Field evaluation of microfluidic paper-based analytical devices for microbial source tracking

Animal-specialty crop interface poses risk factors that can lead to the contamination of fresh produce with foodborne pathogens. Current practices include collecting samples from the crop and sending them to a lab for testing. These methods, typically based on culturing or quantitative polymerase chain reaction, are slow and can require several days to provide a result. Thus, it is challenging to obtain detailed spatial information (for example, a heat map of proximity zones from animal feeding operations to plan growing strategies) or to obtain rapid results (for example, on an hourly basis during harvest to determine when the tools should be cleaned). In this proposal, our overall goal is to build and test a field-deployable microfluidic paper-based analytical device to determine contamination events. We will determine the levels of fecal and pathogenic contamination that are naturally present in fields, on harvest tools, and around animal feeding operations to establish a baseline (Objective 1). We will also optimize our microfluidic paper-based analytical device by testing samples in the lab and the field (Objective 2).
We will use Bacteroidetes as indicator organisms for fecal contamination because of differences between the types of Bacteroidetes found in different hosts (humans, poultry, swine, and ruminants). These bacteria are currently used for tracking the source of fecal contamination in water and this process is known as microbial source tracking. To detect these bacteria, we will target specific sequences of DNA within their genome using an isothermal amplification method call loop-mediated isothermal amplification. Since this method only requires heating at a constant temperature (instead of cycling of temperature as in polymerase chain reaction), it is easier to design a portable device to conduct DNA amplification. Additionally, storing the reagents required for loop-mediated isothermal amplification on microfluidic paper-based analytical devices makes the assay user-friendly because the user does not need to handle multiple reagents. Using the same method, we will also detect Shiga toxin-producing Escherichia coli and Salmonella to enable a tool for making decisions during harvest.
For objective 1, we will collect almost 2000 samples in the form of culture swabs from romaine lettuce, harvest tools, and animal feeding operations. We will characterize the fecal and pathogenic bacterial levels in these samples using an established method (quantitative polymerase chain reaction) and compare it to our novel method (quantitative loop-mediated isothermal amplification). With these data, we will be able to provide insight into methods for characterizing proximity zones around animal feeding operations and animal intrusion. For objective 2, we will test 150 samples in the lab and 200 samples in the field after optimizing the microfluidic paper-based analytical devices and portable detection system. We will compare the results of our portable system to a commercially available lab-based system and aim to provide similar results in under an hour. The anticipated outcome of this project is a validated field-deployable growers’ risk assessment biomarkers investigative tool that enables science-based approaches to measure and manage risk at the interface of animals and specialty crops.