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Streptococcus halichoeri: Comparative Genomics of an Emerging Pathogen
International Journal of Genomics ( IF 2.9 ) Pub Date : 2020-02-18 , DOI: 10.1155/2020/8708305
Kirsi Aaltonen 1, 2 , Ravi Kant 1, 2 , Marjut Eklund 3 , Mirja Raunio-Saarnisto 4 , Lars Paulin 5 , Olli Vapalahti 1, 2, 6 , Thomas Grönthal 3 , Merja Rantala 3 , Tarja Sironen 1, 2
Affiliation  

Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.

中文翻译:

嗜盐链球菌:新兴病原体的比较基因组学。

嗜盐链球菌是一种新兴病原体,具有多种宿主物种和人畜共患病潜力。它已从灰海豹和其他海洋哺乳动物以及人类感染中分离出来。从2010年开始,在芬兰发现了两种并发流行病,分别是毛皮动物和家犬。毛皮动物患有一种新的疾病,即毛皮动物流行性坏死性脓皮病(FENP),犬只出现耳部感染,治疗反应较差。尽管有其他病原体,但在两项研究中均分离到了哈利链霉菌,这表明其可能在疾病病因中起作用。目的是找到毛皮动物和狗分离物的可能的共同起源,并研究毒力因子以评估致病性。获得海豹,人,狗和毛皮动物的分离株用于比较。使用Illumina MiSeq平台对20个不同菌株的整个基因组进行测序,并使用自动注释管道RAST对其进行注释。核心基因组和泛基因组是通过对基因组的相互比较而形成的。使用核心基因组的基因构建了系统树。使用集中于先前确认的链球菌因子的毒力因子数据库(VFDB)评估毒力因子。形成了一个核心基因组,该基因组涵盖了哈里链球菌中大约一半的基因。所得的核心几乎饱和,并且不会通过添加更多的基因组而发生显着变化。剩下的基因形成了全基因组,该基因组高度可变,并且在附加基因组后仍将进化。结果突出了这种细菌的巨大适应性,可能解释了它容易改变宿主和环境的原因。还分析了毒力因子,主要在核心基因组中发现。它们代表许多类别和功能,但最大的单一类别是粘附素,它再次支持了该物种的海洋起源。
更新日期:2020-02-18
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