Salmonella nomenclature in the genomic era: a time for change.
Salmonella nomenclature in the genomic era: a time for change.
复制标题
DOI：
10.1038/s41598-021-86243-w
复制
发表时间：
2021-04-05
影响因子：
4.6
通讯作者：
Wain J
中科院分区：
文献类型：
--
作者：
Chattaway MA;Langridge GC;Wain J
在过去的一百年中，沙门氏菌命名法已经发展成为基于特异性抗体识别抗原的高度复杂的命名惯例。该血清分型方案已导致超过2500种血清型的定义，这些血清型已被充分理解，在命名中具有地位，并且对于大多数而言具有生物学相关性。因此，非常希望命名约定的任何更改都能保持与这些血清型相关信息的向后兼容性。全基因组测序的常规使用以及序列类型和血清型之间的良好建立的联系提供了一个机会，可以通过合并遗传学相关序列数据来更新方案，同时保留最佳的血清型命名法。优点包括：克服了抗体制备的可变性;消除了使用实验室动物的需要，并实现了真正的通用系统。然而，如果我们要完全拥抱基因组时代，就需要放松试图复制表型金标准的问题。我们使用了来自超过46，000株肠道沙门氏菌肠道亚种分离株的全基因组序列数据，分两个阶段定义聚类：多位点序列分型，然后是抗原预测。使用核心SNP聚类来解决序列类型-血清型差异以确定系统发生组，并且这通过将抗原预测覆盖到核心SNP聚类上并使用cgMLST分层聚类测试聚类的分离来确认。这使我们能够定义ST中的任何主要抗原簇-这里称为MAC型，并写作ST血清型。使用这种方法，99.96%的沙门氏菌分离株报告在英国被指定为MAC型，并链接到一个血清型名称从考夫曼和白色计划。我们建议使用ST和血清型报告肠道沙门氏菌亚型。
Salmonella enterica nomenclature has evolved over the past one hundred years into a highly sophisticated naming convention based on the recognition of antigens by specific antibodies. This serotyping scheme has led to the definition of over 2500 serovars which are well understood, have standing in nomenclature and, for the majority, biological relevance. Therefore, it is highly desirable for any change in naming convention to maintain backwards compatibility with the information linked to these serovars. The routine use of whole genome sequencing and the well-established link between sequence types and serovars presents an opportunity to update the scheme by incorporating the phylogenetically relevant sequence data whilst preserving the best of serotyping nomenclature. Advantages include: overcoming the variability in antibody preparations; removing the need to use laboratory animals and implementing a truly universal system. However, the issue of trying to reproduce the phenotyping gold standard needs to be relaxed if we are to fully embrace the genomic era. We have used whole genome sequence data from over 46,000 isolates of Salmonella enterica subspecies enterica to define clusters in two stages: Multi Locus Sequence Typing followed by antigen prediction. Sequence type—serotype discrepancies were resolved using core SNP clustering to determine the phylogenetic groups and this was confirmed by overlaying the antigenic prediction onto the core SNP clusters and testing the separation of clusters using cgMLST Hierarchical Clustering. This allowed us to define any major antigenic clusters within an ST—here called the MAC type and written as ST-serovar. Using this method, 99.96% of Salmonella isolates reported in the UK were assigned a MAC type and linked to a serovar name taken from the Kauffmann and White scheme. We propose a change for reporting of Salmonella enterica sub-types using the ST followed by serovar.
登录
查看更多内容
影响因子：
3.8
作者：
Aldrich, Cassandra;Hartman, Hassan;Eibach, Daniel
通讯作者：
Eibach, Daniel
影响因子：
10.7
作者：
Nguyen LT;Schmidt HA;von Haeseler A;Minh BQ
通讯作者：
Minh BQ
影响因子：
1.7
作者：
Bankevich, Anton;Nurk, Sergey;Pevzner, Pavel A.
通讯作者：
Pevzner, Pavel A.
影响因子：
14.9
作者：
Letunic, Ivica;Bork, Peer
通讯作者：
Bork, Peer
影响因子：
9.4
作者：
Zhang, Shaokang;Yin, Yanlong;Deng, Xiangyu
通讯作者：
Deng, Xiangyu