Whole genome sequencing of bacteria is routine in microbiology, epidemiology, and food safety. The extraction step is a persistent bottleneck: column methods take around 2 hours before sequencing can begin.

A collaborative study by Exymes scientists Jo Stanton and David Saul, published in BioTechniques (Vol. 66, No. 5, 2019), compared PDQeX extraction against QIAGEN DNeasy for WGS-ready DNA from six bacterial cultures including thermophilic aerobes with varying cell morphologies.

1. PDQeX: prepGEM Bacteria chemistry in a sealed cartridge. Pre-wash to WGS-ready DNA: under 30 minutes.

2. Comparator: two incubations, multiple pipetting and transfer steps, centrifugation. Approximately 2 hours total.

3. Both methods sequenced on Ion Torrent PGM. On all performance measures: yield, quality, sequencing parameters; PDQeX extracts were comparable to column-purified DNA.

4. 75% time saving per sample. At scale, the operational difference is substantial.