151. A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing
- Author
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Beth Blane, Danielle Leek, Sharon J. Peacock, Nicholas M. Brown, Kathy E. Raven, Asha Akram, Sophia T. Girgis, Peacock, Sharon [0000-0002-1718-2782], and Apollo - University of Cambridge Repository
- Subjects
0301 basic medicine ,DNA, Bacterial ,Time Factors ,Molecular biology ,Science ,030106 microbiology ,631/208/325/2482 ,Computational biology ,Biology ,Microbiology ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Antibiotic resistance ,Bacterial genetics ,Humans ,Gene ,631/326 ,Whole genome sequencing ,Protocol (science) ,692/700/478 ,Public health ,Multidisciplinary ,Bacteria ,Whole Genome Sequencing ,Lysostaphin ,DNA extraction ,Clinical microbiology ,030104 developmental biology ,chemistry ,692/699/255/1318 ,Medicine ,Bacterial infection ,DNA ,631/337 ,Genome, Bacterial - Abstract
Whole-genome sequencing is likely to become increasingly used by local clinical microbiology laboratories, where sequencing volume is low compared with national reference laboratories. Here, we describe a universal protocol for simultaneous DNA extraction and sequencing of numerous different bacterial species, allowing mixed species sequence runs to meet variable laboratory demand. We assembled test panels representing 20 clinically relevant bacterial species. The DNA extraction process used the QIAamp mini DNA kit, to which different combinations of reagents were added. Thereafter, a common protocol was used for library preparation and sequencing. The addition of lysostaphin, lysozyme or buffer ATL (a tissue lysis buffer) alone did not produce sufficient DNA for library preparation across the species tested. By contrast, lysozyme plus lysostaphin produced sufficient DNA across all 20 species. DNA from 15 of 20 species could be extracted from a 24-h culture plate, while the remainder required 48–72 h. The process demonstrated 100% reproducibility. Sequencing of the resulting DNA was used to recapitulate previous findings for species, outbreak detection, antimicrobial resistance gene detection and capsular type. This single protocol for simultaneous processing and sequencing of multiple bacterial species supports low volume and rapid turnaround time by local clinical microbiology laboratories.
- Published
- 2021