Academic Journal
Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis
| العنوان: | Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis |
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| المؤلفون: | Hall, M. B., Rabodoarivelo, M. S., Koch, A., Dippenaar, A., George, S., Grobbelaar, M., Warren, R., Walker, T. M., Cox, H., Gagneux, S., Crook, D., Peto, T., Rakotosamimanana, N., Grandjean Lapierre, S., Iqbal, Z. |
| سنة النشر: | 2023 |
| المجموعة: | University of Basel: edoc |
| الوصف: | BACKGROUND: Mycobacterium tuberculosis whole-genome sequencing (WGS) has been widely used for genotypic drug susceptibility testing (DST) and outbreak investigation. For both applications, Illumina technology is used by most public health laboratories; however, Nanopore technology developed by Oxford Nanopore Technologies has not been thoroughly evaluated. The aim of this study was to determine whether Nanopore sequencing data can provide equivalent information to Illumina for transmission clustering and genotypic DST for M tuberculosis. METHODS: In this genomic analysis, we analysed 151 M tuberculosis isolates from Madagascar, South Africa, and England, which were collected between 2011 and 2018, using phenotypic DST and matched Illumina and Nanopore data. Illumina sequencing was done with the MiSeq, HiSeq 2500, or NextSeq500 platforms and Nanopore sequencing was done on the MinION or GridION platforms. Using highly reliable PacBio sequencing assemblies and pairwise distance correlation between Nanopore and Illumina data, we optimise Nanopore variant filters for detecting single-nucleotide polymorphisms (SNPs; using BCFtools software). We then used those SNPs to compare transmission clusters identified by Nanopore with the currently used UK Health Security Agency Illumina pipeline (COMPASS). We compared Illumina and Nanopore WGS-based DST predictions using the Mykrobe software and mutation catalogue. FINDINGS: The Nanopore BCFtools pipeline identified SNPs with a median precision of 99.3% (IQR 99.1-99.6) and recall of 90.2% (88.1-94.2) compared with a precision of 99.6% (99.4-99.7) and recall of 91.9% (87.6-98.6) using the Illumina COMPASS pipeline. Using a threshold of 12 SNPs for putative transmission clusters, Illumina identified 98 isolates as unrelated and 53 as belonging to 19 distinct clusters (size range 2-7). Nanopore reproduced 15 out of 19 clusters perfectly; two clusters were merged into one cluster, one cluster had a single sample missing, and one cluster had an additional sample adjoined. ... |
| نوع الوثيقة: | article in journal/newspaper |
| وصف الملف: | application/pdf |
| اللغة: | English |
| تدمد: | 2666-5247 |
| Relation: | https://edoc.unibas.ch/93561/1/20230210103859_63e610b322662.pdf; Hall, M. B. and Rabodoarivelo, M. S. and Koch, A. and Dippenaar, A. and George, S. and Grobbelaar, M. and Warren, R. and Walker, T. M. and Cox, H. and Gagneux, S. and Crook, D. and Peto, T. and Rakotosamimanana, N. and Grandjean Lapierre, S. and Iqbal, Z. (2023) Evaluation of nanopore sequencing for Mycobacterium tuberculosis drug susceptibility testing and outbreak investigation: a genomic analysis. Lancet Microbe, 4 (2). e84-e92.; info:pmid/36549315; urn:ISSN:2666-5247 (Electronic)2666-5247 (Linking) |
| DOI: | 10.1016/S2666-5247(22)00301-9 |
| الاتاحة: | https://edoc.unibas.ch/93561/ https://edoc.unibas.ch/93561/1/20230210103859_63e610b322662.pdf https://doi.org/10.1016/S2666-5247(22)00301-9 |
| Rights: | cc_by ; info:eu-repo/semantics/openAccess |
| رقم الانضمام: | edsbas.2C626D4E |
| قاعدة البيانات: | BASE |
Full Text Finder | تدمد: | 26665247 |
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| DOI: | 10.1016/S2666-5247(22)00301-9 |