Di Martino Maria Letizia, Jenniches Laura, Bhetwal Anjeela, Eriksson Jens, Lopes Ana C C, Ntokaki Angelika, Pasqua Martina, Sundbom Magnus, Skogar Martin, Graf Wilhelm, Webb Dominic-Luc, Hellström Per M, Mateus André, Barquist Lars, Sellin Mikael E
Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden.
Helmholtz Institute for RNA-based Infection Research (HIRI), Helmholtz Centre for Infection Research (HZI), Würzburg, Germany.
Nat Genet. 2025 Jun 12. doi: 10.1038/s41588-025-02218-x.
Studying the pathogenesis of human-adapted microorganisms is challenging, since small animal models often fail to recapitulate human physiology. Hence, the comprehensive genetic and regulatory circuits driving the infection process of principal human pathogens such as Shigella flexneri remain to be defined. We combined large-scale Shigella infections of enteroids and colonoids with transposon-directed insertion sequencing and Bayesian statistical modeling to address infection bottlenecks, thereby establishing the comprehensive genome-wide map of Shigella genes required to infect human intestinal epithelium. This revealed the Shigella virulence effectors essential for epithelial cell colonization across geometries and intestinal segments, identified over 100 chromosomal genes involved in the process and uncovered a post-transcriptional mechanism whereby tRNA-modification enzymes and differential codon usage exert global control of a bacterial virulence program. Our findings provide a broadly applicable framework for combining advanced organotypic tissue culture with functional genomics and computational tools to map human-microorganism interactions at scale.
研究适应人类的微生物的发病机制具有挑战性，因为小动物模型往往无法重现人类生理学特征。因此，驱动诸如福氏志贺氏菌等主要人类病原体感染过程的全面遗传和调控回路仍有待确定。我们将肠道类器官和结肠类器官的大规模志贺氏菌感染与转座子定向插入测序和贝叶斯统计建模相结合，以解决感染瓶颈问题，从而建立了感染人类肠道上皮所需的志贺氏菌基因的全基因组综合图谱。这揭示了志贺氏菌毒力效应因子对于跨几何形状和肠道节段的上皮细胞定植至关重要，确定了该过程中涉及的100多个染色体基因，并发现了一种转录后机制，即tRNA修饰酶和密码子使用差异对细菌毒力程序进行全局控制。我们的研究结果提供了一个广泛适用的框架，用于将先进的器官型组织培养与功能基因组学和计算工具相结合，以大规模绘制人类与微生物的相互作用图谱。
