Author Readme:		Führer; Laura

Date Readme:		2026-03-04
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Titel:						Supplementary data to the publication: A screen of Salmonella enterica mutants interacting with fresh onions and alfalfa sprouts. 
						Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene.
						International Journal of Food Microbiology (2026); DOI:10.1016/j.ijfoodmicro.2026.111696

Location of data collection:			Munich, Bavaria, Germany

Version:					1.0

Corresponding Author:				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: 					Laura Führer, Competence Center for Food Safety, Chair of Food Safety and Analytics, Veterinary Faculty, LMU Munich, Oberschleissheim, Germany (ORCID ID: 0000-0003-3010-0611)
						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:					A screen of Salmonella enterica mutants interacting with fresh onions and alfalfa sprouts
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Abstract:					Illumina Sequencing FASTQ files to the publication: A screen of Salmonella enterica mutants interacting with fresh onions and alfalfa sprouts. 
						Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene.
						International Journal of Food Microbiology (2026); DOI:10.1016/j.ijfoodmicro.2026.111696

Salmonella enterica is a zoonotic pathogen that primarily causes disease through the contamination of food products. Foodborne salmonellosis outbreaks have frequently been associated with the consumption of contaminated ready-to-eat foods, including sprouts and fresh diced onions. To better control Salmonella throughout the food chain and enhance food safety, it is crucial to understand the interaction mechanisms of S.
enterica with relevant food matrices. To identify the genetic determinants underlying the persistence of Salmonella on sprouts and onions, we analyzed barcoded transposon mutant libraries in two relevant S. enterica serovars, Typhimurium and Enteritidis, on these two food matrices for five days under refrigerated storage conditions. Key fitness determinants of S. enterica were observed to be under selection, including virulence factors, two-component systems, flagellar assembly, cell wall integrity, RNA degradation, and mismatch repair systems. The phenotype of selected S. Typhimurium mutants was subsequently verified in competition assays. Our study showed that disruption of tolC, encoding a multidrug efflux pump, resulted in a stronger fitness disadvantage on onions than on sprouts and nutrient-rich media. Furthermore, the fitness disadvantage of mutants in oxyR, a key regulator of the oxidative stress response, was much reduced on sprouts, compared to onions or standard growth conditions. This study provides a comprehensive overview of the genetic determinants that influence the interaction of S. enterica with these fresh produce items under real-world conditions.


Keywords:					food safety; foodborne pathogen; ready-to-eat products; salmonellosis; microbial contamination; fresh produce; transposon insertion sequencing 

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 files are sorted by the primers used and the download includes a sample key with samples and their corresponding file names.

File format: 					FASTQ

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