Tomatoes left on the ground for 2–3 weeks pose a food safety risk. While tomato acidity inhibits some bacteria, pathogens like Salmonella, E. coli, and Clostridium botulinum can still contaminate fruit through cracks or soil contact. Mold and mycotoxins are also concerns.
When removing plants at season's end, harvest all usable fruit immediately. Till remaining fruit into the soil as green manure. This eliminates the hazard and enriches the garden for next year.
When in doubt, discard. The risk of foodborne illness outweighs the value of a few tomatoes.
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