Dichelobacter nodosus MLST Databases

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/.全基因组测序数据的应用不仅可开展多位点序列分型（MLST），还可通过核心基因组MLST与全基因组MLST实现更高分辨率的菌株分型，且实验成本增幅可忽略不计。本研究利用序列读取档案（Sequence Read Archive, SRA）中的公开全基因组测序数据，开发了一套包含7个基因座的MLST分型方案，并配套搭建了对应的MLST数据库。通过与已发表文献中的数据进行比对，验证了序列型别判定与菌株分型结果的可重复性。研究将英国农场分离得到的多株节瘤拟杆菌（Dichelobacter nodosus, D. nodosus）与其他国家的菌株群体开展了直接比对。英国分离株在全球节瘤拟杆菌种群中界定出了新的进化枝，其血清群主要为A、B、H型，同时也检测到了C、D、E及I型血清群。该分型方案可通过https://pubmlst.org/dnodosus/公开获取。

搜集汇总

背景与挑战

背景概述

该数据集为Dichelobacter nodosus的MLST数据库，基于公开的全基因组数据开发，包含等位基因定义和序列类型（ST）索引，用于高分辨率菌株鉴别。数据库由诺丁汉大学团队创建，并得到BBSRC资助，涵盖了英国农场分离株与其他国家种群的比较，显示英国分离株定义了新的进化枝。数据库提供等位基因序列、分离株记录和基因组组装信息，并定期更新。