Design and preliminary results of a DNA chip for the detection of microorganisms in water samples

Waterborne pathogens are responsible for several diseases, either due to the consumption of contaminated drinking water or due to the contact with polluted recreational waters. There is an increasing awareness that emergent and viral pathogens should also be monitored for determining water quality. Conventional detection methodologies present several shortcomings, such as reliance in indicator species, low throughput and increasing resources as more species are to be detected. DNA chips have the potential to serve as surveillance systems for the simultaneous detection of pathogens, overcoming these limitations. In the present study, a rapid method for the detection of multiple waterborne pathogens (bacteria and viruses) was developed, using a DNA chip (AQUACHIP®). Species and group specific probes were implemented on a DNA chip, both for mandatory and non-mandatory microorganisms. Considerations regarding the AQUACHIP® design (probe layout, replicates and dilutions), DNA labelling and amplification, and preliminary results of the application of the chip for the detection of E. coli DNA are presented.