Two months ago, when the Centers for Disease Control and Prevention released revised estimates of foodborne illness in the United States, plenty of people tried to put a positive spin on the long-awaited analysis.

Even though CDC experts cautioned against comparing the old estimates with the new to discern a trend, some saw the new estimate of 48 million episodes of foodborne illnesses per year, in contrast with the 1999 estimate of 76 million, as a dramatic drop — a sign the food supply was becoming safer.

Not so fast, say the publishers of the New England Journal of Medicine.

In a perspective published Wednesday in the Journal, Michael Osterholm, director of the University of Minnesota Center for Infectious Disease Research and Policy and a preeminent authority on food safety, channels the ghost of Paul Harvey with “Foodborne Disease in 2011 – The Rest of the Story.”

Food safety improvements made in the late 1990s are still having a positive effect, Osterholm writes, “but we’ve made little additional progress in the past decade.”

“Although the media and some food producers, processors, wholesalers, and retailers may conclude that the recent CDC estimates offer evidence of major improvements in food safety since 1999, data from active population-based surveillance offer a more nuanced and neutral picture.”

Osterholm says data collected by the Foodborne Disease Active Surveillance Network (FoodNet)– the 10 states that track lab-confirmed infections–are a better “measuring stick of the incidence of foodborne disease across geographic areas and over time” than the CDC estimates.

Based on the FoodNet data, Osterholm says, “even with improvements made during the past decade, the burden of foodborne disease persists” and only the infection rates from Shigella and E. coli O157:H7 have declined significantly.

Additionally, the increase in disease caused by non-O157 toxic E. coli suggests “that surveillance for O157 is no longer sufficient to determine the effect” of foodborne E. coli infections, he notes.

The same edition of the Journal also discusses previously unrecognized sources of foodborne disease that have caused nationwide outbreaks – such as contaminated jalapeno peppers. That outbreak, with 1,500 illnesses and two fatalities, was initially thought to be caused by tomatoes.

Outbreaks caused by contaminated fresh produce are difficult to track to their source, Osterholm points out, because like the peppers, produce from a single farm can be distributed widely and yet the food is quickly gone–consumed because it is perishable.

But will the new FDA Food Safety Modernization Act make the food supply safer?

Osterholm calls the FDA’s expanded authority and other provisions “long overdue,” but adds that without adequate funding “requiring the FDA to carry out the law’s required activities will be like trying to get blood out of a rock.”

Unless Congress appropriates enough money to implement the new law, Osterholm predicts that  “in the end, food safety in the United States cannot be expected to improve in more than an incremental manner.”