Table_10_Crucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1.docx

Acinetobacter baumannii is one of the most important nosocomial pathogens able to rapidly develop extensive drug resistance. Here, we study the role of accessory genome in the success of the globally disseminated clone 1 (GC1) with functional and genomic approaches. Comparative genomics was performed with available GC1 genomes (n = 106) against other A. baumannii high-risk and sporadic clones. Genetic traits related to accessory genome were found common and conserved along time as two novel regions of genome plasticity, and a CRISPR-Cas system acquired before clonal diversification located at the same loci as “sedentary” modules. Although identified within hotspot for recombination, other block of accessory genome was also “sedentary” in lineage 1 of GC1 with signs of microevolution as the AbaR0-type genomic island (GI) identified in A144 and in A155 strains which were maintained one month in independent experiments without antimicrobial pressure. The prophage YMC/09/02/B1251_ABA_BP was found to be “mobile” since, although it was shared by all GC1 genomes, it showed high intrinsic microevolution as well as mobility to different insertion sites. Interestingly, a wide variety of Insertion Sequences (IS), probably acquired by the flow of plasmids related to Rep_3 superfamily was found. These IS showed dissimilar genomic location amongst GC1 genomes presumably associated with promptly niche adaptation. On the other hand, a type VI secretion system and three efflux pumps were subjected to deep processes of genomic loss in A. baumannii but not in GC1. As a whole, these findings suggest that preservation of some genetic modules of accessory genome harbored by strains from different continents in combination with great plasticity of IS and varied flow of plasmids, may be central features of the genomic structure of GC1. Competition of A144 and A155 versus A118 (ST 404/ND) without antimicrobial pressure suggested a higher ability of GC1 to grow over a clone with sporadic behavior which explains, from an ecological perspective, the global achievement of this successful pandemic clone in the hospital habitat. Together, these data suggest an essential role of still unknown properties of “mobile” and “sedentary” accessory genome that is preserved over time under different antibiotic or stress conditions.

鲍曼不动杆菌(Acinetobacter baumannii)是最重要的医院病原菌之一，可快速演化出广泛耐药性。本研究采用功能基因组学与基因组学方法，探究附属基因组(accessory genome)在全球传播克隆1（GC1）的成功定植与流行过程中所发挥的作用。研究团队针对106株已公开的GC1基因组，与其他鲍曼不动杆菌高风险克隆及散发克隆开展比较基因组学分析。结果显示，与附属基因组相关的遗传特征普遍存在且长期保守：包括两个全新的基因组可塑性区域，以及在克隆分化前获取的、与“定居型”模块位于同一基因座的CRISPR-Cas系统(CRISPR-Cas system)。尽管该区域被鉴定为重组热点，但GC1谱系1中的另一附属基因组区块同样呈现“定居型”特征，并存在微进化迹象——例如在A144和A155菌株中鉴定到的AbaR0型基因组岛（GI），这两株菌在无抗菌药物压力的独立实验中被持续培养长达一个月。前噬菌体YMC/09/02/B1251_ABA_BP被鉴定为“移动型”元件：尽管所有GC1基因组均携带该前噬菌体，但其展现出高度的固有微进化特性，且可移动至不同插入位点。值得注意的是，研究发现了大量插入序列(Insertion Sequences, IS)，这些序列大概率通过与Rep_3超家族相关的质粒流转获得；它们在GC1基因组中的基因组位置存在显著差异，推测与GC1的快速生态位适应密切相关。另一方面，VI型分泌系统(type VI secretion system)与三种外排泵(efflux pumps)在鲍曼不动杆菌中经历了显著的基因组丢失过程，但在GC1中并未出现此类丢失。综合来看，上述研究结果表明：不同大陆来源菌株所携带的部分附属基因组遗传模块得以保留，结合插入序列的高度可塑性与多样的质粒流转，或许是GC1基因组结构的核心特征。在无抗菌药物压力的条件下开展的A144、A155与A118（序列型404/ND，ST 404/ND）的竞争实验显示，GC1相较于散发型克隆具备更强的生长能力，这从生态学视角解释了该成功流行克隆在医院生境中的全球传播优势。综上，本研究数据表明，在不同抗生素或胁迫条件下长期保留的“移动型”与“定居型”附属基因组的未知特性，可能发挥着至关重要的作用。