Mycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate secondline genotypic drug susceptibility testing and spoligotyping

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dc.contributor.authorVenter, Rouxjeaneen_ZA
dc.contributor.authorDerendinger, Brigittaen_ZA
dc.contributor.authorDe Vos, Margarethaen_ZA
dc.contributor.authorPillay, Samanthaen_ZA
dc.contributor.authorDolby, Tanyaen_ZA
dc.contributor.authorSimpson, Johnen_ZA
dc.contributor.authorKitchin, Natashaen_ZA
dc.contributor.authorRuiters, Ashleyen_ZA
dc.contributor.authorVan Helden, Paul D.en_ZA
dc.contributor.authorWarren, Robin M.en_ZA
dc.contributor.authorTheron, Granten_ZA
dc.date.accessioned2018-01-22T06:50:54Z
dc.date.available2018-01-22T06:50:54Z
dc.date.issued2017-11-01
dc.descriptionCITATION: Venter, R., et al. 2017. Mycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate secondline genotypic drug susceptibility testing and spoligotyping. Scientific Reports, 7:14854, doi:10.1038/s41598-017-14385-x.
dc.descriptionThe original publication is available at http://www.nature.com
dc.descriptionPublication of this article was funded by the Stellenbosch University Open Access Fund.
dc.description.abstractENGLISH ABSTRACT: Xpert MTB/RIF (Xpert) is a widely-used test for tuberculosis (TB) and rifampicin-resistance. Second-line drug susceptibility testing (DST), which is recommended by policymakers, typically requires additional specimen collection that delays effective treatment initiation. We examined whether cartridge extract (CE) from used Xpert TB-positive cartridges was, without downstream DNA extraction or purification, suitable for both genotypic DST (MTBDRplus, MTBDRsl), which may permit patients to rapidly receive a XDR-TB diagnosis from a single specimen, and spoligotyping, which could facilitate routine genotyping. To determine the limit-of-detection and diagnostic accuracy, CEs from dilution series of drug-susceptible and -resistant bacilli were tested (MTBDRplus, MTBDRsl). Xpert TB-positive patient sputa CEs (n = 85) were tested (56 Xpert-rifampicin-susceptible, MTBDRplus and MTBDRsl; 29 Xpert-rifampicin-resistant, MTBDRsl). Spoligotyping was done on CEs from dilution series and patient sputa (n = 10). MTBDRplus had high non-valid result rates. MTBDRsl on CEs from dilutions ≥103CFU/ml (CT ≤ 24, >“low” Xpert semiquantitation category) was accurate, had low indeterminate rates and, on CE from sputa, highly concordant with MTBDRsl isolate results. CE spoligotyping results from dilutions ≥103CFU/ml and sputa were correct. MTBDRsl and spoligotyping on CE are thus highly feasible. These findings reduce the need for additional specimen collection and culture, for which capacity is limited in high-burden countries, and have implications for diagnostic laboratories and TB molecular epidemiology.en_ZA
dc.description.urihttps://www.nature.com/articles/s41598-017-14385-x
dc.description.versionPublisher's version
dc.format.extent9 pages : illustrationsen_ZA
dc.identifier.citationVenter, R., et al. 2017. Mycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate secondline genotypic drug susceptibility testing and spoligotyping. Scientific Reports, 7: 14854, doi:10.1038/s41598-017-14385-x
dc.identifier.issn2045-2322 (Online)
dc.identifier.issn2045-2322 (Print)
dc.identifier.otherdoi:10.1038/s41598-017-14385-x
dc.identifier.urihttp://hdl.handle.net/10019.1/103063
dc.language.isoen_ZAen_ZA
dc.publisherSpringer Natureen_ZA
dc.rights.holderAuthors retain copyrighten_ZA
dc.subjectMycobacterium tuberculosisen_ZA
dc.subjectGenomes -- DNAen_ZA
dc.subjectPharmacogenomics -- Testingen_ZA
dc.titleMycobacterial genomic DNA from used Xpert MTB/RIF cartridges can be utilised for accurate secondline genotypic drug susceptibility testing and spoligotypingen_ZA
dc.typeArticleen_ZA
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