Blanchard Adam M, Jolley Keith A, Maiden Martin C J, Coffey Tracey J, Maboni Grazieli, Staley Ceri E, Bollard Nicola J, Warry Andrew, Emes Richard D, Davies Peers L, Tötemeyer Sabine
School of Veterinary Medicine and Science, University of Nottingham, Nottingham, United Kingdom.
Department of Zoology, University of Oxford, Oxford, United Kingdom.
Front Microbiol. 2018 Mar 23;9:551. doi: 10.3389/fmicb.2018.00551. eCollection 2018.
() 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 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 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 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/.
（）是绵羊腐蹄病的致病病原体，该病对全球养羊业有着重大的福利和经济影响。此前对（）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，这意味着对英国种群目前的多样性及其在全球范围内的关系了解甚少。有多种流行病学方法可用于细菌分型；然而，很少有方法考虑到全基因组多样性或为未来新计算技术的应用提供机会。多位点序列分型（MLST）测量几个位点内的核苷酸变异，变异积累缓慢，以便指定等位基因编号来确定序列类型。全基因组序列数据的使用不仅能应用MLST，还能应用核心和全基因组MLST进行更高水平的菌株鉴别，而实验成本的增加可忽略不计。利用来自序列读取存档的公开全基因组数据，开发了一个MLST数据库以及一个七基因座方案。将序列类型指定和菌株鉴别与先前发表的数据进行比较，以确保可重复性。将来自英国农场的多个（）分离株与其他国家的种群直接进行比较。英国的分离株在全球（）种群中定义了新的进化枝，主要由血清群A、B和H组成，但也发现了血清群C、D、E和I。该方案可在https://pubmlst.org/dnodosus/上公开获取。
