An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI.
An evaluation of the species and subspecies of the genus Salmonella with whole genome sequence data: Proposal of type strains and epithets for novel S. enterica subspecies VII, VIII, IX, X and XI.
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DOI：
10.1016/j.ygeno.2021.07.003
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发表时间：
2021-09
期刊：
影响因子：
4.4
通讯作者：
Chattaway MA
中科院分区：
文献类型：
--
作者：
Pearce ME;Langridge GC;Lauer AC;Grant K;Maiden MCJ;Chattaway MA
出于公共卫生目的，沙门氏菌属内的种和亚种已通过生物化学特性定义;然而，参考实验室越来越多地采用基于序列的方法，尤其是全基因组序列（WGS）方法进行监测和常规鉴定。这导致亚种定义、常规分型和检测新亚种的能力存在潜在差异。对来自临床分离株常规测序的WGS数据进行大规模分析，以确定和鉴定沙门氏菌亚种种群结构，证明沙门氏菌种和亚种在遗传上是不同的，包括先前通过系统发育方法鉴定的那些，即：S. enterica londinensis亚种（VII）、巴西亚种（VIII）、冬眠亚种（IX）和essexiensis亚种（X）。该分析还确定了一个新的亚种，爬行动物（XI）。此外，这些分析表明，S。肠道沙门氏菌亚利桑那亚种（IIIa）分离株与其它沙门氏菌不同。enterica亚种聚在一起，根据ANI分析，亚种IIIa足够明显，可以被分类为一个单独的种，S.亚利桑那州。多个系统发育和统计方法产生一致的结果，表明拟议的物种和亚种结构是足够的生物学稳健的常规应用。生物化学分析表明，并非所有的亚种是可区分的，这些手段和生化方法没有捕捉到的属的基因组多样性。我们建议采用标准化的物种和亚种的基因组定义，以及基于基因组序列的方法来识别和定义新的亚种。对基因组数据的大规模分析表明沙门氏菌物种和亚种在遗传上是不同的。生化分析不能捕获沙门氏菌属的基因组多样性，但可以用rMLST平均核苷酸鉴定（ANI）实现常规种和亚种鉴定，其中95%的标准适于区分种，98%适于区分亚种。五部小说S.定义了肠亚种（VII-XI）型菌株。重新分类S。亚利桑那州作为一个单独的物种被推荐。
Species and subspecies within the Salmonella genus have been defined for public health purposes by biochemical properties; however, reference laboratories have increasingly adopted sequence-based, and especially whole genome sequence (WGS), methods for surveillance and routine identification. This leads to potential disparities in subspecies definitions, routine typing, and the ability to detect novel subspecies. A large-scale analysis of WGS data from the routine sequencing of clinical isolates was employed to define and characterise Salmonella subspecies population structure, demonstrating that the Salmonella species and subspecies were genetically distinct, including those previously identified through phylogenetic approaches, namely: S. enterica subspecies londinensis (VII), subspecies brasiliensis (VIII), subspecies hibernicus (IX) and subspecies essexiensis (X). The analysis also identified an additional novel subspecies, reptilium (XI). Further, these analyses indicated that S. enterica subspecies arizonae (IIIa) isolates were divergent from the other S. enterica subspecies, which clustered together and, on the basis of ANI analysis, subspecies IIIa was sufficiently distinct to be classified as a separate species, S. arizonae. Multiple phylogenetic and statistical approaches generated congruent results, suggesting that the proposed species and subspecies structure was sufficiently biologically robust for routine application. Biochemical analyses demonstrated that not all subspecies were distinguishable by these means and that biochemical approaches did not capture the genomic diversity of the genus. We recommend the adoption of standardised genomic definitions of species and subspecies and a genome sequence-based approach to routine typing for the identification and definition of novel subspecies. A large-scale analysis of genomic data demonstrate Salmonella species and subspecies are genetically distinct. Biochemical analysis does not capture the genomic diversity of the Salmonella genus but routine species and subspecies identification can be achieved with rMLST Average Nucleotide Identify (ANI) with a 95% criteria was suitable to distinguish species and 98% to distinguish subspecies. Five novel S. enteric subspecies (VII-XI) type strains are defined. Reclassification of S. arizonae as a separate species is recommended.
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影响因子：
6.4
作者：
Desai PT;Porwollik S;Long F;Cheng P;Wollam A;Bhonagiri-Palsikar V;Hallsworth-Pepin K;Clifton SW;Weinstock GM;McClelland M
通讯作者：
McClelland M
影响因子：
3.3
作者：
Gay, Noellie;Le Hello, Simon;Berger, Franck
通讯作者：
Berger, Franck
影响因子：
4.6
作者：
Chattaway MA;Langridge GC;Wain J
通讯作者：
Wain J
影响因子：
4.5
作者：
Didelot X;Bowden R;Street T;Golubchik T;Spencer C;McVean G;Sangal V;Anjum MF;Achtman M;Falush D;Donnelly P
通讯作者：
Donnelly P
DOI：
10.2307/2992355
发表时间：
1990-12-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
GOLDMAN, N
通讯作者：
GOLDMAN, N