Genotyping of bacteria belonging to the former Erwinia genus by PCR-RFLP analysis of a recA gene fragment.
Genotypic characterization, based on the analysis of restriction fragment length polymorphism of the recA gene fragment PCR product (recA PCR-RFLP), was performed on members of the former Erwinia genus. PCR primers deduced from published recA gene sequences of Erwinia carotovora allowed the amplification of an approximately 730 bp DNA fragment from each of the 19 Erwinia species tested. Amplified recA fragments were compared using RFLP analysis with four endonucleases (Alul, Hinfl, Tasl and Tru1l), allowing the detection of characteristic patterns of RFLP products for most of the Erwinia species. Between one and three specific RFLP groups were identified among most of the species tested (E. amylovora, E. ananas [Pantoea ananatis], E. cacticida, E. cypripedii, E. herbicola [P. agglomerans], E. mallotivora, E. milletiae [P. agglomerans pv. millettiae], E. nigrifluens, E. persicina [E. persicinus], E. psidii, E. quercina, E. rhapontici, E. rubrifaciens, E. salicis, E. stewartii [P. stewartii], E. tracheiphila, E. uredovora [P. ananatis pv. uredovora], E. carotovora subsp. atroseptica, E. carotovora subsp. betavasculorum, E. carotovora subsp. odorifera and E. carotovora subsp. wasabiae). However, in two cases, E. chrysanthemi and E. carotovora subsp. carotovora, 15 and 18 specific RFLP groups were detected, respectively. The variability of genetic patterns within these bacteria could be explained in terms of their geographic origin and/or wide host-range. The results indicated that PCR-RFLP analysis of the recA gene fragment is a useful tool for identification of species and subspecies belonging to the former Erwinia genus, as well as for differentiation of strains within E. carotovora subsp. carotovora and E. chrysanthemi.