Similar comparisons have not been performed forP. agglomerans, leaving a gap in knowledge critical to regulatory authorities. The aim of our study was to perform a polyphasic genotypic and phenotypic analysis ofP. agglomeransisolates of diverse origin in order to understand whether clinical and biocontrol (environmental) isolates can be distinguished and have undergone a discrete evolution that would indicate specialization towards human
pathogenicity or an epiphytic lifestyle. The taxonomy of a collection of clinical and plant isolates was assessed using fluorescent amplified fragment length polymorphism CA3 datasheet (fAFLP) analysis of total genomic DNA and sequence analyses of specific genes (such as 16S rDNA generrs,gyrBencoding DNA gyrase subunit B, and theP. agglomeransquorum-sensing regulatory genespagRIencoding homoserine lactone receptor and synthase) [34]. The fAFLP analysis was used as well to search for CX-5461 clinical trial random molecular markers that could serve as a simple and rapid discriminatory marker for clinical and biocontrol strains. Additionally, we examined the distribution of some phenotypic and genotypic traits among strains that may reflect adaptation to the different lifestyles proposed forP. agglomerans, such as growth at 37°C for clinical isolates, presence of pantocin
A genes or sorbitol utilization for biocontrol strains, and presence of type III secretion system (T3SS) for plant pathogenic pathovars. Methods Bacterial strains Thirty-two clinical isolates designated asP. agglomerans,E. agglomerans,E. herbicolaorPantoeaspp. were obtained from the American Type Culture Collection (ATCC,http://www.atcc.org/), the Belgian Coordinated Collection of Microorganisms (BCCM/LMG,http://bccm.belspo.be), the Institut Pasteur Collection (CIP,http://www.crbip.pasteur.fr/), the Spanish Type Culture Collection (CECT,http://www.cect.org/) Ribonucleotide reductase or received from the Hospital de la Santa Crei Sant Pau (Barcelona, Spain) and the Istituto Cantonale di Microbiologia (ICM, Bellinzona, Switzerland). ElevenP. agglomeransstrains with established
biocontrol activity obtained from several sources (including the three currently registered commercial strains), twenty environmental isolates and three phytopathogenic strains, together with representative strains of otherPantoeaspecies and closely related genera such asErwinia,PectobacteriumandBrenneria, were included in the study for comparison (see Additional file 1 – Table S1). DNA extraction and PCR amplification DNA of each bacterial isolate was extracted with the Wizard®Genomic DNA Purification Kit (Promega, Dübendorf, Switzerland) from 1.5 ml aliquots of overnight cultures at 28°C in Luria Bertani (LB) Histone Methyltransferase inhibitor medium. Obtained genomic DNA was quantified on a NanoDrop 1000 spectrophotometer (Thermo Scientific, Wilmington, U.S.A.) and 10-20 ng of genomic DNA were used for each PCR reaction.