Development and evaluation of a loop-mediated isothermal amplification assay for rapid detection and identification of Pectobacterium atrosepticum

Through exploration of available genomic sequence data for pectolytic bacterial plant pathogens, we identified genomic fragments best suited for developing specific diagnostic assays. A gene cluster encoding a pathogenicity-related phytotoxin similar to coronafacic acid of Pseudomonas syringae was identified as suitable for developing a loop-mediated isothermal amplification (LAMP) assay for rapid identification and detection of Pectobacterium atrosepticum, the causal agent of potato blackleg disease. The LAMP assay differentiates P. atrosepticum from other pectolytic potato pathogens and other bacteria and has a detection sensitivity of 2.5 x 10(2) CFU/mL(-1). Together with a simplified DNA extraction method, the LAMP assay could serve as an easy and rapid method with potential application for on-site disease diagnosis and field surveys.