小柯机器人

美国哈佛大学Deborah T. Hung研究团队利用基于细菌液滴的单细胞RNA-seq揭示抗生素相关的异质细胞状态。该项研究成果于2023年1月27日在线发表在《细胞》杂志上。

研究人员报道了BacDrop，一种高度可扩展的细菌单细胞RNA测序技术，其克服了阻碍细菌scRNA-seq发展的许多挑战。BacDrop可以应用于数百万来自革兰氏阴性和革兰氏阳性物种的细胞。它具有通用核糖体RNA损耗和组合条形码，可实现多路复用和大规模并行测序。研究人员应用BacDrop研究了肺炎克雷伯菌临床分离株，并阐明其异种菌对抗生素应激的反应。在一个假定为同质的未受干扰的种群中，研究人员发现种群内的异质性主要是由促进抗生素耐药性演化的移动遗传元件表达所驱动。在抗生素干扰下，BacDrop揭示了与不同表型结果（包括抗生素持久性）相关的转录差异亚群。因此，BacDrop可以捕获无法被批量RNA-seq检测到的细胞状态，这将解锁细菌对扰动和更大的细菌群落（如微生物组）反应的微生物学新见解。

附：英文原文

Title: Bacterial droplet-based single-cell RNA-seq reveals antibiotic-associated heterogeneous cellular states

Author: Peijun Ma, Haley M. Amemiya, Lorrie L. He, Shivam J. Gandhi, Robert Nicol, Roby P. Bhattacharyya, Christopher S. Smillie, Deborah T. Hung

Issue&Volume: 2023-01-27

Abstract: We introduce BacDrop, a highly scalable technology for bacterial single-cell RNA sequencingthat has overcome many challenges hindering the development of scRNA-seq in bacteria.BacDrop can be applied to thousands to millions of cells from both gram-negative andgram-positive species. It features universal ribosomal RNA depletion and combinatorialbarcodes that enable multiplexing and massively parallel sequencing. We applied BacDropto study Klebsiella pneumoniae clinical isolates and to elucidate their heterogeneous responses to antibiotic stress.In an unperturbed population presumed to be homogeneous, we found within-populationheterogeneity largely driven by the expression of mobile genetic elements that promotethe evolution of antibiotic resistance. Under antibiotic perturbation, BacDrop revealedtranscriptionally distinct subpopulations associated with different phenotypic outcomesincluding antibiotic persistence. BacDrop thus can capture cellular states that cannotbe detected by bulk RNA-seq, which will unlock new microbiological insights into bacterialresponses to perturbations and larger bacterial communities such as the microbiome.

DOI: 10.1016/j.cell.2023.01.002

Source: https://www.cell.com/cell/fulltext/S0092-8674(23)00002-8