Stability of short sequence repeats and their application for the characterization of Erwinia amylovora strains

Abstract

A motif of eight nucleotides (GAATTACA) reiterated 3 to 15 times within the PstI fragment of the pEa29 plasmid was found in Erwinia amylovora strains representing a valuable typing method for this pathogen. The stability of short sequence DNA repeat (SSR) numbers was investigated to determine the suitability of this marker for strain differentiation. The number of SSR units was found to be stable under laboratory and certain stress conditions. This meets the requirements for a suitable genetic marker that should be stable upon cultivation of strains. Therefore, this SSR marker was used for strain differentiation from SSR-3 to SSR-15 and a large number of E. amylovora strains from Austria was screened for their SSR numbers for epidemiological identification purposes. Traceability was possible if strains had very high or very low SSR numbers.