The targets were set as part of the ‘Winnable Battles’ program launched in 2010 and covering seven public health areas.
CDC said less progress was seen in efforts to meet targeted goals in foodborne illness than other areas.
Salmonella and E. coli targets missed
It wanted to reduce the rate of foodborne illness caused by Salmonella by 14.5% from 15.2 in 2006-08 to 13 per 100,000 but the rate was 15.9 according to preliminary 2015 data.
The agency said Salmonella infections result in more hospitalizations and deaths than any other bacteria in food and incur $365m in direct medical costs annually.
Another target was the reduction of Shiga toxin-producing E. coli (STEC) O157:H7 by 29%.
From a baseline of 1.2 in 2006-08 it wanted to achieve 0.85 per 100,000 but preliminary 2015 data had the rate at 0.9.
CDC estimates prevention of a single fatal case of E. coli O157 infection saves $7m.
Tom Frieden, CDC director, said the approach was about accountability, setting ambitious goals, working with partners and rapid health improvement.
"Although there is much more to be done, because of the great work of CDC doctors, scientists, and public health specialists, and our partners at the federal, state and local levels, in hospitals and health care systems, and in the community, Americans are living longer, healthier lives and avoiding expensive and painful diseases."
Not all bad news
However, since CDC adopted whole genome sequencing (WGS) for Listeria outbreaks, the median number of Listeria illnesses per outbreak has declined by 50%.
The agency said data and results from CDC-led investigations helped shape FDA regulations for the produce safety and preventive controls rules of the Food Safety Modernization Act.
Data were also used by USDA for its performance standards, limiting Salmonella allowed in poultry carcasses, parts and ground poultry.
An analysis published this year found PulseNet, the national laboratory network that detects foodborne outbreaks, prevents an estimated 270,000 illnesses a year from the most common causes of foodborne illness: Salmonella, E. coli O157 and Listeria monocytogenes.
So an estimated $507m is saved every year in medical costs and lost productivity.
CDC said it would continue to use the approach and framework for a variety of issues and reasons despite the end of the program.
“Winnable Battles has fundamentally changed the way we work on high priority health issues,” said Kathleen Ethier, director of the Program Performance and Evaluation Office at CDC.