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

In this study, we introduce BacDrop, a bacterial droplet-based high throughput scRNA-seq technology that can be applied to large cell numbers. We applied BacDrop to study Klebsiella pneumoniae clinical isolates and elucidated their critical, genome-wide heterogeneity in the absence and presence of antibiotic perturbations. Overall design: An antibiotic-susceptible K. penumoniae isolate, MGH66, was treated separately with three different antibiotics, including meropenem, ciprofloxacin, and gentamicin. BacDrop was applied to these three samples as well as the untreated control. We profiled the within population heterogeneity in these 4 samples. In addition, we also applied BacDrop to a multi-drug resistant K. pneumoniae BIDMC35, and demonstrated the within population heterogeneity in this strain.

本研究介绍了BacDrop技术，一种可适配大细胞量样本的基于微滴的细菌高通量单细胞RNA测序（single-cell RNA sequencing, scRNA-seq）技术。我们利用该技术开展肺炎克雷伯菌（Klebsiella pneumoniae）临床分离株的相关研究，揭示了该菌在有无抗生素扰动条件下的全基因组层面关键异质性。

实验设计概述：选取一株抗生素敏感型肺炎克雷伯菌分离株MGH66，分别以美罗培南、环丙沙星及庆大霉素三种不同抗生素进行处理；将BacDrop技术应用于上述三个处理样本及未处理对照样本，对这4组样本的种群内异质性进行了表征分析。此外，我们还将BacDrop技术应用于一株多重耐药肺炎克雷伯菌BIDMC35，证实了该菌株的种群内异质性。