Table 1.
Methods of DNA extraction used in this study, including additional enzymatic and mechanical (bead-beating) cell disruption steps.
| Method | Extraction Method | Commercially Available Kit | Enzymatic Lysis Step Added | Bead-beating |
|---|---|---|---|---|
| M1 | Phenol/chloroform | No | No | No |
| M2 | QIAamp DNA Mini Kit | Yes | No | No |
| M3 | QIAamp DNA Mini Kit | Mutanolysin | No | |
| Yes | Lysozyme | |||
| Lysostaphin | ||||
| M4 | QIAamp DNA Mini Kit | Mutanolysin | 0.1 mm-diameter zirconia/silica beads (BioSpec) | |
| Yes | Lysozyme | |||
| Lysostaphin | ||||
| M5 | PowerLyzer PowerSoil DNA Isolation Kit | Mutanolysin | 0.1 mm-diameter glass beads (MoBio) | |
| Yes | Lysozyme | |||
| Lysostaphin | ||||
| M6 | PowerSoil DNA Isolation Kit | Yes | No | 0.7 mm-diameter garnet (MoBio) |
| M7 | UltraClean Microbial DNA Isolation Kit | Yes | No | 0.7 mm-diameter garnet (MoBio) |
| M8 | BiOstic Bacteremia DNA Isolation Kit | Yes | No | 0.15 mm-diameter garnet (MoBio) |
Enzymes listed in this table are in addition to any lysis buffer included in each kit (either specified, such as proteinase K, or proprietary). All bead-beating was conducted on a FastPrep-24 Instrument (MP Biomedicals) at 6.0 m/s for 40 seconds.