As Tests for Foodborne Illness Evolve, Disease-Tracking Systems Must Adapt

A Q&A with the CDC’s Dr. Rima Khabbaz

As Tests for Foodborne Illness Evolve, Disease-Tracking Systems Must Adapt

Foodborne illness

Doctors can use new diagnostic tools for intestinal infections to obtain faster results, but health care providers still need to collect specimens from patients for additional tests that provide details vital to treatment and foodborne outbreak detection.


When facing the painful, sometimes life-threatening symptoms associated with foodborne illness, patients and their doctors want to know quickly if a bacterial infection is the cause. That’s one reason health care providers are turning to new tools, called culture-independent diagnostic tests (CIDTs), that can identify Salmonella and other dangerous bacteria in a few hours. These tests are much faster than the one to three days often needed for traditional methods that involve growing, or culturing, bacteria taken from a patient to produce an isolate—a pure sample of the disease-causing strain.

Today’s CIDTs, however, have limitations with serious implications for the nation’s disease surveillance systems, including those that track foodborne illness outbreaks and antibiotic-resistant bacteria. To understand these challenges and how public health officials are working to overcome them, Pew spoke with Dr. Rima Khabbaz, director of the National Center for Emerging and Zoonotic Infectious Diseases at the Centers for Disease Control and Prevention.

Foodborne illness

Q. How are CIDTs affecting the public health system’s ability to find foodborne disease outbreaks and track illness trends over time?

A. Unlike some traditional laboratory methods, CIDTs do not provide an isolate that we can test to determine an organism’s strain or subtype, sometimes called a DNA fingerprint, antimicrobial resistance pattern, or other attributes. This hinders our ability to make informed public health decisions about foodborne disease outbreaks and trends. For example, PulseNet—CDC’s national laboratory network that connects foodborne illnesses using DNA fingerprinting—relies on subtype and strain information to detect outbreaks and link them to specific foods.

When these links cannot be made or are delayed, contaminated food products may remain on shelves and in pantries, outbreaks may go unsolved, more people may become sick, and valuable opportunities to improve the safety of our food may be lost. It is therefore critical that the public and private sectors collaborate to find ways to obtain isolates when a CIDT indicates a foodborne infection so that we can maintain effective public health surveillance.

In addition to being faster, a single CIDT can detect multiple harmful organisms, including some that traditional tests are unable to identify. Although this offers public health and medical professionals the opportunity to understand a wider range of organisms, it also may make interpretation of test results difficult. For example, if multiple pathogens are detected, which one needs to be reported? And are there false-positive errors?

Q. How has CDC already adapted its foodborne disease surveillance systems to account for the increasing use of CIDTs?

A. CDC and many of our partner organizations have been anticipating this shift and have implemented several strategies to begin transforming public health surveillance. To start with, CDC, state health departments, and the Council of State and Territorial Epidemiologists revised the clinical criteria for reportable diseases to make sure that foodborne illnesses identified with CIDTs are captured in CDC’s historically culture-based surveillance system called FoodNet. This allows us to evaluate how CIDTs are being used and their impact on surveillance. We also can compare those results with traditional surveillance data.

Another key step is enhancing our surveillance systems with technologies that eliminate the need for a separate bacterial culture. Although technology that allows characterization of bacteria directly from a patient specimen is not yet available, CDC and its PulseNet partners, including state public health laboratories, are paving the way by implementing whole genome sequencing in all 50 states as the primary DNA fingerprinting method to link illnesses and predict a bacterium’s antibiotic resistance characteristics. CDC is also developing advanced disease-tracking technologies that can obtain foodborne bacteria’s genomic sequence information directly from a patient’s urine or blood specimen. Other CDC surveillance programs—including those for tuberculosis, legionellosis, and hospital-acquired infections—are pursuing similar approaches.

Q. What strategies are you considering to ensure the integrity of our surveillance system during these transitions to more advanced testing technologies?

A. To maintain effective surveillance in the near future, we will continue to need bacterial isolates from CIDT-identified cases. We are working with partners on ways to make this happen that include providing incentives and materials in CIDT kits to encourage clinical, diagnostic, and public health laboratories to culture CIDT-positive specimens. We are also evaluating new approaches to collecting, transporting, and culturing CIDT-positive specimens to improve recovery of isolates.

Q. How is CDC working with public health groups and companies to speed the development of advanced technologies?

A. CDC is committed to continued investment in the development of next-generation technologies through its Advanced Molecular Detection initiative. With AMD support, CDC and state public health laboratories are working to create and expand the diagnostic tools that will enable us to detect diseases and identify outbreaks without a need for culture.

CDC also works with multiple companies to foster and prepare for further changes in diagnostic testing. In the coming years, we expect to see older, less-accurate CIDTs replaced by technologies that can more accurately identify pathogen characteristics directly from specimens. We are in the final stages of creating an agreement so we can provide data to test manufacturers to help inform development of new tools such as these.

