Rapid diagnostic tests help diagnose infections quicker than traditional culture methods.
But as they do not provide isolates (the organism that caused illness), it is not possible to run tests that determine an organism’s DNA fingerprint, strain, subtype or resistance pattern which could lead to contaminated products remaining on shelves longer and more people becoming sick.
Without DNA fingerprints from the bacteria, PulseNet, a laboratory network that connects foodborne illness cases to detect outbreaks, won’t be able to detect clusters. Without cluster detection outbreaks may not be recognized.
The agency made the comments as it revealed Campylobacter and Salmonella caused the most reported bacterial foodborne illnesses in 2016.
CDC’s Foodborne Diseases Active Surveillance Network (FoodNet) collects data on 15% of the US population.
It describes preliminary surveillance data for 2016 on the nine pathogens and changes in incidence compared with 2013-2015.
FoodNet identified 24,029 infections, 5,512 hospitalizations and 98 deaths caused by these pathogens.
Reported illnesses by germ are Campylobacter (8,547), Salmonella (8,172), Shigella (2,913), Shiga toxin-producing E. coli (1,845), Cryptosporidium (1,816), Yersinia (302), Vibrio (252), Listeria (127) and Cyclospora (55).
It is the first time calculations include bacterial infections diagnosed only by rapid diagnostic tests as well as those confirmed by traditional culture-based methods.
The observed increases in incidence of confirmed or CIDT positive–only infections could be due to increased testing, varying test sensitivity, an increase in infections or a combination of reasons.
The use of culture-independent diagnostic tests (CIDTs) by clinical labs to detect enteric pathogens has been increasing since FoodNet began surveying clinical labs in 2010.
CIDTs detect bacterial pathogen antigen, nucleic acid sequences, or for STEC, Shiga toxin or Shiga toxin genes, in a stool specimen or enrichment broth.
A large proportion of CIDT positive specimens were not reflex cultured, which is needed to obtain isolates for distinguishing pathogen subtypes and monitoring trends.
Robert Tauxe, director of CDC’s division of Foodborne, Waterborne and Environmental Diseases, said the report identifies changes in ways clinicians are testing for foodborne illness and gaps in information as a result.
“We need foodborne-illness trend data to monitor progress toward making our food supply safer," he said.
“It’s important that laboratories continue to do follow-up cultures on CIDT-positive patients so public health officials can get the information needed to protect people from foodborne illness.”
A CIDT positive–only bacterial infection is a positive CIDT result not confirmed by culture.
The proportion of infections CIDT positive without culture confirmation in 2016 was largest for Campylobacter (32%) and Yersinia (32%), followed by STEC (24%), Shigella (23%), Vibrio (13%) and Salmonella (8%).
The overall increase in CIDT positive-only infections for these pathogens was 114% compared with 2013–2015.
When including confirmed and CIDT positive–only infections, incidence rates in 2016 were higher for each of them.
Susan Mayne, director of FDA’s Center for Food Safety and Applied Nutrition, said progress is being made in detecting and responding to foodborne illness but the focus remains on prevention.
“The final rules we are implementing under the FDA Food Safety Modernization Act focus on prevention, and we will continue to work closely with other government agencies at the local, state and federal levels, as well as our tribal and territorial partners, to support industry compliance with the new requirements.”
Jim O’Hara, director of health promotion policy at the Center for Science in the Public Interest, said the progress combatting foodborne illness was a ‘mixed bag’.
“For example, the 2016 incidence of confirmed Campylobacter was lower, but confirmed rates of incidence were higher for pathogens such as Shiga toxin-producing E. coli. The burden of foodborne illness in the US continues to be high and progress in food safety, especially prevention, is slow.
“FDA, CDC and state health departments that often receive funding from federal sources need more investments, not the 18 percent across-the-board cut for the Department of Health and Human Services offered by the Trump Administration.”
Interpreting incidence and comparisons
Increasing use of CIDTs presents challenges when interpreting increases in incidence, said CDC.
It is difficult to interpret whether changes are true or how much is due to moves in diagnostic testing practices and procedures, added the agency.
“For example, the incidence of confirmed Campylobacter infections in 2016 was significantly lower than the 2013–2015 average. However, when including CIDT positive–only infections, a slight but not significant increase occurred.
“For STEC and Yersinia, the incidence of confirmed infections alone and confirmed or CIDT positive–only infections in 2016 were both significantly higher than the 2013–2015 average; the magnitude of change approximately doubled when analyzing CIDT positive–only infections.
“Listeria infections, for which CIDTs have not previously been available, and cases of HUS, which do not rely on CIDT, did not change significantly in 2016 compared with the previous three years.”
Compared with 2013–2015, the 2016 incidence of Campylobacter infection was lower (11%) when including only confirmed infections but was not significantly different when including confirmed or CIDT positive–only infections.
Incidence of STEC infection was significantly higher for confirmed infections (21%) and confirmed or CIDT positive–only infections (43%).
Incidence of Yersinia infection was higher for confirmed (29%) and confirmed or CIDT positive–only infections (91%).
Incidence of confirmed Cryptosporidium infection was also higher compared with 2013–2015 (45%).
The Consumer Federation of America said the data demonstrates little progress on reducing illnesses.
“The data underscores the urgent need for policy reforms to address Salmonella and other foodborne pathogens, particularly in meat and poultry,” said Thomas Gremillion, director of CFA’s Food Policy Institute.
Gremillion said technological change is one of many factors that complicate surveillance.
“Despite the uncertainty, however, we must set goals and attempt to determine whether we are moving towards them, taking advantage of all the resources available. CDC has said that the agencies are developing new tools to continue to track progress toward reducing foodborne illness, and we look forward to learning how those will be applied.”
“Incidence and Trends of Infections with Pathogens Transmitted Commonly Through Food and the Effect of Increasing Use of Culture-Independent Diagnostic Tests on Surveillance - Foodborne Diseases Active Surveillance Network, 10 U.S. Sites, 2013–2016"
Authors: Marder EP, Cieslak PR, Cronquist AB, et al.