Team:NYU Abu Dhabi/Description
The most common type of bacterial infection stems from contact with Escherichia coli , which when ingested can cause a variety of symptoms ranging from nausea to diarrhea. Shiga toxin-producing E. coli (STECs) are responsible for the majority of foodborne E. coli infections because the shiga toxin produced inhibits protein synthesis in all cells. While most countries now have stringent food safety regulations in place to prevent the sale of contaminated foods, small scale manufacturers, particularly street food vendors, often do not have access, time or pressure to consult laboratories about the safety of their food. Therefore, STEC-illnesses are still a major problem in countries that revolve around street food.
Our project aims to produce a portable device that allows for the detection of STEC through the use of loop-mediated isothermal amplification (LAMP), a technique that is similar to, but more sensitive than, polymerase chain reaction (PCR). Using the LAMP technique, we are targeting the genes that have been identified in shiga-toxin producing E. coli, namely stx1B, stx2B, rfbE, and eae. For each gene, we designed a set of 4-6 primers, which includes the forward and backward outer primers, the forward and backward inner primers, and the forward and backward loop primers if applicable. The forward inner primer initiates the amplification, followed by the strand-displacing DNA polymerase which separates the target DNA duplex. Synthesis initiated by the forward outer primer at an upstream target region subsequently displaces the first product, causing a stem-loop structure to form at the end of the first product due to the inner primer sequence complementarity. The annealing and strand-displacing processes continue from the opposite direction, yielding a dumbbell-shaped structure that contains more annealing sites at the inner primer sequences for further amplification.
In order to ease the use of this technique for food vendors, we are building a device that will consist of two main components: the heater and a custom-made cartridge. The cartridge will contain three different chambers connected by pipes and valves. The first chamber is a cooking chamber where the samples will be heated to 95℃ to trigger the lysis process. The second chamber is where the LAMP technique will occur, with a chamber temperature of approximately 65℃ for the amplification reaction to occur. The result of the amplification can be visualized by a colorimetric assay using a color-changing dye in the third chamber. The reaction tubes will be prepared in powder form and premixed, ensuring that the user only needs to insert their food sample for testing. The device is also designed such that the cartridge is easily disposable and a new cartridge can be inserted every time the customer want to check a food sample. This ensures that the whole setup will be clear from contamination.
The end goal of our project is to provide food vendors an opportunity to easily and quickly detect for the presence of STEC in their products to ensure that they are complying with government standards efficiently and conveniently. The results of each test will eventually be uploaded into a database that provides consumers with the date, location and result of each STEC test. This will ensure that both vendor and consumer are safe, leading to a decrease in the incidence of foodborne E.coli infections.