Q. What steps can medical providers and clinical labs using CIDTs take to help ensure that bacterial cultures are collected and culture results are reported to public health agencies?

A. Medical providers and clinical laboratories can reach out to their state public health departments to understand requirements for collecting patient specimens for culture after a CIDT shows an infection. They can also work collaboratively with CDC and public health laboratories to identify interim and long-term solutions that support both clinical care and public health surveillance. Medical providers can help educate patients, too, about the need for additional specimens to get an isolate and run tests to determine, for example, whether a particular antibiotic will be able to successfully treat an illness. Together, we can do more to help patients understand why CIDTs do not provide all the necessary information for clinical treatment.

Q. What steps can the public health system take to help improve foodborne illness surveillance and outbreak detection and adapt to the use of CIDTs?

A. We can act to bring about changes at the state and federal levels to help fight foodborne illnesses. With support from CDC’s Antibiotic Resistance Solutions Initiative, AMD program, and Food Safety Office, PulseNet is building infrastructure in labs in all 50 states to support whole genome sequencing of pathogens.

State agencies can help maintain the integrity of foodborne disease surveillance by adding language about CIDTs to their reporting and sample submission requirements. CDC is working with its partners on model legal and regulatory language for state requirements. State agencies can also work directly with clinical laboratories and health care providers to monitor and encourage compliance with reporting requirements and to conduct surveys to monitor the types of diagnostic tests being used. Finally, states can begin to plan for and allocate resources to pay for the additional lab tests necessary to recover bacterial isolates.

CDC is partnering with The Pew Charitable Trusts, the Association of Public Health Laboratories, and other public health groups to bring together stakeholders from federal, state, and local governments, clinical laboratories, and diagnostic manufacturers to discuss the opportunities and challenges associated with adoption of CIDTs and to generate additional short- and long-term strategies to address public health needs.

This is an exciting time of transformation that we believe will offer new opportunities for public health. However, CDC and these key stakeholders will need to strategically invest our time, resources, and energies in ways that ensure we can maintain public health surveillance in the short term and be prepared to capitalize on these new technologies in the future.

Spotlight on Mental Health

Antibiotic resistance
Antibiotic resistance

New FDA Web Tool Will Help Doctors Prescribe the Right Antibiotic

Launch implements provision of 21st Century Cures law focused on fight against antibiotic resistance

Quick View

For health care professionals, choosing the right antibiotic to treat a bacterial infection is not only critical for protecting patients’ safety and helping them get well as quickly as possible. Improved antibiotic selection is also essential to slowing the emergence of resistant pathogens and safeguarding public health.

flip to find out


flip to find out

The increase in the overall number of Campylobacter, Listeria, Salmonella, Shigella, Vibrio, and Yersinia infections diagnosed by CIDT in 2017 compared with the 2014–2016 average. TWEET
Food spread
Food spread

U.S. Should Improve Estimates of Illnesses Linked to Particular Foods

New methods and more data would advance food safety

Quick View

In December, the Interagency Food Safety Analytics Collaboration (IFSAC)—a partnership that includes the Centers for Disease Control and Prevention, Food and Drug Administration, and U.S. Department of Agriculture—released new illness estimates for 17 food categories and four major disease-causing bacteria. The data and methods used in the study demonstrate the complexity of the task, but the results also show that IFSAC’s approach needs to be improved.

Composite image of modern city network communication concept

Learn the Basics of Broadband from Our Limited Series

Sign up for our four-week email course on Broadband Basics

Quick View

How does broadband internet reach our homes, phones, and tablets? What kind of infrastructure connects us all together? What are the major barriers to broadband access for American communities?

Pills illustration
Pills illustration

What Is Antibiotic Resistance—and How Can We Fight It?

Sign up for our four-week email series The Race Against Resistance.

Quick View

Antibiotic-resistant bacteria, also known as “superbugs,” are a major threat to modern medicine. But how does resistance work, and what can we do to slow the spread? Read personal stories, expert accounts, and more for the answers to those questions in our four-week email series: Slowing Superbugs.

Explore Pew’s new and improved
Fiscal 50 interactive

Your state's stats are more accessible than ever with our new and improved Fiscal 50 interactive:

  • Maps, trends, and customizable charts
  • 50-state rankings
  • Analysis of what it all means
  • Shareable graphics and downloadable data
  • Proven fiscal policy strategies


Welcome to the new Fiscal 50

Key changes include:

  • State pages that help you keep track of trends in your home state and provide national and regional context.
  • Interactive indicator pages with highly customizable and shareable data visualizations.
  • A Budget Threads feature that offers Pew’s read on the latest state fiscal news.

Learn more about the new and improved Fiscal 50.