Agdia, Inc has commercialized a rapid and user-friendly DNA test kit, based on their AmplifyRP XRT+ platform, for detection of Clavibacter michiganensis ssp. sepedonicus (Cms).
Cms is the causal agent of bacterial ring rot (BRR) in potato. It is primarily spread through infected seedstock and/or through contaminated farm equipment. Cms is a zero-tolerance pathogen in U.S. seed potato certification programs and can have substantial financial implications for a grower if his stock or field is found to be Cms-positive.
AmplifyRP XRT+ for Cms is an isothermal amplification technology that utilizes recombinase polymerase amplification (RPA) to rapidly amplify and detect fragments of Cms DNA. It does so with the same level of sensitivity and specificity as laboratory-based PCR methods but offers some clear advantages. AmplifyRP XRT+ can be used with crude sample extracts and does not require nucleic acid purification. Impressively, the total assay time is only about 20 minutes, including sample preparation. This is a stark contrast to PCR methods, which can take hours or days to complete. PCR analysis must also be completed in a laboratory by trained, skilled technicians, whereas AmplifyRP XRT+ can be performed on-site.
Agdia has validated its new assay against a collection of more than 30 Cms strains and 24 other strains of plant pathogenic bacteria. During this analysis, the assay classified 100 percent of the isolates correctly as either positive or negative. In comparison to commonly used PCR methods, such as those using CelA and Cms50 primer sets, the AmplifyRP XRT+ assay was equally as sensitive analytically.
Agdia’s AmplifyRP XRT+ platform is highly flexible and provides results in real time using a portable fluorometer called the AmpliFire (Image 1). Alternatively, the assay can be performed using a small portable heat block (Image 2), with results being visualized post-amplification in an Amplicon Detection Chamber. This allows end users who don’t want to invest in a fluorometer as an alternative method of running the test.
Agdia’s AmplifyRP XRT+ kit for Cms includes 48 reactions and the necessary buffers to perform the test. If performing the test as a real-time assay, the end user will need to purchase the AmpliFire separately. The AmpliFire is battery-operated and has a small footprint, making it possible to test in remote locations. Setup is simple because all the assay parameters are loaded into the AmpliFire using a barcode affixed to the test packaging. It also has a large, intuitive touchscreen interface that is used to initiate reactions and view results. More information on the AmpliFire can be found on Agdia’s website.
If the end user runs the test as an end-point detection assay, the user will need to purchase Amplicon Detection Chambers, as well as a starter pack, separately. The starter pack includes a heat block (necessary for the amplification step) as well as pipettes, pipette tips and a tube rack.