Strain CECT 4842, is retrievable asE. herbicolabut listed asP. agglomeransdespite the fact that our 16S rDNA data suggests this
strain isKlebsiella, and strain CECT 842 received by us asE. agglomeransisolated from human feces has now been designated as the type strain of BL-2Cedecea davisae[56]. In the BCCM/LMG collection (Belgian Co-ordinated Collections of Micro-organisms/Laboratorium voor Microbiologie, Universiteit Gent) many strains received as clinicalE. agglomeransisolates are awaiting reclassification and are now considered “”unidentified”" BIX 1294 manufacturer (see Additional file 1 – Table S1). Most of theP. agglomeransstrains obtained from the ATCC, particularly those of clinical origin, were found in our analysis to belong to other species. Thus, incorrect taxonomy is a major problem in terms of biosafety classification ofP. agglomerans. Figure 8 Taxonomic rearrangements undergone by the E. agglomerans/E. Selleck GDC-0449 herbicola complex in the last decades and attempts to assign still unassigned biotypes to known species. Strains belonging to theE. agglomerans/E. herbicolacomplex were described
as early as 1888 [59] and included organisms that were saprophytes or plant pathogens [60,61] or (opportunistic) pathogens in humans [61]. The nameE. agglomeranswas proposed by Ewing and Fife [50] after comparing plant and animal isolates as a subjective synonym for all threeErwiniaspecies in the Herbicola group which was created in the meantime, i.e.,E. herbicola,E. stewartii(nowP. stewartii) andE. uredvora[62]. In this process, otherEnterobacterstrains may have been included in the new species. Brenner et al. [41] attempted to classifyE. agglomeransstrains by DNA hybridization and phenotypic tests deciding upon 13 biotypes. Subsequent classification efforts assigned several of the Brenner biotypes to new species, includingP. agglomerans,P. dispersa,P. ananatisorLeclercia adecarboxylata[1,52,54], but for most reclassification with definitive assignment remains open.
For these still unnamed biotypes an approximate classification, based on strain Bay 11-7085 phylogeny (Figure 1 & 2) or 16S rDNA andgyrBsequence similarity (see Additional file 2- Table S2) is projected above. We identified a single discriminatory marker for biocontrol strains using fAFLP which may be of use in biosafety decisions for registration of beneficial isolates. Only biocontrol isolates had this fAFLP band, eventhough all strains ofP. agglomerans sensu strictohave indication of the gene found within the band. For MAPK inhibitor differentiation purposes this is irrelevant since the purpose is to identify a genomic marker, not a specific gene. Our polyphasic analysis indicated that clinical and biocontrol strains co-cluster withinP. agglomerans sensu stricto.