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Abstract：
Staphylococcus epidermidis, a common commensal bacterium found on human skin, can cause infections in clinical settings, and the presence of antibiotic resistance genes (ARGs) impedes the treatment of S. epidermidis infections. However, studies characterizing the ARGs in S. epidermidis with regard to genomic and ecological diversities are limited. Thus, we performed a comprehensive and comparative analysis of 405 high-quality S. epidermidis genomes, including those of 35 environmental isolates from the Han River, to investigate the genomic diversity of antibiotic resistance in this pathogen. Comparative genomic analysis revealed the prevalence of ARGs in S. epidermidis genomes associated with multi-locus sequence types. The genes encoding dihydrofolate reductase (dfrC) and multidrug efflux pump (norA) were genome-wide core ARGs. β-Lactam class ARGs were also highly prevalent in the S. epidermidis genomes, which was consistent with the resistance phenotype observed in river isolates. Furthermore, we identified chloramphenicol acetyltransferase genes (cat) in the plasmid-like sequences of the six river isolates, which have not been reported previously in S. epidermidis genomes. These genes were identical to those harbored by the Enterococcus faecium plasmids and associated with the insertion sequence 6 family transposases, homologous to those found in Staphylococcus aureus plasmids, suggesting the possibility of horizontal gene transfer between these Gram-positive pathogens. Comparison of the ARG and virulence factor profiles between S. epidermidis and S. aureus genomes revealed that these two species were clearly distinguished, suggesting genomic demarcation despite ecological overlap. Our findings provide a comprehensive understanding of the genomic diversity of antibiotic resistance in S. epidermidis.
OBJECTIVE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
OBJECTIVE: A comprehensive understanding of the antibiotic resistance gene (ARG) profiles of the skin commensal bacterium and opportunistic pathogen Staphylococcus epidermidis needs to be documented from a genomic point of view. Our study encompasses a comparative analysis of entire S. epidermidis genomes from various habitats, including those of 35 environmental isolates from the Han River sequenced in this study. Our results shed light on the distribution and diversity of ARGs within different S. epidermidis multi-locus sequence types, providing valuable insights into the ecological and genetic factors associated with antibiotic resistance. A comparison between S. epidermidis and Staphylococcus aureus revealed marked differences in ARG and virulence factor profiles, despite their overlapping ecological niches.
摘要：
表皮葡萄球菌，在人类皮肤上发现的一种常见共生细菌，会在临床环境中引起感染，抗生素抗性基因（ARGs）的存在阻碍了表皮葡萄球菌感染的治疗。然而,在基因组和生态多样性方面表征表皮葡萄球菌中ARGs的研究有限。因此，我们对405个高质量的表皮葡萄球菌基因组进行了全面和比较分析，包括汉江的35个环境分离物，研究该病原体中抗生素抗性的基因组多样性。比较基因组分析揭示了与多位点序列类型相关的表皮葡萄球菌基因组中ARG的流行。编码二氢叶酸还原酶（dfrC）和多药外排泵（norA）的基因是全基因组核心ARGs。β-内酰胺类ARGs在表皮葡萄球菌基因组中也非常普遍，这与在河流分离株中观察到的抗性表型一致。此外，我们在六个河流分离株的质粒样序列中鉴定了氯霉素乙酰转移酶基因（cat），以前在表皮葡萄球菌基因组中没有报道过。这些基因与屎肠球菌质粒所携带的基因相同，并与插入序列6家族转座酶相关，与在金黄色葡萄球菌质粒中发现的那些同源，提示这些革兰氏阳性病原体之间水平基因转移的可能性。表皮葡萄球菌和金黄色葡萄球菌基因组之间的ARG和毒力因子谱的比较表明，这两个物种是明确区分的，尽管存在生态重叠，但仍表明基因组划界。我们的发现为表皮葡萄球菌抗生素抗性的基因组多样性提供了全面的理解。
目的：需要从基因组的角度全面了解皮肤共生菌和条件致病菌表皮葡萄球菌的抗生素耐药基因（ARG）谱。我们的研究包括对来自不同栖息地的整个表皮葡萄球菌基因组的比较分析，包括本研究中测序的汉江环境分离株。我们的结果揭示了不同表皮葡萄球菌多基因座序列类型中ARGs的分布和多样性，为与抗生素抗性相关的生态和遗传因素提供有价值的见解。表皮葡萄球菌和金黄色葡萄球菌之间的比较揭示了ARG和毒力因子谱的显着差异，尽管它们的生态位重叠。
目的：需要从基因组的角度全面了解皮肤共生菌和条件致病菌表皮葡萄球菌的抗生素耐药基因（ARG）谱。我们的研究包括对来自不同栖息地的整个表皮葡萄球菌基因组的比较分析，包括本研究中测序的汉江环境分离株。我们的结果揭示了不同表皮葡萄球菌多基因座序列类型中ARGs的分布和多样性，为与抗生素抗性相关的生态和遗传因素提供有价值的见解。表皮葡萄球菌和金黄色葡萄球菌之间的比较揭示了ARG和毒力因子谱的显着差异，尽管它们的生态位重叠。
