Author Readme:		Beck; Maximilian

Date Readme:		2026-09-16
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Titel:						Data to: Host-associated fitness determinants support Salmonella Choleraesuis persistence on fresh-cut onions
                                                Beck, Maximilian; Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene.
						DOI will be published soon

Location of data collection:			Munich, Bavaria, Germany

Version:					1.0

Corresponding Authors:				Maximilian Beck, e-mail: M.Beck@ls.vetmed.uni-muenchen.de, Irene Esteban-Cuesta, e-mail: Irene.Esteban@ls.vetmed.uni-muenchen.de, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich Oberschleissheim, Germany
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Authors: 					Maximilian Beck, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany (ORCID ID: 0009-0003-7853-6745)
                                                Laura Führer, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany
						Steffen Porwollik, Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, United States of America
						Weiping Chu, Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, United States of America
						Verena Hohenester, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany
						Irmak Sah, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany
						Michael McClelland, Department of Microbiology and Molecular Genetics, School of Medicine, University of California, Irvine, CA, United States of America
						Claudia Guldimann, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany
						Irene Esteban-Cuesta, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany (ORCID ID: 0000-0002-5004-9529)
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Project name:					Host-associated fitness determinants support Salmonella Choleraesuis persistence on fresh-cut onions
Abstract:					Illumina Sequencing FASTQ files to the publication: Host-associated fitness determinants support Salmonella Choleraesuis persistence on fresh-cut onions.
						Beck, Maximilian; Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene.
						DOI will be published soon

Fresh diced onions are increasingly consumed as ready-to-eat ingredients in the growing convenience food market. Because in this context onions do not undergo heat treatment, understanding the genetic mechanisms controlling Salmonella persistence on this food matrix is critical for developing precision food safety strategies. In this study, a barcoded transposon mutant library comprising 35,432 unique insertion mutants in a plant-derived S. enterica serovar Choleraesuis strain was used to identify genetic mechanisms contributing to fitness on onions during cold storage at 8°C. Insertions in 350 insertion mutants resulted in negative fitness effects, including 138 located in intergenic regions, 42 hypothetical proteins and 170 genes with assigned functions, 42 of which are classically associated with host-infection or virulence. Competitive fitness assays confirmed food matrix-specific fitness effects for mutants with disruptions in ail_1, encoding a cell attachment and invasion protein, and spaP_1, a key type III secretion system component. Furthermore, no growth was observed for mutants with insertions in acrB_1, encoding an acridine efflux pump component, and spaQ_1, also involved in the type III secretion system. Polar effects were identified for four genes (oxyR_1, csgD, mnmG, and yciF), where fitness impact depended on the insertion orientation. Our study highlights how onions provide an environment that elicits mechanisms similar to those encountered during host infection. Comparative analysis reveals shared pathways with S. Enteritidis but limited overlap with S. Typhimurium, underscoring serovar-specific variations in their environmental adaptive response. These insights support the identification of control targets for precision food safety interventions along the production and storage chain.

Keywords:					transposon insertion sequencing, salmonellosis, microbial contamination, transposon library, food safety

Method of data collection:	 		Illumina sequencing was performed as a dual-indexed paired-end 100 or 150 base run on a NovaSeq 6000 with one million reads/sample.

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Files:						The dataset contains raw Illumina sequencing files generated from the barcoded transposon mutant library screen. The files are organized according to the primers used. A sample key is included, linking each sample to the corresponding file name.
File format: 					Illumina FASTQ files, provided as compressed FASTQ files where applicable.

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Funding: 					The project was funded by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG). Grant No. 494875429.