Genetic fingerprinting of Erwinia amylovora strains isolated from tree-fruit crops and Rubus spp.

Genetic fingerprints were determined for 189 strains of Erwinia amylovora isolated from different hosts from fruit-producing regions in North America and New Zealand using two polymerase chain reaction (PCR)-based techniques. For repetitive element PCR (rep-PCR), outward-facing oligonucleotide primers complementary to the ends of highly conserved, repetitive, extragenic sequences directed amplification of DNA between adjacent repetitive elements. Identical rep-PCR fingerprints were detected among 87% of the tree fruit strains, and similarity coefficients based on shared rep-PCR products ranged from 96 to 99% among tree-fruit strains that differed in at least one rep-PCR product. Strains isolated from Rubus spp. were genetically more heterogeneous, with no predominant rep-PCR fingerprints, and similarity coefficients based on shared rep-PCR products ranged from 89 to 97%. Several major rep-PCR products distinguished tree-fruit strains from Rubus strains. For PCR ribotyping, oligonucleotide primers directed amplification of the 16S-23S spacer region of the rrn operon(s). Four distinct PCR-ribotype fingerprints (PCR-ribotypes 1 through 4) were detected among strains of E. amylovora. PCR-ribotype 1 was common among 100, 97, and 27% of tree-fruit isolates from New Zealand, eastern North America, and the western United States, respectively. Strains of PCR-ribotype 2 were rare, accounting for only 4% of the strains from the western United States. Strains of PCR-ribotype 3 were found primarily in the western United States, and strains of PCR-ribotype 4 were all isolated from Rubus spp. Out of 11 strains of E. herbicola isolated from various hosts and locations, no 2 strains produced identical rep-PCR fingerprints using any of the three rep-PCR primer sets, but all strains of E. herbicola were PCR-ribotype 5. We conclude that strains of E. amylovora isolated from fruit trees are genetically homogeneous and can be distinguished from strains isolated from Rubus spp. using simple, rapid PCR techniques.