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Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens

Clark, SA; Doyle, R; Lucidarme, J; Borrow, R; Breuer, J; (2018) Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens. International Journal of Medical Microbiology , 308 (2) pp. 256-262. 10.1016/j.ijmm.2017.11.004. Green open access

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Abstract

In England and Wales, approximately one half of all laboratory-confirmed meningococcal disease cases fail to yield a viable invasive isolate, primarily due to the use of antibiotics. Characterisation of non-culture meningococci has been restricted to the detection or sequencing of specific gene targets within clinical specimens. In this study we investigated the ability of the Agilent SureSelectXT kit to facilitate DNA enrichment and genome sequencing of meningococcal DNA within a small panel of blood and CSF specimens. A target-specific RNA oligonucleotide bait library was used to capture and enrich the bacterial DNA prior to next generation sequencing. A positive correlation between meningococcal DNA amount and genome coverage was observed with eight of the ten specimens producing genomes of acceptable quality. All commonly-used typing information derived from each acceptable non-culture genome matched those of an isolate from the same patient and the paired genomes showed a high level of congruence across indexed loci. We estimate that this technique could be used to perform whole genome sequencing on up to ∼45% of the positive specimens received by the Public Health England's Meningococcal Reference Unit. Further optimisation of the extraction and/or enrichment processes may, however, increase the proportion of non-culture cases from which quality genomes can be obtained.

Type: Article
Title: Targeted DNA enrichment and whole genome sequencing of Neisseria meningitidis directly from clinical specimens
Location: Germany
Open access status: An open access version is available from UCL Discovery
DOI: 10.1016/j.ijmm.2017.11.004
Publisher version: http://dx.doi.org/10.1016/j.ijmm.2017.11.004
Language: English
Additional information: Crown Copyright © 2017 Published by Elsevier GmbH. This is an open access article under the OGL license (http://www.nationalarchives.gov.uk/doc/open-government-licence/version/3/).
Keywords: Clinical specimens, DNA enrichment, Meningococcal, RNA baits, Whole genome sequencing
UCL classification: UCL
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health
UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Population Health Sciences > UCL GOS Institute of Child Health > Infection, Immunity and Inflammation Dept
URI: https://discovery.ucl.ac.uk/id/eprint/10041551
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