Oxford Gene Technology, Oxford, UK.
Texas A&M Veterinary Medical Diagnostic Laboratory (TVMDL), College Station, TX, USA.
Methods Mol Biol. 2021;2314:459-480. doi: 10.1007/978-1-0716-1460-0_20.
Whole-genome sequencing is a powerful, high-resolution tool that can be used to generate accurate data on bacterial population structure, phylogeography, and mutations associated with antimicrobial resistance. The ability to sequence pathogen genomes directly from clinical specimens, without the requirement for in vitro culturing, is attractive in terms of time- and labor-saving, especially in the case of slow growing pathogens, such as Mycobacterium tuberculosis. However, clinical samples typically contain too low levels of pathogen nucleic acid, plus relatively high levels of human and natural microbiota DNA/RNA, to make this a viable option. Using a combination of whole-genome enrichment and deep sequencing, which has been proven to be a nonmutagenic approach, we can capture all known variations found within M. tuberculosis genomes. The method is a consistent and sensitive tool that enables rapid whole-genome sequencing of M. tuberculosis directly from clinical samples and has the potential to be adapted to other pathogens with a similar clonal nature.
全基因组测序是一种强大的、高分辨率的工具，可用于生成有关细菌种群结构、系统地理学和与抗生素耐药性相关突变的准确数据。能够直接从临床标本中对病原体基因组进行测序，而无需体外培养，这在节省时间和劳动力方面具有吸引力，尤其是对于生长缓慢的病原体，如结核分枝杆菌。然而，临床样本中病原体核酸的含量通常太低，加上人类和天然微生物群落的 DNA/RNA 含量相对较高，因此无法实现这一目标。使用全基因组富集和深度测序的组合，该方法已被证明是非致突变性的方法，我们可以捕获结核分枝杆菌基因组中所有已知的变异。该方法是一种一致且敏感的工具，可直接从临床样本中快速进行结核分枝杆菌的全基因组测序，并有可能适应具有类似克隆性质的其他病原体。
