment and duplex amplification targeting both chromosomal and virulence plasmid genes. Key reaction parameters—including annealing temperature, primer and probe concentrations, and PMAxx treatment conditions—were systematically optimized. Singleplex and duplex assays were compared to verify amplification consistency. Additionally, three DNA concentration methods (direct centrifugation, PEG precipitation, and a commercial kit) were evaluated for their suitability in field applications using fecal-spiked water samples.

The optimized PMAxx-ddPCR assay enabled simultaneous detection of viable S. flexneri and S. sonnei with excellent specificity. Duplex amplification showed amplification efficiencies comparable to those of singleplex assays across all targets. The method achieved a detection limit of ≤10 CFU/reaction in fecal-spiked water, and PMAxx treatment effectively suppressed signals from dead cells. Comparative evaluation of concentration methods identified effective protocols suitable for field deployment.

This PMAxx-ddPCR approach enables the simultaneous quantification of viable, virulent Shigella in water samples, offering a robust tool for advancing water safety monitoring and public health protection.

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