Abstract：
Staphylococcus aureus is a versatile pathobiont, exhibiting a broad host range, including humans, other mammals, and avian species. Host specificity determinants, virulence, and antimicrobial resistance genes are often shared by strains circulating at the animal-human interface. While transmission dynamics studies have shown strain exchange between humans and livestock, knowledge of the source, genetic diversification, and transmission drivers of S. aureus in wildlife lag behind. In this work, we explore a wide array of S. aureus genomes from different sources in the Iberian Peninsula to understand population structure, gene content and niche adaptation at the human-livestock-wildlife nexus. Through Bayesian inference, we address the hypothesis that S. aureus strains in wildlife originate from humanized landscapes, either from contact with humans or through interactions with livestock. Phylogenetic reconstruction applied to whole genome sequence data was completed with a dataset of 450 isolates featuring multiple clones from the 1990-2022 period and a subset of CC398 strains representing the 2008-2022 period. Phylodynamic signatures of S. aureus from the Iberian Peninsula suggest widespread circulation of most clones among humans before jumping to other hosts. The number of transitions of CC398 strains within each host category (human, livestock, wildlife) was high (88.26 %), while the posterior probability of transitions from livestock to wildlife was remarkably high (0.99). Microbial genome-wide association analysis did not evidence genome rearrangements nor biomarkers suggesting S. aureus niche adaptation to wildlife, thus supporting recent spill overs. Altogether, our findings indicate that S. aureus isolates collected in the past years from wildlife most likely represent multiple introduction events from livestock. The clonal origin of CC398 and its potential to disseminate and evolve through different animal host species are highlighted, calling for management practices at the livestock-wildlife axis to improve biosecurity and thus restrict S. aureus transmission and niche expansion along gradients of human influence.
摘要：
金黄色葡萄球菌是一种多才多艺的病原体,表现出广泛的宿主范围，包括人类,其他哺乳动物,和鸟类。宿主特异性决定因素，毒力,抗生素抗性基因通常由在动物-人类界面上循环的菌株共享。虽然传播动力学研究表明，人与牲畜之间的菌株交换，来源的知识，遗传多样化，金黄色葡萄球菌在野生动物中的传播驱动因素落后。在这项工作中,我们探索了伊比利亚半岛不同来源的金黄色葡萄球菌基因组，以了解种群结构，人-畜-野生动物关系的基因含量和生态位适应。通过贝叶斯推理，我们解决了这样一个假设，即野生动物中的金黄色葡萄球菌菌株来自人性化的景观，要么通过与人类接触，要么通过与牲畜的互动。应用于全基因组序列数据的系统发育重建完成了450个分离株的数据集，这些分离株具有1990-2022年期间的多个克隆和代表2008-2022年期间的CC398菌株子集。来自伊比利亚半岛的金黄色葡萄球菌的系统动力学特征表明，大多数克隆在跳入其他宿主之前在人类中广泛传播。每个宿主类别(人，牲畜,野生动物)很高(88.26%)，而从牲畜到野生动物过渡的后验概率非常高(0.99)。微生物全基因组关联分析没有证据表明基因组重排或生物标志物表明金黄色葡萄球菌生态位适应野生动物，从而支持最近的溢出。总之,我们的研究结果表明,过去几年从野生动物中收集的金黄色葡萄球菌分离株很可能代表来自家畜的多次引入事件.强调了CC398的克隆起源及其在不同动物宿主物种中传播和进化的潜力，呼吁在家畜-野生动物轴心采取管理措施，以改善生物安全性，从而限制金黄色葡萄球菌的传播和沿人类影响梯度的生态位扩展。
