Studying human-adapted pathogens like Shigella flexneri is challenging because animal models poorly mimic human physiology and suffer from infection bottlenecks. We developed a scalable workflow combining human organoid infections with Transposon Insertion Sequencing to map disruptions of Shigella genes affecting colonization. Systematic optimization of mutant library size, infection and culture conditions along with Bayesian...

Summary Contaminated water is a major risk factor associated with the transmission of Salmonella enterica serovar Typhi ( S. Typhi), the aetiological agent of human typhoid. However, little is known about how this pathogen adapts to living in the aqueous environment. We used transcriptome analysis (RNA‐seq) and transposon mutagenesis (TraDIS) to characterize these adaptive changes and identify multiple genes that contribute to...