The tomato has been getting a bad rap recently, both justifiably and unjustifiably. Not long ago, tomatoes were blamed for a Salmonella outbreak, when the bad guys were really serraños (hot peppers) and jalapeños. However, raw tomatoes have been responsible for some outbreaks, mostly caused by restaurants.
You don't want Salmonella in your BLT, because you may end up with vomiting, diarrhea (including bloody diarrhea), and fever.
Salmonella is often traced back to the raw tomato; even though the tomato’s acidic level is often at a range that most bacteria don’t like, Salmonella is able to live on sliced or cut tomatoes. In the past, many restaurants would let tomatoes sit on the counter, giving any Salmonella that might be present a chance to grow. Tomatoes are now deemed a potentially hazardous food (PHF/TCS food in restaurant terms), and restaurants must abide by stricter rules when they use them. When you prepare any raw tomatoes in your home, make sure to refrigerate them right away to keep Salmonella from growing.