Results of modelling by the FSA estimate this equates to more than 100,000 fewer cases of Campylobacter across the UK compared to that baseline.
There were 59,142 confirmed lab reports of Campylobacter in 2016 and 63,083 in 2015.
Figures come from Public Health England, Public Health Wales, Health Protection Scotland and Public Health Agency in Northern Ireland.
How baseline was calculated
The baseline was calculated as the average of confirmed lab reports between 2009 and 2013 which was 71,261.
The decrease is scaled up to take account of underreporting at a rate of 9.3. This gives an overall reduction of 113,000 cases when applied to the 12,119 decrease in confirmed laboratory reports.
The 100,000 fewer cases refers to the figures once they have been scaled up to take account of underreporting. 12,119 x 9.3 = 113,000 (which has been rounded to 100,000).
Heather Hancock, chair of the FSA, said: “In the absence of any other clear indicators, we can reasonably say that the work that we and the food industry have done from farm to fork has given us this really positive result for public health.”
First results using new method
The agency also published the first set of results from the third year survey of Campylobacter on fresh shop-bought whole chickens from August to December 2016.
A total of 7% of chickens tested positive within the highest band of contamination (more than 1,000 colony forming units per gram).
This was down from 12% for the same period in 2015 and 20% in 2014.
Chickens that tested positive for the pathogen at any level was at 56%, down from 66% in 2015 and 78% in 2014.
However, it was up from 50% during the third quarter of testing, from January to March 2016.
These are the first results since the survey was suspended and method changed from measuring the amount of Campylobacter on 25g of chicken neck skin - generally the most contaminated part.
The current method involves measuring it on the 10g portion of neck skin only. It was changed as the old method could not be relied upon to give accurate retailer comparisons.
The FSA said it is changing the way it looks at levels of Campylobacter on chickens at the slaughterhouse by ending the current monitoring programme.
The agency said this will not impact the retail survey and will be the method through which the large processors and retailers will be measured.
To focus on the processors which are not making significant improvements (generally small-medium sized poultry plants), the FSA is considering targeting specific sites with inspections.
Hancock said large retailers and major processing plants had invested a lot of effort and money into interventions to tackle the problem.
“We commend the efforts of the larger retailers and the major processing plants who supply them, all of which have shown significant improvement and many have achieved the target we set to reduce the highest levels of Campylobacter,” she said.
“But there is more to be done and our focus now is on encouraging the smaller retailers and processors, who generally haven’t met target levels, to follow the lead of the major players and we are considering how we can best help them and monitor their progress.”
Alex Neill, Which? managing director of home services, said: “It is encouraging to see that overall levels of Campylobacter in chickens are falling and that major retailers are meeting the FSA’s target.
“However there is no room for complacency as the survey shows that over half of chickens are contaminated and that this can vary greatly depending on where consumers shop.”
Meanwhile in Scotland, research shows Campylobacter is the biggest cause of food poisoning and that 55-75% of cases are associated with chicken.
Health Protection Scotland said there had been a decline of 15.5% in laboratory reports of human cases of Campylobacter in 2016, compared to the previous year.
Professor Norval Strachan, FSS chief scientific adviser, said it was the second year of decline.
“The reported reduction in the levels of Campylobacter in chicken is encouraging. However, it is important for Food Standards Agency, Food Standards Scotland and industry to continue working in partnership to protect public health.”
A total of 5,296 laboratory reports of Campylobacter were received by HPS last year.
This was a decrease of 968 (15.5%) compared to 2015 when 6,262 isolates were reported. Figures from 2016 represent a decline of 1,340 (20.2%) on the peak of 6,636 reports in 2014.
Incidence rates are higher in children under one year compared with older children and young adults and then increase with the highest rates among those 50 years and older.
No outbreaks of Campylobacter were reported to ObSurv last year (the surveillance system for all general outbreaks of infectious intestinal disease in Scotland).
Since ObSurv was established in 1996 there have been 35 general outbreaks of Campylobacter.
HPS received reports of 836 isolates of non-typhoidal Salmonella last year – an increase of around 4% on the 803 in 2015. This compares to 717 and 814 in 2014 and 2013 respectively.
There were 362 reports of Salmonella Enteritidis in 2016 compared to 315 in 2015. The most commonly reported phage type of S. Enteritidis was PT8 with 138 reports (compared to 102 in 2015).
Salmonella Typhimurium decreased slightly with 128 reports compared to 133 in 2015.
In 2016 there were seven outbreaks of Salmonella reported to ObSurv compared with six in 2015. Five reported in 2016 were part of UK outbreaks.