Enterococci are commensals that proliferated as animals crawled ashore hundreds of millions of years ago. They are also leading causes of multidrug-resistant hospital-acquired infections. While most studies are driven by clinical interest, comparatively little is known about enterococci in the wild or the effect of human activity on them. Pharmaceutical pollution and runoff from other human activities are encroaching widely into natural habitats. To assess their reach into remote habitats, we investigated the identity, genetic relatedness, and presence of specific traits among 172 enterococcal isolates from wild Magellanic penguins. Four enterococcal species, 18 lineage groups, and different colonization patterns were identified. One Enterococcus faecalis lineage, sequence type 475 (ST475), was isolated from three different penguins, making it of special interest. Its genome was compared to those of other E. faecalis sequence types (ST116 and ST242) recovered from Magellanic penguins, as well as to an existing phylogeny of E. faecalis isolated from diverse origins over the past 100 years. No penguin-derived E. faecalis strains were closely related to dominant clinical lineages. Most possessed intact CRISPR defenses, few mobile elements, and antibiotic resistances limited to those intrinsic to the species and lacked pathogenic features conveyed by mobile elements. Interestingly, plasmids were identified in penguin isolates that also had been reported for other marine mammals. Enterococci isolated from penguins showed limited anthropogenic impact, indicating that they are likely representative of those naturally circulating in the ecosystem inhabited by the penguins. These findings establish an important baseline for detecting the encroachment of human activity into remote planetary environments.

中文翻译：

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来自野生麦哲伦企鹅（Spheniscus magellanicus）的肠球菌是海洋生态系统健康和人类影响的指标。

肠球菌是数亿年前动物在岸上爬行时所产生的赞誉。它们也是导致多药耐药的医院获得性感染的主要原因。尽管大多数研究是由临床兴趣驱动的，但对于野生肠球菌或人类活动对其的影响知之甚少。药物污染和其他人类活动的径流正广泛侵蚀自然栖息地。为了评估它们到达偏远生境的范围，我们调查了来自野生麦哲伦企鹅的172个肠球菌分离株的身份，遗传相关性和特定性状的存在。确定了四个肠球菌物种，18个血统族群和不同的定殖模式。其中粪肠球菌从三种不同的企鹅中分离出了475型序列（ST475），这使得它特别受关注。将其基因组与从麦哲伦企鹅中回收的其他粪肠球菌序列类型（ST116和ST242）的基因组进行了比较，并与过去100年来从不同来源分离的粪肠球菌的系统发育进行了比较。没有来自企鹅的粪肠球菌菌株与优势临床谱系密切相关。大多数具有完整的CRISPR防御，很少的活动元件，并且抗生素抗性仅限于物种固有的那些，并且缺乏活动元件传递的致病特征。有趣的是，在企鹅分离物中也鉴定出了质粒，而其他海洋哺乳动物也有报道。从企鹅中分离出来的肠球菌对人为的影响有限，表明它们很可能代表了企鹅所居住的生态系统中自然循环的那些。这些发现为检测人类活动侵入偏远的行星环境奠定了重要的基础。