Whole-genome sequencing of M. tuberculosis

Genomic DNA from M. tuberculosis isolates was extracted as per standard protocol [11 (link)]. Libraries were constructed using the Nextera XT DNA preparation kit (Illumina, San Diego, California) and genome sequencing was performed on NextSeq500 (Illumina) with 2 × 150-bp paired-end chemistry. Sequencing reads were mapped to the reference genome M. tuberculosis H37Rv (GenBank NC_000962) and single nucleotide polymorphism (SNP) variants identified using CLC Genomics Workbench version 10.0.1 (Qiagen, Denmark). Reads were processed through the RedDog pipeline (https://github.com/katholt/RedDog) and Snippy v3.1 and screened for mutations associated with drug resistance.

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Parvaresh L., Crighton T., Martinez E., Bustamante A., Chen S, & Sintchenko V. (2018). Recurrence of tuberculosis in a low-incidence setting: a retrospective cross-sectional study augmented by whole genome sequencing. BMC Infectious Diseases, 18, 265.

Publication 2018

Nextera XT DNA preparation kit NextSeq500 CLC Genomics Workbench version 10.0.1

Drug resistance Genome M tuberculosis M tuberculosis h37rv Mutations Single nucleotide polymorphism

Corresponding Organization : Westmead Hospital

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Variable analysis

independent variables

DNA extraction method
Library construction using Nextera XT DNA preparation kit
Genome sequencing on NextSeq500 (Illumina) with 2 × 150-bp paired-end chemistry
Mapping sequencing reads to the reference genome M. tuberculosis H37Rv (GenBank NC_000962)
Identifying single nucleotide polymorphism (SNP) variants using CLC Genomics Workbench
Processing reads through the RedDog pipeline and Snippy v3.1
Screening for mutations associated with drug resistance

dependent variables

Sequencing reads obtained
SNP variants identified
Mutations associated with drug resistance

control variables

Not explicitly mentioned

positive controls

Not explicitly mentioned

negative controls

Not explicitly mentioned

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