Panel of three loop-mediated isothermal amplification assays differentiates Rathayibacter toxicus populations RT-I, RT-II, RT-III, RT-IV and RT-V

Abstract

Rathayibacter toxicus is a nematode-vectored (Anguina sp.) plant-pathogenic (Poaceae; grasses) bacterium that secretes a toxin, which can cause fatalities in livestock and horses that ingest diseased plant material. The lethal toxicoses associated with R. toxicus are annual ryegrass toxicity and flood plain staggers. Currently, this bacterium is confined to certain areas of Australia and South Africa. Previous studies have shown that populations from Western Australia (RT-III) are genetically distinct from populations from South Australia (RT-II). A recent study discovered a newly emerged population in South Australia (RT-I), distinct from both Western and South Australian populations studied previously. In this study, a six-gene MLST delineated five distinct genetic populations. Phenotypic significance of these different populations is not yet known. A set of molecular-based assays for the specific detection of R. toxicus has been developed. Described here are loop-mediated isothermal amplification (LAMP) assays for rapid identification and differentiation of R. toxicus populations in the field or laboratory. These assays can be used subsequent to an R. toxicus-specific field assay, allowing on-site determination of population type. This will allow informed field sampling to collect populations of interest, as well as track the movement of populations to new areas.