Background The Salmonella enterica subsp. diarizonae serovar 61:k:1,5,(7) (SASd) has been found to be host-adapted to sheep, with a high prevalence in sheep herds worldwide. Infections are usually sub-clinical, however the serovar has the potential to cause diarrhea, abortions and chronic proliferative rhinitis. Although occurrence and significance of SASd infections in sheep have been extensively studied, the genetic mechanism underlying this unusual host-adaptation have remained unknown, due to a lack of (a) available high-quality genome sequence(s). Results We utilized Nanopore and Illumina sequencing technologies to generate a de novo assembly of the 4.88-Mbp complete genome sequence of the SASd strain 16-SA00356, isolated from the organs of a deceased sheep in 2016. We annotated and analyzed the genome sequence with the aim to gain a deeper understanding of the genome characteristics associated with its pathogenicity and host adaptation to sheep. Overall, we found a number of interesting genomic features such as several prophage regions, a VirB4/D4 plasmid and novel genomic islands. By comparing the genome of 16-SA00356 to other S. enterica serovars we found that SASd features an increased number of pseudogenes as well as a high level of genomic rearrangements, both known indicators of host-adaptation. Conclusions With this sequence, we provide the first complete and closed genome sequence of a SASd strain. With this study, we provide an important basis for an understanding of the genetic mechanism that underlie pathogenicity and host adaptation of SASd to sheep.

中文翻译：

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肠沙门氏菌亚种的第一个完整基因组序列和比较分析。diarizonae serovar 61:k:1,5,(7) 表明宿主对绵羊的适应性特征。

背景 肠沙门氏菌亚种。已发现 diarizonae serovar 61:k:1,5,(7) (SASd) 对绵羊具有宿主适应性，在全世界的羊群中流行率很高。感染通常是亚临床的，但血清型有可能导致腹泻、流产和慢性增殖性鼻炎。尽管已经广泛研究了绵羊 SASd 感染的发生和意义，但由于缺乏（a）可用的高质量基因组序列，这种不寻常的宿主适应背后的遗传机制仍然未知。结果 我们利用 Nanopore 和 Illumina 测序技术生成了 SASd 菌株 16-SA00356 的 4.88-Mbp 完整基因组序列的从头组装，该菌株于 2016 年从一只死羊的器官中分离出来。我们对基因组序列进行了注释和分析，旨在更深入地了解与其致病性和宿主对绵羊的适应性相关的基因组特征。总体而言，我们发现了许多有趣的基因组特征，例如几个前噬菌体区域、VirB4/D4 质粒和新的基因组岛。通过将 16-SA00356 的基因组与其他 S. enterica 血清型进行比较，我们发现 SASd 具有增加的假基因数量以及高水平的基因组重排，这两者都是宿主适应的已知指标。结论 通过该序列，我们提供了 SASd 菌株的第一个完整且封闭的基因组序列。通过这项研究，我们为了解 SASd 对绵羊的致病性和宿主适应的遗传机制提供了重要基础。