ArticlePloS one2016
Comparison of Sample Preparation Methods Used for the Next-Generation Sequencing of Mycobacterium tuberculosis.
Article in PloS one, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers, 2 of them syntheses that pooled it.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
35 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Pooled it
- Whole-Genome Sequencing as Tool for Investigating International Tuberculosis Outbreaks: A Systematic Review.Frontiers in public health · 2019Pooled it
- Biases from Oxford Nanopore library preparation kits and their effects on microbiome and genome analysis.BMC genomics · 2025Article
- Article
- Molecular typing of Mycobacterium tuberculosis: a review of current methods, databases, softwares, and analytical tools.FEMS microbiology reviews · 2025Review
- Genotypic drug resistance and transmission clusters of Mycobacterium tuberculosis isolates among Ethiopian returnees from Saudi Arabia.PloS one · 2025Article
- Preassembly Read Processing and Quality Control in Fungal Genomes, Exemplified by the Chytrid Batrachochytrium salamandrivorans.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Development of a Tagmentation-Based Next-Generation Sequencing Clinical Assay as an Alternative to Capillary Electrophoresis-Based Sequencing.Molecular genetics & genomic medicine · 2024Article
- Distribution of Common and Rare Genetic Markers of Second-Line-Injectable-Drug Resistance in Mycobacterium tuberculosis Revealed by a Genome-Wide Association Study.Antimicrobial agents and chemotherapy · 2022Article
- The efficiency of Nextera XT tagmentation depends on G and C bases in the binding motif leading to uneven coverage in bacterial species with low and neutral GC-content.Frontiers in microbiology · 2022Article
- Integrative utility of long read sequencing-based whole genome analysis and phenotypic assay on differentiating isoniazid-resistant signature of Mycobacterium tuberculosis.Journal of biomedical science · 2021Article
- Evaluation of a high-throughput, cost-effective Illumina library preparation kit.Scientific reports · 2021Article
- Benchmarking DNA Extraction Methods for Phylogenomic Analysis of Sub-AntarcticMicroorganisms · 2021Article
- Exact mapping of Illumina blind spots in theMicrobial genomics · 2021Article
- Article
- Article
- Article
- Review
- Reply to Li et al., "GC Content-Associated Sequencing Bias Caused by Library Preparation Method May Infrequently AffectApplied and environmental microbiology · 2020Article
- Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The advent and widespread application of next-generation sequencing (NGS) technologies to the study of microbial genomes has led to a substantial increase in the number of studies in which whole genome sequencing (WGS) is applied to the analysis of microbial genomic epidemiology. However, microorganisms such as Mycobacterium tuberculosis (MTB) present unique problems for sequencing and downstream analysis based on their unique physiology and the composition of their genomes. In this study, we compare the quality of sequence data generated using the Nextera and TruSeq isolate preparation kits for library construction prior to Illumina sequencing-by-synthesis. Our results confirm that MTB NGS data quality is highly dependent on the purity of the DNA sample submitted for sequencing and its guanine-cytosine content (or GC-content). Our data additionally demonstrate that the choice of library preparation method plays an important role in mitigating downstream sequencing quality issues. Importantly for MTB, the Illumina TruSeq library preparation kit produces more uniform data quality than the Nextera XT method, regardless of the quality of the input DNA. Furthermore, specific genomic sequence motifs are commonly missed by the Nextera XT method, as are regions of especially high GC-content relative to the rest of the MTB genome. As coverage bias is highly undesirable, this study illustrates the importance of appropriate protocol selection when performing NGS studies in order to ensure that sound inferences can be made regarding mycobacterial genomes.
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