Salmonella enterica is comprised of genetically distinct “serovars”, that together provide an intriguing model for exploring the genetic basis of pathogen evolution. While the genomes of numerous Salmonella isolates with broad variations in host range and human disease manifestations have been sequenced, the functional links between genetic and phenotypic differences among these serovars remain poorly understood. Here, we conduct high-throughput functional genomics on both generalist (Typhimurium) and human-restricted (Typhi & Paratyphi A) Salmonella at unprecedented scale in the study of this enteric pathogen. Using a comprehensive systems biology approach, we identify gene networks with serovar-specific fitness effects across 25 host-associated stresses encountered at key stages of human infection. By experimentally perturbing these networks, we characterize previously undescribed pseudogenes in human-adapted Salmonella. Overall, this work highlights specific vulnerabilities encoded within human-restricted Salmonella that are linked to the degradation of their genomes, shedding light into the evolution of this enteric pathogen.
Overall design: This is a Rb-Tn-seq project using barcoded transposons to rapidly identify changes in gene fitness. We tested 4 Salmonella isolates against 25 stress conditions each. Tn libraries were grown to an OD~1, then back-diluted 1:50 into either a media control or stressor. The concentration of each stressor was optimized such that growth of the library decreased by ~30-50% on average. The Tn libraries were allowed to grow overnight, then DNA was extracted using a Qiagen gDNA extraction kit. A barcoding PCR was performed to amplify all Tn-associated barcodes and sent for Illumina sequencing on a Hiseq4000. Fitness changes were calculated according to published scripts. This submission includes experiments from Barseq round 6, including anaerobic LB, GMM, zinc overload, Nmedia, and protamine (second set of samples).
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