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dc.contributor.authorRaven, Kathy E.
dc.contributor.authorGirgis, Sophia T.
dc.contributor.authorAkram, Asha
dc.contributor.authorBlane, Beth
dc.contributor.authorLeek, Danielle
dc.contributor.authorBrown, Nicholas
dc.contributor.authorPeacock, Sharon J.
dc.date.accessioned2021-01-08T17:22:14Z
dc.date.available2021-01-08T17:22:14Z
dc.date.issued2021-01-08
dc.date.submitted2020-06-08
dc.identifier.others41598-020-80031-8
dc.identifier.other80031
dc.identifier.urihttps://www.repository.cam.ac.uk/handle/1810/315931
dc.description.abstractAbstract: 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.
dc.languageen
dc.publisherNature Publishing Group UK
dc.rightsAttribution 4.0 International (CC BY 4.0)en
dc.rights.urihttps://creativecommons.org/licenses/by/4.0/en
dc.subjectArticle
dc.subject/631/208/325/2482
dc.subject/692/699/255/1318
dc.subject/692/700/478
dc.subject/631/326
dc.subject/631/337
dc.subjectarticle
dc.titleA common protocol for the simultaneous processing of multiple clinically relevant bacterial species for whole genome sequencing
dc.typeArticle
dc.date.updated2021-01-08T17:22:13Z
prism.issueIdentifier1
prism.publicationNameScientific Reports
prism.volume11
dc.identifier.doi10.17863/CAM.63042
dcterms.dateAccepted2020-12-09
rioxxterms.versionofrecord10.1038/s41598-020-80031-8
rioxxterms.versionVoR
rioxxterms.licenseref.urihttp://creativecommons.org/licenses/by/4.0/
dc.identifier.eissn2045-2322
pubs.funder-project-idHealth Innovation Challenge Fund (WT098600, HICF-T5-342)


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Attribution 4.0 International (CC BY 4.0)
Except where otherwise noted, this item's licence is described as Attribution 4.0 International (CC BY 4.0)