Evolutionarily stable gene clusters shed light on the common grounds of pathogenicity in the Acinetobacter calcoaceticus-baumannii complex.

Nosocomial pathogens of the Acinetobacter calcoaceticus-baumannii (ACB) complex are a cautionary example for the world-wide spread of multi- and pan-drug resistant bacteria. Aiding the urgent demand for novel therapeutic targets, comparative genomics studies between pathogens and their apathogenic relatives shed light on the genetic basis of human-pathogen interaction. Yet, existing studies are limited in taxonomic scope, sensing of the phylogenetic signal, and resolution by largely analyzing genes independent of their organization in functional gene clusters. Here, we explored more than 3,000 Acinetobacter genomes in a phylogenomic framework integrating orthology-based phylogenetic profiling and microsynteny conservation analyses. We delineate gene clusters in the type strain A. baumannii ATCC 19606 whose evolutionary conservation indicates a functional integration of the subsumed genes. These evolutionarily stable gene clusters (ESGCs) reveal metabolic pathways, transcriptional regulators residing next to their targets but also tie together sub-clusters with distinct functions to form higher-order functional modules. We shortlisted 150 ESGCs that either co-emerged with the pathogenic ACB clade or are preferentially found therein. They provide a high-resolution picture of genetic and functional changes that coincide with the manifestation of the pathogenic phenotype in the ACB clade. Key innovations are the remodeling of the regulatory-effector cascade connecting LuxR/LuxI quorum sensing via an intermediate messenger to biofilm formation, the extension of micronutrient scavenging systems, and the increase of metabolic flexibility by exploiting carbon sources that are provided by the human host. We could show experimentally that only members of the ACB clade use kynurenine as a sole carbon and energy source, a substance produced by humans to fine-tune the antimicrobial innate immune response. In summary, this study provides a rich and unbiased set of novel testable hypotheses on how pathogenic Acinetobacter interact with and ultimately infect their human host. It is a comprehensive resource for future research into novel therapeutic strategies. The spread of multi- and pan-drug resistant bacterial pathogens is a worldwide threat to human health. Understanding the genetics of host colonization and infection can substantially help in devising novel ways of treatment. Acinetobacter baumannii, a nosocomial pathogen ranked top by the World Health Organization in the list of bacteria for which novel therapeutic approaches are needed, is a prime example. Here, we have carved out the genetic make-up that distinguishes A. baumannii and its pathogenic next relatives from other and mostly apathogenic Acinetobacter species. We found a rich spectrum of pathways and regulatory modules that reveal how the pathogens have modified biofilm formation, iron scavenging, and their carbohydrate metabolism to adapt to their human host. Among these, the capability to metabolize kynurenine is particularly intriguing. Humans produce this substance to contain bacterial invaders and to fine-tune the innate immune response. But A. baumannii and closely related pathogens found a way to feed on kynurenine. This suggests that the pathogens might be able to dysregulate the human immune response. In summary, our study substantially deepens the understanding of how a highly critical pathogen interacts with its host, which substantially eases the identification of novel targets for innovative therapeutic strategies.

醋酸钙不动杆菌 - 鲍曼不动杆菌（ACB）复合群的医院病原体是多重耐药和泛耐药细菌在全球传播的一个警示例子。为了满足对新型治疗靶点的迫切需求，病原体与其非致病性近亲之间的比较基因组学研究揭示了人类 - 病原体相互作用的遗传基础。然而，现有的研究在分类学范围、系统发育信号的感知以及通过在很大程度上分析独立于其在功能基因簇中组织的基因的分辨率方面存在局限性。在此，我们在一个整合了基于直系同源的系统发育谱分析和微共线性保守性分析的系统基因组学框架中探索了3000多个不动杆菌基因组。我们描绘了鲍曼不动杆菌标准菌株ATCC 19606中的基因簇，其进化保守性表明所包含基因的功能整合。这些进化稳定基因簇（ESGCs）揭示了代谢途径、位于其靶标附近的转录调节因子，还将具有不同功能的子簇连接在一起形成高阶功能模块。我们筛选出了150个ESGCs，它们要么与致病性ACB分支共同出现，要么在其中优先被发现。它们提供了与ACB分支中致病表型的表现相一致的遗传和功能变化的高分辨率图像。关键的创新包括通过中间信使将LuxR/LuxI群体感应连接到生物膜形成的调节 - 效应级联的重塑、微量营养素清除系统的扩展以及通过利用人类宿主提供的碳源增加代谢灵活性。我们通过实验表明，只有ACB分支的成员使用犬尿氨酸作为唯一的碳源和能源，犬尿氨酸是人类产生的一种用于微调先天免疫抗菌反应的物质。总之，这项研究提供了一组丰富且无偏见的关于致病性不动杆菌如何与人类宿主相互作用并最终感染宿主的可检验假设。它是未来研究新型治疗策略的综合资源。 多重耐药和泛耐药细菌病原体的传播是对全球人类健康的威胁。了解宿主定植和感染的遗传学对于设计新的治疗方法有很大帮助。鲍曼不动杆菌是一种医院病原体，被世界卫生组织列为最需要新型治疗方法的细菌之首，是一个主要例子。在这里，我们找出了将鲍曼不动杆菌及其致病性近亲与其他大多数非致病性不动杆菌物种区分开来的基因组成。我们发现了丰富的途径和调节模块，揭示了病原体如何改变生物膜形成、铁摄取以及它们的碳水化合物代谢以适应人类宿主。其中，代谢犬尿氨酸的能力特别有趣。人类产生这种物质是为了抑制细菌入侵并微调先天免疫反应。但是鲍曼不动杆菌及其密切相关的病原体找到了以犬尿氨酸为食的方法。这表明病原体可能能够扰乱人类免疫反应。总之，我们的研究极大地加深了对一种高度关键的病原体如何与其宿主相互作用的理解，这极大地简化了创新治疗策略的新型靶点的识别。