The use of two complementary DNA assays, AFLP and MLSA, for epidemic and phylogenetic studies of pectolytic enterobacterial strains with focus on the heterogeneous species Pectobacterium carotovorum

Amplified fragment length polymorphism (AFLP) markers and multilocus sequence analysis (MLSA) were used to analyse 63 bacterial strains, including 30 soft-rot-causing bacterial strains collected from Syrian potato fields and 33 reference strains. For the MLSA, additional sequences of 41 strains of Pectobacterium and Dickeya, available from the NCBI GenBank, were included to produce a single alignment of the 104 taxa for the seven concatenated genes (acnA, gapA, proA, icd, mtlD, mdh and pgi). The results indicate the need for a revision of the previously classified strains, as some potato-derived Pectobacterium carotovorum strains were re-identified as P.similar to wasabiae. The strains that were classified as P.similar to carotovorum during the analyses demonstrated high heterogeneity and grouped into five P.similar to carotovorum highly supported clusters (PcI to PcV). The strains represented a wide range of host plants including potatoes, cabbage, avocados, arum lilies, sugar cane and more. Host specificity was detected in PcV, in which four of the six strains were isolated from monocotyledonous plants. The PcV strains formed a clearly distinct group in all the constructed phylogenetic trees. The number of strains phylogenetically classified as subspecies P.similar to c.similar to subsp.similar to brasiliensis in PcIV dramatically increased in size as a result of the characterization of new isolates or re-identification of previous P.similar to carotovorum and P.similar to atrosepticum strains. The P.similar to carotovorum strains from Syria were grouped into PcI, PcII and PcIV. This grouping indicates a lack of correlation between the geographical origin and classification of these pathogens.