Although the FDA issued a recall of fresh tomatoes in June 2008 because of a statistical link to a salmonella outbreak, further research determined that jalapeno peppers were actually the culprit. Tomatoes, like other fresh fruit and vegetables, can become contaminated with pathogens such as salmonella and E. coli when they come into contact with these contaminants. But the food-borne illness most commonly associated with tomatoes is botulism, which incubates as a result of improper canning techniques.
How Botulism Spreads
According to the Colorado State University Extension, botulism bacteria and their spores exist naturally in the soil, especially in the Western United States. These spores reproduce and release toxins at pH levels near 7, or extremely non-acidic environments, and also in the absence of oxygen. The canning process can produce conditions especially hospitable to the spread of botulism, especially when fully ripe tomatoes are used because they are less acidic than unripe tomatoes.
Canning Techniques
Adding bottled lemon juice or food grade citric acid to each batch of tomatoes that you process will ensure that they have the proper acidity. Canning jars should be washed in hot soapy water and rinsed well before you fill them. Bring water to a full boil before loading your canning jars into the canner and maintain a full boil for the entire time you are processing them. When in doubt, use a recipe from a trusted source such as a canning book and follow it precisely.
Warning Signs
According to the Iowa State Extension, if the seal on your home canned tomatoes opens, you should discard these tomatoes because they have been exposed to air, facilitating the spread of pathogens that can cause food poisoning. Also discard canned tomatoes if they are cloudy looking, because this can be a sign of food-borne illness as well.
Recognition
Botulism and other pathogens liable to cause food poisoning can also be present in commercially canned tomato products. Avoid cans of tomato products that are bulging on the top or the bottom. Also avoid cans of tomato products that appear to be improperly welded, or have leaks or punctures. Glass jars of tomatoes should always pop when you open them, indicating that you have broken an intact seal.
Salmonella
According to CBS News, outbreaks of salmonella traced to raw tomatoes occur periodically. Because the agricultural industry is growing increasingly consolidated, these outbreaks have the potential to affect hundreds of people in dozens of states. The only way to absolutely ensure that you will not be exposed to pathogens on fresh tomatoes is to fully cook all tomatoes before eating them.


