PDF(Pubmed)
Abstract：
UNASSIGNED: Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil\'s relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses.
UNASSIGNED: Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.
UNASSIGNED: wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.
UNASSIGNED: The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
UNASSIGNED: Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.
UNASSIGNED: wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes. Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.
UNASSIGNED: The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.
摘要：
■肠沙门氏菌（沙门氏菌婴儿）是一种人畜共患，遍布全球的食源性病原体。尽管巴西作为主要的肉类出口国，在这个国家，很少有研究通过基因组分析来表征这种血清型菌株。因此,这项研究旨在评估从兽医分离的80个婴儿沙门氏菌菌株的多样性，通过比较基因组分析，2013年至2018年巴西的食物和人类来源。在一些分析中，出于比较目的，包括了非巴西国家（n=18）的其他基因组。
■全基因组多位点序列分型（wgMLST）的分析，使用PGAdb-builder，以及零散的基因组，利用Gegenees，进行了80个巴西菌株与18个非巴西基因组的比较。对所分析的所有婴儿沙门氏菌基因组进行Pangenome分析和计算。使用PHASTER对80种巴西菌株确定了原虫的存在。对来自巴西的20个选定的婴儿沙门氏菌基因组和来自非巴西国家的10个基因组，评估了使用BLAST环形图像生成器（BRIG）的基因组可塑性和使用紫红色的基因同步。在来自巴西的十个选定的婴儿沙门氏菌基因组和来自非巴西国家的十个中搜索了独特的直系同源蛋白质簇。
wgMLST和Gegenees在一些巴西婴儿沙门氏菌基因组中显示出高度的基因组相似性，以及一些集群与非巴西基因组的相关性。Gegenees在所有婴儿沙门氏菌基因组中也显示出>91％的总体相似性。Pangenome计算揭示了所有分析的沙门氏菌婴儿亚群的开放pangenome，以及核心基因组中的高基因含量。在97.5％的巴西菌株中检测到15种类型的原噬菌体。BRIG和Mauve在巴西和非巴西分离株之间表现出高度的结构相似性。与生物过程相关的独特直系同源蛋白质簇，分子功能，在巴西和非巴西基因组中检测到细胞成分。
■使用不同基因组方法得出的结果强调了巴西沙门氏菌Infantis基因组之间的显着基因组相似性分析，这表明巴西不同来源中密切相关的基因型分布广泛。所产生的数据有助于提供有关巴西和非巴西婴儿沙门氏菌基因组多样性的新信息。来自巴西的不同遗传相关的婴儿沙门氏菌亚型可以仅在该国境内发生，或者在其他国家，这表明巴西基因型的一些出口可能已经发生。
■全基因组多位点序列分型（wgMLST）的分析，使用PGAdb-builder，以及零散的基因组，利用Gegenees，进行了80个巴西菌株与18个非巴西基因组的比较。对所分析的所有婴儿沙门氏菌基因组进行Pangenome分析和计算。使用PHASTER对80种巴西菌株确定了原虫的存在。对来自巴西的20个选定的婴儿沙门氏菌基因组和来自非巴西国家的10个基因组，评估了使用BLAST环形图像生成器（BRIG）的基因组可塑性和使用紫红色的基因同步。在来自巴西的十个选定的婴儿沙门氏菌基因组和来自非巴西国家的十个中搜索了独特的直系同源蛋白质簇。
wgMLST和Gegenees在一些巴西婴儿沙门氏菌基因组中显示出高度的基因组相似性，以及一些集群与非巴西基因组的相关性。Gegenees在所有婴儿沙门氏菌基因组中也显示出>91％的总体相似性。Pangenome计算揭示了所有分析的沙门氏菌婴儿亚群的开放pangenome，以及核心基因组中的高基因含量。在97.5％的巴西菌株中检测到15种类型的原噬菌体。BRIG和Mauve在巴西和非巴西分离株之间表现出高度的结构相似性。与生物过程相关的独特直系同源蛋白质簇，分子功能，在巴西和非巴西基因组中检测到细胞成分。
■使用不同基因组方法得出的结果强调了巴西沙门氏菌Infantis基因组之间的显着基因组相似性分析，这表明巴西不同来源中密切相关的基因型分布广泛。所产生的数据有助于提供有关巴西和非巴西婴儿沙门氏菌基因组多样性的新信息。来自巴西的不同遗传相关的婴儿沙门氏菌亚型可以仅在该国境内发生，或者在其他国家，这表明巴西基因型的一些出口可能已经发生。
