Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, New Hampshire, USA.
Department of Biological Sciences, University at Albany, State University of New York, New York, USA.
Genome Biol Evol. 2021 Sep 1;13(9). doi: 10.1093/gbe/evab206.
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.
基于凝固酶蛋白的诊断表现，革兰氏阳性菌葡萄球菌属的成员历来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）和重组在更为人熟知的 CoPS 物种金黄色葡萄球菌中的重要性，然而，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，我们旨在阐明 CoNS 的系统发育关系、基因组特征和 HGT 频率，这些 CoNS 现在被认为是人类的主要机会性病原体。我们编译了一个由 1876 个公开可得的命名为 CoNS 的基因组组成的数据集。这些基因组可以根据 462 个核心基因的等位基因差异和辅助基因内容的变化划分为 55 个种。CoNS 物种是与多种类别的抗生素耐药性相关的可转移基因的储库。我们还鉴定了 9 种可移动遗传元件 SCCmec，其携带耐甲氧西林的决定子 mecA。其他经常转移的基因包括与重金属耐药性、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、重组和代谢酶相关的基因。在表皮葡萄球菌、山羊葡萄球菌、人葡萄球菌、溶血葡萄球菌和腐生生物种组的成员中，重组 DNA 片段的接收和捐赠频率最高。重组的可变速率和转移伙伴的偏倚表明，某些 CoNS 物种作为基因流动的枢纽和整个属遗传多样性的主要库发挥作用。
