Genome assemblies utilized in this study.

Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17–19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.Agnetis葡萄球菌（Staphylococcus agnetis）是鸡的一种新兴病原菌，但此前最常从牛的亚临床乳腺炎中分离得到。此前针对已知毒力基因的全基因组分析，未能识别出其从牛的轻度导管感染转向鸡的严重感染的相关致病决定因子。本研究首次报道鉴定出一类长度为15 kbp、编码17~19个基因的移动遗传元件（mobile genetic elements, MGEs），该类元件特异性存在于Agnetis葡萄球菌的鸡骨髓炎与皮炎分离株中。此类移动遗传元件可在单个基因组中以多拷贝形式存在。该移动遗传元件由一株葡萄球菌噬菌体介导，该噬菌体可分别溶原化两株Agnetis葡萄球菌骨髓炎菌株。一株来自肉种鸡溃疡性皮炎病例的Agnetis葡萄球菌基因组中，含有两个该移动遗传元件的直系同源拷贝，且未与前噬菌体相关联。BLASTn比对与系统发育分析显示，在金黄色葡萄球菌（Staphylococcus aureus）的基因组中存在与之密切相关的完整移动遗传元件。1980年代从爱尔兰鸡群中分离得到的一株菌株基因组中，含有三个该移动遗传元件的拷贝。源自该菌株的近期鸡分离株（2009年波兰株、2010年俄克拉荷马州株以及2018年阿肯色州株）中，含有2~4个与之相关的拷贝。在其他金黄色葡萄球菌鸡分离株的基因组不同区域中，可识别出该移动遗传元件的多个基因。对NCBI数据库的BLAST搜索结果显示，除金黄色葡萄球菌与Agnetis葡萄球菌外，未在其他物种中发现类似的移动遗传元件。此类移动遗传元件所编码的蛋白质，与金黄色葡萄球菌致病岛所产生的蛋白质无同源性，而后者与金黄色葡萄球菌从人类宿主转向鸡宿主的转变过程相关。除移动功能相关基因外，这类新型移动遗传元件中的大多数基因注释为假设蛋白。本研究描述的这类移动遗传元件，代表了一类共享于Agnetis葡萄球菌与金黄色葡萄球菌之间的新型染色体岛（Chromosomal Islands, CIs）家族。仍需开展进一步研究以阐明此类染色体岛/移动遗传元件在致病过程中的作用。对葡萄球菌属不同分离株与物种间的遗传元件水平转移进行分析，可为宿主-病原体互作的演化过程提供线索，同时也能揭示影响动物福利与人类疾病的关键决定因子。