Rapid method developed for water, soil pathogen screening

A highly sensitive, cost-effective technology can perform rapid bacterial pathogen screening of air, soil, water and agricultural produce in as little as 24 hours.

The technology, developed by researchers at Israel’s Ben-Gurion University of the Negev (BGU) and the Massachusetts Institute of Technology (MIT), could prove suitable for real-time monitoring of activities such as dairy farming, wastewater and run-off treatment. Current methods used in food, water or clinical applications rely on labour- and time-intensive culturing techniques, according to Ezra Orlofsky PhD, who led the research while working on his doctorate at the BGU Zuckerberg Institute for Water Research.

The study, published online in the Water, Air & Soil Pollution journal, defines an accurate, inexpensive, high-throughput and rapid alternative for screening of pathogens from various environmental samples. “This is the first study to comprehensively assess pathogen concentrations in such a broad variety of environmental sample types while achieving multiple pathogen detection with complete parallel testing by standard (or traditional) methods,” Orlofsky explained.

“We accurately identified Salmonella (S. enterica) in environmental soil samples within 24 hours, while traditional methods take four to five days and require sorting,” Orlofsky said. “We also successfully identified a sometimes-fatal infection, Pseudomonas aeruginosa, in aerosols generated by a domestic wastewater treatment system. The results suggest that the developed method presents a broad approach for the rapid, efficient and reliable detection of relatively low densities of pathogenic organisms in challenging environmental samples.”

To evaluate the technology, a variety of environmental samples, including aerosols, various soil types, wastewater and vegetable surface (tomato), was concurrently spiked with Salmonella enteric and/or Pseudomonas aeruginosa. The researchers chose these pathogens because they are leading causes of illness, have high survival potential in the environment and are considered difficult to detect accurately at low concentration.

“When applied to non-spiked field samples, our method outperformed the standard methods substantially, while detecting pathogens within a day of receiving the samples,” says Orlofsky. “Since this focused and economical screening procedure tells us exactly where to look within a day, we don’t need to monitor hundreds of samples and sub-samples over several days.”

The two techniques used concomitantly are an evolved ‘MPN-type enrichment’ (most probable number) used in microbiology testing, coupled with 'qPCR' (quantitative polymerase chain reaction) widely used in molecular biology to monitor the amplification of DNA in real time.

“We considerably shortened previous protocols, do not use any name-brand expensive reagents for DNA extraction and purification, and increased the procedure and workflow to segue easily from raw sample to qPCR assays,” said Orlofsky.

While detection in soil, water and vegetable samples was highly sensitive (as low as one cell per test), the researchers believe additional steps are required to further improve the detection levels such that they reflect low pathogen concentrations (especially ones with low infective doses) in aerosols.

The researchers recommend applying this method in the future to other pathogens such as Legionella pneumophilia (Legionnaire's Disease), Staphylococcus aureus (Staph infection) and Campylobacter jejuni, the second most common cause of foodborne illness.