Sera mag speedbeads

PCR products were cleaned using Sera-Mag™ SpeedBeads (Merck KGaA, Darmstadt, Germany) in a Zephyr NGS Workstation (Caliper Lifesciences, Perkin-Elmer; Waltham, MA, USA) and quantified using a Promega dsDNA Quantifluor System Kit (Ref: E2670, 00002484139; Madison, WI, USA) on an Enspire Workstation (Perkin-Elmer; Waltham, MA, USA). The PCR products of all fragments were pooled and normalized to 0.2 ng/µL with 10 mM Tris-HCl (pH 8.0) for library preparation, and final accuracy checks of concentration were performed using the Illumina Nextera XT DNA Library Prep Kit (Illumina, San Diego, CA, USA).

MagnaExtract uses sera‐mag SpeedBeads (MERCK, Germany) magnetic beads that have been diluted and optimized to be more cost‐effective than neat, see supplementary material 1 (S1) (Fouet et al., 2017 ; Rohland & Reich, 2012 (link)). During development of this protocol numerous factors were considered and tested, outlined in Box 1. Each variable was tested in triplicate using an E. coli isolate incubated overnight in buffered peptone water (BPW), a non‐selective enrichment broth and evaluated by comparison of cycle threshold (Ct) values using high‐resolution melt (HRM) PCR for the detection of bla_CTXM‐1, and bla_SHV ARGs, as described by Edwards et al. (2020 (link)). The final method for MagnaExtract is shown in Box 2, incorporating the optimized strategy.