Department of Zoology, University of Oxford, Peter Medawar Building for Pathogen Research, South Parks Road, Oxford OX1 3SY, United Kingdom; National Institute for Health Research, Health Protection Research Unit, Gastrointestinal Infections, University of Oxford, United Kingdom.
Public Health England, Gastrointestinal Bacteria Reference Unit, 61 Colindale Avenue, London NW9 5EQ, United Kingdom.
Genomics. 2020 Jan;112(1):371-378. doi: 10.1016/j.ygeno.2019.02.016. Epub 2019 Mar 21.
The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations.
沙门氏菌存在于广泛的动物宿主和许多供人类食用的食品中。大多数人类疾病病例是由 S. enterica 亚种 I 引起的；然而，作为机会性病原体，其他亚种（II-VI）和 S. bongori 也能够引起疾病。在先前提出的核心基因组方案（EBcgMLSTv2.0）中，去除了未在所有物种和亚种中一致存在的基因座，去除这 252 个基因座导致了核心属方案（SalmcgMLSTv1.0）的产生。与 EBcgMLSTv2.0 相比，SalmcgMLSTv1.0 更快地聚类来自同一亚种的分离株，并且更准确地将来自不同亚种的分离株分组。EBcgMLSTv2.0 方案中的所有基因座均存在于超过 98%的 S. enterica 亚种 I 分离株中，因此，应该继续用于亚种 I 分析，而 SalmcgMLSTv1.0 方案更适合于跨属研究。
