skirrowii (Tables 1 and 2). Furthermore, the

expected amplicons for A. butzleri and A. skirrowii in individual reactions were also obtained for the eight and three strains of A. CB-839 cibarius, respectively (Table 2). Nevertheless, no cross-reaction with non-targeted species occurred when using primers designed for A. cibarius that reacted only with the eight strains of this species. The combined method of Douidah et al.[9] and De Smet et al.[17], misidentified four of the non-targeted species (Arcobacter defluvii, Arcobacter ellisii, Arcobacter venerupis, and Arcobacter suis) as A. butzleri, and two of the three strains of A. ellisii as A. cryaerophilus (Table 2). The method performed correctly for the four remaining targeted species. Finally, the 16S rRNA-RFLP designed by Figueras et al. [18] was found to misidentify three species (A. trophiarum, A. thereius, and some A. cryaerophilus strains) as A. butzleri. Further to this, A. suis, and A. defluvii produced the same pattern, and two species (A. venerupis, and Arcobacter marinus)

a very PF-562271 chemical structure similar one (Table 2). Because of these limitations, this method has recently been updated selleck kinase inhibitor with new endonucleases; these produced specific results for all strains and species [19]. This updated protocol was the one used to identify all strains used in this study. Comparative evaluation of the targeted genes and designed primers When the results were evaluated in relation to genes used to identify the species, it was observed that the 23S rRNA gene regions targeted in the Kabeya et al.[15] method for A. butzleri, A. cryaerophilus, and A. skirrowii were Galeterone unreliable, as was the region employed in the Houf et al. method [14] for A. cryaerophilus (Tables 1 and Additional file 1: Table S2). However, the regions of the 23S rRNA gene targeted by the m-PCR method of Douidah et al. [9] were 100% reliable for the detection of A. skirrowii, A. cibarius, and A. thereius, but not for A. butzleri (Tables 1, 2 and Additional file 1: Table S2). With regard to the gyrA gene, the region used for the identification of A. cryaerophilus in the latter method, and the one in the method of Pentimalli et al. [16] were unreliable. Despite all strains of A. cryaerophilus being

correctly identified, A. ellisii was confused with this species when using the Douidah et al.[9] method, and with A. skirrowii when using the Pentimalli et al. [16] method (Tables 1 and 2). The main reason for the poor performance of the targeted regions of 23S rRNA or gyrA genes (Additional file 1: Table S2) is the limited amount of sequences used to derive the primers. For instance, the sequences of the 23S rRNA gene are, at the time of writing, only available for eight of the seventeen known Arcobacter species (A. butzleri, A. cryaerophilus, A. skirrowii, A. cibarius, A. nitrofigilis, A. thereius, Arcobacter mytili, and A. trophiarum), and the gyrA gene is only available for seven species (A. butzleri, A. cryaerophilus, A. skirrowii, A. cibarius, A. nitrofigilis, A.