The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.
The Applied Development of a Tiered Multilocus Sequence Typing (MLST) Scheme for Dichelobacter nodosus.
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DOI：
10.3389/fmicb.2018.00551
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发表时间：
2018
影响因子：
5.2
通讯作者：
Tötemeyer S
中科院分区：
文献类型：
--
作者：
Blanchard AM;Jolley KA;Maiden MCJ;Coffey TJ;Maboni G;Staley CE;Bollard NJ;Warry A;Emes RD;Davies PL;Tötemeyer S
结节双歧杆菌是引起绵羊蹄疾的病原体，这种疾病对全球养羊业具有重大的福利和经济影响。以前对结节毛虫系统发育的研究主要集中在澳大利亚和斯堪的纳维亚半岛，这意味着英国目前的多样性。在全球范围内，人们对人口及其关系知之甚少。有许多流行病学方法可用于细菌分型；然而，很少有方法考虑全基因组多样性或为未来新的计算技术的应用提供机会。多位点序列分型(MLST)测量几个基因座内的核苷酸变异，这些变异累积缓慢，从而能够指定等位基因数来确定序列类型。全基因组序列数据的使用使MLST的应用成为可能，而且核心和全基因组MLST也可以用于更高水平的菌株识别，而实验成本的增加可以忽略不计。MLST数据库是利用来自序列读取档案的公开可用的全基因组数据与七个基因座方案一起开发的。序列类型命名和菌株识别与以前发表的数据进行了比较，以确保重复性。来自英国农场的多个结节圆线虫分离株直接与其他国家的种群进行了比较。这些英国分离株在全球节结线虫种群中定义了新的分支，主要由A、B和H血清组组成，但也发现了C、D、E和I血清组。该计划可在https://pubmlst.org/dnodosus/.上公开获得。
Dichelobacter nodosus (D. nodosus) is the causative pathogen of ovine footrot, a disease that has a significant welfare and financial impact on the global sheep industry. Previous studies into the phylogenetics of D. nodosus have focused on Australia and Scandinavia, meaning the current diversity in the United Kingdom (U.K.) population and its relationship globally, is poorly understood. Numerous epidemiological methods are available for bacterial typing; however, few account for whole genome diversity or provide the opportunity for future application of new computational techniques. Multilocus sequence typing (MLST) measures nucleotide variations within several loci with slow accumulation of variation to enable the designation of allele numbers to determine a sequence type. The usage of whole genome sequence data enables the application of MLST, but also core and whole genome MLST for higher levels of strain discrimination with a negligible increase in experimental cost. An MLST database was developed alongside a seven loci scheme using publically available whole genome data from the sequence read archive. Sequence type designation and strain discrimination was compared to previously published data to ensure reproducibility. Multiple D. nodosus isolates from U.K. farms were directly compared to populations from other countries. The U.K. isolates define new clades within the global population of D. nodosus and predominantly consist of serogroups A, B and H, however serogroups C, D, E, and I were also found. The scheme is publically available at https://pubmlst.org/dnodosus/.