Ion Torrent whole genome sequencing of Klebsiella pnemoniae OXA-48 strain 1191100241
Concentration of reconstituted genomic DNA was determined with the Qubit dsDNA BR Assay (Life Technologies). Library preparation was performed with the Ion Fragment Library Kit (Life Technologies) according to the protocol (part no. 4467320 rev. A, 04/2011) with minor modifications. Size selection was done with the Caliper LabChip® XT (Caliper Life Sciences, Mainz, Germany).  Template preparation was carried out with the Ion XpressTM Template Kit (Life Technologies) according to the Ion XpressTM Template Kit User Guide (part no. 4467389 Rev. B, 05/2011) with a modified protocol for Ion SphereTM recovery (Recovery Steps 1.f to 4.b). Emulsified Ion SphereTM particles were collected by centrifugation (2200 g for 8 min) in a SOLiD® emulsion collection tray (Life Technologies). After centrifugation a clear oil phase developed above a white solid  pellet. The oil layer was decanted and pelleted Ion Spheres were resuspended with 700 µl of breaking solution followed by two washes of the emulsion collection tray with breaking solution. In a departure from the User Guide, all three fractions were pooled in the same 2.0 ml reaction tube. Washing of the recovered Ion Sphere particles was performed as described in the original protocol (Steps 4.c and following).
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Klebsiella pnemoniae OXA-48 strain 1191100241