According to the Tribune-Democrat of La Junta, CO:

The Laboratory Services Division of the Colorado Department of Public Health and Environment has confirmed that a jalapeno pepper provided by an ill individual from Montezuma County has tested positive with the same DNA pattern of Salmonella Saintpaul-the strain that has caused a large, multistate outbreak of salmonella.

This comes on the heels of 1307 cases of Salmonella Saintpaul across 43 states since April 2008. As of this writing, it's still unclear where the Salmonella was introduced to the peppers. What is clear is the tainted jalapeno peppers originated in Mexico and not from United States farms. You can see the number of cases by state by clicking on the map at the left.

Best practices in avoiding Salmonella Saintpaul are currently to verify where jalapenos you purchase originated from before buying them. If you must buy jalapenos sourced from Mexico, be sure to cook them long enough to kill any bacteria before using. More details are available from the CDC link above or from the FDA.