First off, nothing has been said that the culprit is whole tomatoes.
It has been assumed only by knee-jerker reactionists. It may be fresh tomato salsa, etc. that people no longer make themselves and buy it packaged in the produce section.
Many of these products are grown and packaged in Mexico these days.
I find it hard to believe that the list of whole tomato types listed in the article are said to be safe. All of which contact the ground regularly.
It may be contaminated by mechanized picking equipment that breaks the skin after the tomato is harvested. At which point, it stops producing acid and bacteria killing PH.
Here again is much knee-jerking before the actual source or the type is identified or defined.