Universidad Peruana Cayetano Heredia

Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears

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dc.contributor.author Rowneki, M.
dc.contributor.author Aronson, N.
dc.contributor.author Du, P.
dc.contributor.author Sachs, P.
dc.contributor.author Blakemore, R.
dc.contributor.author Chakravorty, S.
dc.contributor.author Levy, S.
dc.contributor.author Jones, A.L.
dc.contributor.author Trivedi, G.
dc.contributor.author Chebore, S.
dc.contributor.author Addo, D.
dc.contributor.author Byarugaba, D.K.
dc.contributor.author Njobvu, P.D.
dc.contributor.author Wabwire-Mangen, F.
dc.contributor.author Erima, B.
dc.contributor.author Ramos, E.S.
dc.contributor.author Evans, Carlton Anthony William
dc.contributor.author Hale, B.
dc.contributor.author Mancuso, J.D.
dc.contributor.author Alland, D.
dc.date.accessioned 2020-12-14T16:10:08Z
dc.date.available 2020-12-14T16:10:08Z
dc.date.issued 2020
dc.identifier.uri https://hdl.handle.net/20.500.12866/8788
dc.description.abstract Background: Drug susceptibility testing for Mycobacterium tuberculosis (MTB) is difficult to perform in resource-limited settings where Acid Fast Bacilli (AFB) smears are commonly used for disease diagnosis and monitoring. We developed a simple method for extraction of MTB DNA from AFB smears for sequencing-based detection of mutations associated with resistance to all first and several second-line anti-tuberculosis drugs. Methods: We isolated MTB DNA by boiling smear content in a Chelex solution, followed by column purification. We sequenced PCR-amplified segments of the rpoB, katG, embB, gyrA, gyrB, rpsL, and rrs genes, the inhA, eis, and pncA promoters and the entire pncA gene. Results: We tested our assay on 1,208 clinically obtained AFB smears from Ghana (n = 379), Kenya (n = 517), Uganda (n = 262), and Zambia (n = 50). Coverage depth varied by target and slide smear grade, ranging from 300X to 12000X on average. Coverage of ≥20X was obtained for all targets in 870 (72%) slides overall. Mono-resistance (5.9%), multi-drug resistance (1.8%), and poly-resistance (2.4%) mutation profiles were detected in 10% of slides overall, and in over 32% of retreatment and follow-up cases. Conclusion: This rapid AFB smear DNA-based method for determining drug resistance may be useful for the diagnosis and surveillance of drug-resistant tuberculosis. This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication. en_US
dc.language.iso eng
dc.publisher Public Library of Science
dc.relation.ispartofseries PLoS ONE
dc.rights info:eu-repo/semantics/restrictedAccess
dc.rights.uri https://creativecommons.org/licenses/by-nc-nd/4.0/deed.es
dc.subject Mutation detection en_US
dc.subject Extensively drug-resistant tuberculosis en_US
dc.subject Tuberculosis en_US
dc.subject Mycobacterium tuberculosis en_US
dc.subject Polymerase chain reaction en_US
dc.subject DNA isolation en_US
dc.subject Mutation en_US
dc.subject Ghana en_US
dc.title Detection of drug resistant Mycobacterium tuberculosis by high-throughput sequencing of DNA isolated from acid fast bacilli smears en_US
dc.type info:eu-repo/semantics/article
dc.identifier.doi https://doi.org/10.1371/journal.pone.0232343
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#3.02.07
dc.subject.ocde https://purl.org/pe-repo/ocde/ford#3.01.05
dc.relation.issn 1932-6203


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