Computational protocol: Mobile Insertion Cassette Elements Found in Small Non-Transmissible Plasmids in Proteeae May Explain qnrD Mobilization

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Protocol publication

[…] Plasmid extraction was performed by the Kieser method from the qnrD-positive strains . Plasmids harboring qnrD were sequenced on both strands using a Walk DS strategy . Nucleotide sequences were aligned using the program BioEdit version 7.09.0 and BLAST searches using the National Center for Biotechnology Information website ( and the blastn algorithms. Putative promoters, ribosome binding site, and transcription start site were searched using BPROM ( and Promoter Prediction by Neural Network .Incompatibility groups of the plasmids were determined using the PCR-based replicon typing (PBRT) as described elsewhere . Briefly, four multiplex PCR were used for the detection of A/C, T, FIIAs, W, N, FIB, L/M, I1-Iγ, X, HI2, FIA, and Y replicons. Replicons P, R, U, F, FIC, and K were detected by simplex PCR, as previously described, and replicons, FII1K, FII2K, NewXXX or also named ZK, LVPK and Amet () as described by D. Decré and G. Arlet. The primer design was based on pGSH500 and pKNP4 (AJ009980 and CP000649 respectively), pLVPK (AY378100) and pK245 (DQ449578), and pMET-1 (EU383016) sequences. […]

Pipeline specifications

Software tools BioEdit, BLASTN, BPROM
Application Genome annotation
Organisms Providencia rettgeri, Proteus vulgaris
Diseases Proteus Syndrome