دورية أكاديمية
A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing
| العنوان: | A common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing |
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| المؤلفون: | Kathy E. Raven, Sophia T. Girgis, Asha Akram, Beth Blane, Danielle Leek, Nicholas Brown, Sharon J. Peacock |
| المصدر: | Scientific Reports, Vol 11, Iss 1, Pp 1-8 (2021) |
| بيانات النشر: | Nature Portfolio, 2021. |
| سنة النشر: | 2021 |
| المجموعة: | LCC:Medicine LCC:Science |
| مصطلحات موضوعية: | Medicine, Science |
| الوصف: | 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. |
| نوع الوثيقة: | article |
| وصف الملف: | electronic resource |
| اللغة: | English |
| تدمد: | 2045-2322 74026658 |
| Relation: | https://doaj.org/toc/2045-2322 |
| DOI: | 10.1038/s41598-020-80031-8 |
| URL الوصول: | https://doaj.org/article/524e6a03bd824fdd928c746c74026658 |
| رقم الأكسشن: | edsdoj.524e6a03bd824fdd928c746c74026658 |
| قاعدة البيانات: | Directory of Open Access Journals |
Full Text Finder | تدمد: | 20452322 74026658 |
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| DOI: | 10.1038/s41598-020-80031-8 |