Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China; Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.
Cell Rep. 2024 Aug 27;43(8):114602. doi: 10.1016/j.celrep.2024.114602. Epub 2024 Aug 12.
Klebsiella aerogenes is an understudied and clinically important pathogen. We therefore investigate its population structure by genome analysis aligned with metadata. We sequence 130 non-duplicated K. aerogenes clinical isolates and identify two inter-patient transmission events. We then retrieve all publicly available K. aerogenes genomes (n = 1,026, accessed by January 1, 2023) and analyze them with our 130 genomes. We develop a core-genome multi-locus sequence-typing scheme. We find that K. aerogenes is a species complex comprising four phylogroups undergoing evolutionary divergence, likely forming three species. We delineate remarkable clonal diversity and identify three worldwide-distributed carbapenemase-encoding clonal clusters, representing high-risk lineages. We uncover that K. aerogenes has an open genome equipped by a large arsenal of antimicrobial resistance genes. We identify two genetic regions specific for K. aerogenes, encoding a type VI secretion system and flagella/chemotaxis for motility, respectively, both contributing to the virulence. These results provide much-needed insights into the population structure and pan-genomes of K. aerogenes.
产酸克雷伯菌是一种研究较少但临床重要的病原体。因此，我们通过与元数据对齐的基因组分析来研究其种群结构。我们对 130 个非重复的产酸克雷伯菌临床分离株进行测序，并确定了两起患者间传播事件。然后，我们检索了所有公开可用的产酸克雷伯菌基因组（n=1026，截至 2023 年 1 月 1 日访问），并使用我们的 130 个基因组进行分析。我们开发了一个核心基因组多位点序列分型方案。我们发现产酸克雷伯菌是一个由四个经历进化分歧的系统发育群组成的种复合体，可能形成三个种。我们描绘了显著的克隆多样性，并确定了三个在全球范围内传播的碳青霉烯酶编码克隆群，代表高风险谱系。我们发现产酸克雷伯菌具有开放的基因组，配备了大量的抗生素耐药基因。我们确定了两个特定于产酸克雷伯菌的遗传区域，分别编码一种 VI 型分泌系统和鞭毛/趋化性以实现运动，这两者都有助于毒力。这些结果为产酸克雷伯菌的种群结构和泛基因组提供了急需的见解。
