Members of the gram-positive bacterial genus Staphylococcus have historically been classified into coagulase-positive Staphylococcus (CoPS) and coagulase-negative Staphylococcus (CoNS) based on the diagnostic presentation of the coagulase protein. Previous studies have noted the importance of horizontal gene transfer (HGT) and recombination in the more well-known CoPS species Staphylococcus aureus, yet little is known of the contributions of these processes in CoNS evolution. In this study, we aimed to elucidate the phylogenetic relationships, genomic characteristics, and frequencies of HGT in CoNS, which are now being recognized as major opportunistic pathogens of humans. We compiled a data set of 1,876 publicly available named CoNS genomes. These can be delineated into 55 species based on allele differences in 462 core genes and variation in accessory gene content. CoNS species are a reservoir of transferrable genes associated with resistance to diverse classes of antimicrobials. We also identified nine types of the mobile genetic element SCCmec, which carries the methicillin resistance determinant mecA. Other frequently transferred genes included those associated with resistance to heavy metals, surface-associated proteins related to virulence and biofilm formation, type VII secretion system, iron capture, recombination, and metabolic enzymes. The highest frequencies of receipt and donation of recombined DNA fragments were observed in Staphylococcus capitis, Staphylococcus caprae, Staphylococcus hominis, Staphylococcus haemolyticus, and members of the Saprophyticus species group. The variable rates of recombination and biases in transfer partners imply that certain CoNS species function as hubs of gene flow and major reservoir of genetic diversity for the entire genus.

中文翻译：

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凝固酶阴性葡萄球菌种内和种间的广泛水平基因转移


历史上，根据凝固酶蛋白的诊断表现，革兰氏阳性细菌属葡萄球菌被分为凝固酶阳性葡萄球菌（CoPS）和凝固酶阴性葡萄球菌（CoNS）。先前的研究已经注意到水平基因转移 (HGT) 和重组在更知名的 CoPS 物种金黄色葡萄球菌中的重要性，但人们对这些过程在 CoNS 进化中的贡献知之甚少。在这项研究中，我们的目的是阐明 CoNS 中 HGT 的系统发育关系、基因组特征和频率，CoNS 现在被认为是人类主要的机会性病原体。我们编制了一个由 1,876 个公开的命名 CoNS 基因组组成的数据集。根据 462 个核心基因的等位基因差异和辅助基因含量的变化，可以将它们划分为 55 个物种。 CoNS 物种是与多种抗菌药物耐药性相关的可转移基因的库。我们还鉴定了九种类型的可移动遗传元件 SCCmec，其携带甲氧西林抗性决定子 mecA。其他经常转移的基因包括与重金属抗性相关的基因、与毒力和生物膜形成相关的表面相关蛋白、VII型分泌系统、铁捕获、重组和代谢酶。在头状葡萄球菌、山羊葡萄球菌、人葡萄球菌、溶血葡萄球菌和腐生菌属物种组中观察到接收和捐赠重组 DNA 片段的频率最高。 重组率的变化和转移伙伴的偏差意味着某些 CoNS 物种充当基因流的枢纽和整个属遗传多样性的主要库。