Peanut butter is primarily three things: peanuts, oil, salt.
Sometimes [they add] sugar or another sweetener.
How, then, does salmonella end up in peanut butter?
– Corey Clark
The ingredient list can even be shorter! Remember, many brands of peanut butter consist of nothing but peanuts.
Your question — which is excellent, by the way — is one that many food safety experts are asking themselves (while vividly remembering the eerily similar E.Coli-infested spinach outbreak of 2007.)
Part of the issue here is that the United States does not have one central agency overseeing issues of food safety.
Consequently, sources of contamination are hard to track and contain.
Additionally, most of the focus on food safety (from random inspections to consistent monitoring) is relegated to meat processing plants, as they are considered “high risk” operations.
In short, the vague answer to your question is: “unsanitary plant conditions.”
This could mean anything from animal feces somehow ending up in the peanut butter (think a bird or two somehow getting inside the facility) or dirty equipment being used in the processing of peanut butter.
What is practically a given is that the contamination had to have occurred after the roasting and grinding process (both of these use extremely high temperatures that kill all strands of the salmonella virus.)