LAMBDR: Long-range amplification and Nanopore sequencing of the Mycobacterium bovis direct-repeat region . A novel method for in-silico spoligotyping of M. bovis directly from badger faeces
LAMBDR: Long-range amplification and Nanopore sequencing of the Mycobacterium bovis direct-repeat region . A novel method for in-silico spoligotyping of M. bovis directly from badger faeces
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LAMBDR：牛分枝杆菌直接重复区域的长程扩增和纳米孔测序。
DOI：
10.1101/791129
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
James R
中科院分区：
文献类型：
--
作者：
James R
环境是一个被忽视的牛分枝杆菌的来源，牛结核病的病原体。跨M.牛基因组被评估为直接从环境样本中获得快速菌株水平分辨率的方法。8份M. bovis、两株BCG（Danish和Pasteur）和一株M.结核型培养物（NCTC 13144）用于产生该方法的数据。用长距离PCR扩增直接重复区，合成约15kb的模板DNA，用于进一步的序列分析。这使得M.存在于环境中的牛spoligotypes。直接重复区的序列水平分析表明，spoligotyping可能低估了菌株的多样性，由于无法识别SNP和引物结合突变，使用生物素化杂交方法。
The environment is an overlooked source of Mycobacterium bovis, the causative agent of bovine TB. Long read, end to end sequencing of variable repeat regions across the M. bovis genome was evaluated as a method of acquiring rapid strain level resolution directly from environmental samples. Eight samples of M. bovis, two BCG strains (Danish and Pasteur), and a single M. tuberculosis type culture (NCTC 13144) were used to generate data for this method. Long range PCR amplification of the direct repeat region was used to synthesize∼ 5kb template DNA for onward sequence analysis. This has permitted culture independent identification of M. bovis spoligotypes present in the environment. Sequence level analysis of the direct repeat region showed that spoligotyping may underestimate strain diversity due to the inability to identify both SNPs and primer binding mutations using a biotinylated hybridisation approach.