Aaltonen Kirsi, Kant Ravi, Eklund Marjut, Raunio-Saarnisto Mirja, Paulin Lars, Vapalahti Olli, Grönthal Thomas, Rantala Merja, Sironen Tarja
Department of Veterinary Biosciences, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland.
Department of Virology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Int J Genomics. 2020 Feb 18;2020:8708305. doi: 10.1155/2020/8708305. eCollection 2020.
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.
海氏链球菌是一种新出现的病原体，可感染多种宿主物种，具有人畜共患病潜力。它已从灰海豹和其他海洋哺乳动物以及人类感染病例中分离出来。从2010年开始，芬兰分别在毛皮动物和家犬中发现了两种同时发生的疫情。毛皮动物患上了一种新疾病——毛皮动物流行性坏死性脓皮病（FENP），而犬类则出现耳部感染且治疗效果不佳。在这两项研究中均分离出了海氏链球菌，尽管同时还存在其他病原体，这表明它可能在疾病病因中发挥作用。目的是寻找毛皮动物和犬类分离株可能的共同起源，并研究毒力因子以评估致病潜力。获取了海豹、人类、犬类和毛皮动物的分离株用于比较。使用Illumina MiSeq平台对20种不同菌株的全基因组进行测序，并使用自动注释管道RAST进行注释。通过全基因组相互比较形成核心基因组和泛基因组。利用核心基因组的基因构建系统发育树。使用毒力因子数据库（VFDB）评估毒力因子，重点关注先前已确认的链球菌因子。形成了一个核心基因组，其包含海氏链球菌中约一半的基因。所得核心基因组几乎已饱和，增加更多基因组后不会有显著变化。其余基因形成泛基因组，其具有高度变异性，增加更多基因组后仍会进化。结果突出了这种细菌的强大适应性，这可能解释了它易于在宿主和环境之间转换的原因。还对毒力因子进行了分析，发现它们主要存在于核心基因组中。它们代表了许多类别和功能，但最大的单一类别是黏附素，这再次支持了该物种的海洋起源。
