Author Readme:		Beck; Maximilian 

Date Readme:		2026-07-23
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Titel:						Data to: Identification of genes promoting fitness of a plant-associated Salmonella Choleraesuis strain on alfalfa sprouts during cold storage.
                                                Beck, Maximilian; Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene. 
						Applied and Environmental Microbiology (2026); 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:					Identification of genes promoting fitness of a plant-associated Salmonella Choleraesuis strain on alfalfa sprouts during cold storage
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Abstract:					Illumina Sequencing FASTQ files to the publication: Identification of genes promoting fitness of a plant-associated Salmonella Choleraesuis strain on alfalfa sprouts during cold storage.
						Beck, Maximilian; Führer, Laura; Porwollik, Steffen; Chu, Weiping; Hohenester, Verena; Sah, Irmak; McClelland, Michael; Guldimann, Claudia; Esteban-Cuesta, Irene.
						Applied and Environmental Microbiology (2026); DOI will be published soon

Consumption of sprouted seeds, such as alfalfa sprouts, has increased in recent years due to their nutritional value and antioxidant content. However, these products have repeatedly been implicated in outbreaks of foodborne pathogens, including Salmonella enterica. Although host-adapted Salmonella serovars are less frequently associated with foodborne illness, infections caused by these serovars often result in invasive and severe outcomes, highlighting the importance of understanding their persistence in food production systems. Moreover, the variability among Salmonella serovars requires characterization beyond the most prevalent types to support the development of precision food safety strategies effective across the diversity of serovars capable of contaminating fresh produce. Here, a plant-internalized S. Choleraesuis strain was used as a model to investigate persistence mechanisms on alfalfa sprouts. A barcoded transposon mutant library comprising approximately 33,000 unique insertions was generated, along with a collection of individual insertion mutants. These resources were used to identify genetic determinants contributing to strain fitness on sprouts under abusive cold storage (8°C) simulating commercial shelf-life environments. Genome-wide analyses identified negative selection for mutants with insertions in eda, fabF, lpp1_2, pnp, stpA, SCHChr_03621 and two intergenic regions. Competition assays confirmed fitness defects associated with eda, encoding a key enzyme of the Entner-Doudoroff pathway; mnmG, encoding a tRNA modification enzyme involved in translational fidelity; and fabF, involved in fatty acid biogenesis. These findings provide a genome-wide perspective on mechanisms enabling persistence on sprouts of a plant-associated, host-adapted Salmonella strain during cold storage and inform risk assessment and intervention design within precision food safety frameworks.

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.