In this study, we detail a novel approach that combines bacterial fitness fluorescent reporter strains with scRNA-seq to simultaneously acquire the host transcriptome, surface marker expression, and bacterial phenotype for each infected cell. This approach facilitates the dissection of the functional heterogeneity of M. tuberculosis–infected alveolar (AMs) and interstitial macrophages (IMs) in vivo. We identify clusters of pro-inflammatory AMs associated with stressed bacteria, in addition to three different populations of IMs with heterogeneous bacterial phenotypes. Finally, we show that the main macrophage populations in the lung are epigenetically constrained in their response to infection, while inter-species comparison reveals that most AMs subsets are conserved between mice and humans. This conceptual approach is readily transferable to other infectious disease agents with the potential for an increased understanding of the roles that different host cell populations play during the course of an infection.

中文翻译：

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受感染肺中结核分枝杆菌表型和巨噬细胞谱系的单细胞分析

在这项研究中，我们详细介绍了一种将细菌适应性荧光报告菌株与 scRNA-seq 相结合的新方法，以同时获取每个感染细胞的宿主转录组、表面标记表达和细菌表型。这种方法有助于剖析结核分枝杆菌的功能异质性– 体内感染的肺泡 (AMs) 和间质巨噬细胞 (IMs)。除了具有异质细菌表型的三个不同的 IMs 群之外，我们还确定了与压力细菌相关的促炎 AMs 簇。最后，我们表明肺中的主要巨噬细胞群在对感染的反应方面受到表观遗传限制，而物种间比较表明大多数 AMs 亚群在小鼠和人类之间是保守的。这种概念方法很容易转移到其他传染病病原体，从而有可能加深对不同宿主细胞群在感染过程中所起的作用的理解。