Targeted and Whole Genome Sequencing of Mycobacterium tuberculosis

Sequencing was performed in a NextSeq 500/550, using a Mid Output Kit (2 × 150 bp) (Illumina). A depth of 4000x was estimated for targeted panel libraries (clinical samples and reference strains) to detect minor populations of Mtb in co-infections and possible heteroresistance (10 (link)). The depth of WGS libraries (reference strains only) was at least 200x.
The quality of all libraries was evaluated on an Agilent 4200 TapeStation System, and their concentration determined with the Qubit high sensitivity dsDNA assay (Qubit 3.0, Thermo Fisher) before sequencing.

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Barbosa-Amezcua M., Cuevas-Córdoba B., Fresno C., Haase-Hernández J.I., Carrillo-Sánchez K., Mata-Rocha M., Muñoz-Torrico M., Bäcker C., González-Covarrubias V., Alaez-Verson C, & Soberón X. (2022). Rapid Identification of Drug Resistance and Phylogeny in M. tuberculosis, Directly from Sputum Samples. Microbiology Spectrum, 10(5), e01252-22.

Publication 2022

NextSeq 500/550 Mid Output Kit Agilent 4200 TapeStation System Qubit high sensitivity dsDNA assay

Assay Co infections Dsdna Populations Sensitivity Strains

Corresponding Organization : Universidad Nacional Autónoma de México

Other organizations : Universidad Veracruzana, Universidad Anáhuac, Mexican Social Security Institute, Centro Medico Nacional Siglo XXI, Instituto Nacional de Enfermedades Respiratorias, Secretaria de Salud

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Variable analysis

independent variables

Sequencing platform (NextSeq 500/550)
Sequencing kit (Mid Output Kit (2 × 150 bp) (Illumina))
Sequencing depth (4000x for targeted panel libraries, at least 200x for WGS libraries)

dependent variables

Detection of minor populations of Mtb in co-infections and possible heteroresistance

control variables

Library quality evaluation (Agilent 4200 TapeStation System)
Library concentration determination (Qubit high sensitivity dsDNA assay)

controls

No positive or negative controls were explicitly mentioned in the provided information.

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