A loop-mediated isothermal amplification assay to detect Bacteroidales and assess risk of fecal contamination

Abstract

Fecal contamination of fresh produce from human and animal sources is a public health concern due to the risk of foodborne illnesses. The current standard laboratory procedures for microbiological analyses usually require an enrichment step that involves several hours. Molecular techniques such as polymerase chain reaction (PCR) have been used to directly detect pathogens from the samples, however, due to the low quantity of pathogen present and small volumes used for PCR, enrichment is usually required. Additionally, the need for specialized equipment and experienced workers hinders the use of these molecular techniques for field testing. Here, we developed a rapid risk-assessment assay for fecal contamination by targeting Bacteroidales using loop-mediated isothermal amplification (LAMP). The assay allows for naked-eye observation of reactions with as few as ∼8 copies of Bacteroidales per cm2 of the surface in the field. We evaluated this assay with complex field samples as well as on-site field studies. Our on-field studies demonstrated that the Bacteroidales LAMP assay enables us to easily and quickly (<50 min) assess the risk of fecal contamination from animal operations, with a concordance of 85.3% when compared to lab-based qPCR. These results were obtained without expensive equipment (when compared to standard laboratory procedures). These assays could be used to determine site-specific risk and help the decision-making process of fresh produce growers.