III. 2018 Forum on Culture-Independent Diagnostics: Charting a Path for Public Health

2018 FSMA Annual Report


Clinical diagnostic microbiology is undergoing one of the most significant technological revolutions since the time of Pasteur. DNA technology is making it possible for physicians to quickly obtain more information about what is making their patients sick without the need for time-consuming culture-based testing. Public health surveillance programs rely on clinical microbiology data for a variety of functions, such as detecting outbreaks, monitoring trends, and informing policy. Adapting practices to the new types of data is essential for public health to maintain its critical functions and to make full use of this expanded potential. The 2018 Forum on Culture-Independent Diagnostics was convened at the Pew headquarters in Washington, DC, to bring together subject matter experts to help public health forge a path in the CIDT era. Because of the importance of the topic, the FSMA-SWG attended the meeting in lieu of one of its biannual meetings.


Foodborne disease is largely preventable, but prevention requires information about the foods that are making people ill and the means by which the foods become contaminated. The programs for tracking and managing specific diseases such as salmonellosis, campylobacteriosis, and pathogenic E. coli diseases have been based on patient culture reports from physicians and clinical microbiology laboratories. “Isolates,” or samples of the bacteria grown as part of the culture process, are sent to public health agencies and play a critical role in disease monitoring, outbreak detection, and outbreak investigation. As the increasing use of CIDTs replaces the use of culture, public health agencies must make a wide range of adjustments to the methods and policies.

Over the years, the lessons learned from outbreak investigations conducted by state and local health departments, CDC, FDA, and USDA have triggered safety improvements by industry for a wide range of foods such as leafy green vegetables, tree nuts, vine vegetables, melons, flour, beef, poultry, eggs, spices, cereal, peanut butter, and ice cream. PulseNet, a collaboration of 83 local, state, and federal laboratories in all 50 states, has been the primary detection mechanism for large multistate outbreaks involving commercial products. A 2016 economic analysis showed that PulseNet prevents at least 270,000 cases and one half billion dollars in costs and productivity losses per year.6 PulseNet works by conducting “DNA fingerprinting” on illness-causing bacteria (pathogen “isolates”) from patients who have become ill with Salmonella, E. coli, Listeria, or other bacteria. Matching DNA fingerprints among multiple cases in a similar timeframe triggers an outbreak investigation, as patients with matching isolates may have consumed the same contaminated food, even if they are physically located in different parts of the country. This process depends on patients seeking medical care, physicians ordering diagnostic tests, and clinical laboratories finding a pathogen and sending an isolate to their local PulseNet laboratory. For the past several years, PulseNet has become even more effective as pulsed-field gel electrophoresis (PFGE), the older “DNA fingerprinting” method, has been replaced by WGS. Both PFGE and WGS depend on isolates.

Although CIDTs have been emerging in clinical microbiology for over 30 years, it wasn’t until the 2010s that FDA cleared “syndromic panels” to simultaneously test for many pathogens, including bacteria, viruses, and parasites. These panels streamlined clinical laboratory processes, saving time and potentially money. The panels also provided data to physicians more rapidly than culture methods. In 2012, syndromic CIDT use was still rare, but it was already clear that the use of this type of testing would rise rapidly as the market matured. In anticipation of this trend, CDC, the Association of Public Health Laboratories (APHL), and the Council for State and Territorial Epidemiologists (CSTE) organized a “Forum on Culture-Independent Diagnostics” to chart a path for public health and to preemptively address expected issues and disruptions. The FSMA-SWG attended the 2012 CIDT Forum and commented on the importance of CIDTs in its annual reports for FY 2013–2017.

2018 CIDT Forum Goals and Composition

By 2018, the trend toward CIDTs had accelerated and was starting to impact both negatively and positively on a number of public health surveillance activities. Through a collaborative effort, CDC, APHL, CSTE, Pew, and The Ohio State University organized a 2nd Forum on Culture-Independent Diagnostics to build upon the 2012 meeting and the intervening 6 years of experience with CIDT trends.

As with the introduction of any transformative technology, the introduction of CIDTs into the medical marketplace is causing wide-ranging effects, including immediate enhancement of clinical medicine and public health but also widespread disruption of existing systems. To more effectively harness the potential of CIDT technology and address its disruptive impacts, the 2018 Forum bought together leaders and subject matter experts from clinical microbiology, medicine, epidemiology, molecular biology, health law, policy, economics, and medical/laboratory regulation who represented government, academia, and the medical device industry. The Forum focused on public health aspects, and its goals included (1) increasing awareness among participants about the scope of the problem, current impacts, and likely impacts; (2) evaluating current efforts to address CIDT issues in public health and identify knowledge gaps; and (3) brainstorming new ideas and potential solutions. To achieve these goals, the Forum included plenary sessions to familiarize participants with all of the major topics, along with three tracts to explore subject-specific issues, including (1) public health practice, (2) strategies for preserving isolate-based surveillance until CIDT-compatible surveillance mechanisms are in place, and (3) technological approaches to characterize pathogens for public health activities without the need for culture.

The FSMA-SWG attended the 2018 CIDT Forum in lieu of its biannual meeting and provided the observations and guidance listed below. Of note, the BSC FSMA-SWG recommends that CDC develop an action plan that CDC and stakeholders can use to guide efforts and ensure continued foodborne illness surveillance into the future.


Public health practice

Adapting reportable enteric disease case definitions to include CIDTs

Local, state, federal, and international case definitions have been based on culture. Since an increasing percentage of total cases are now diagnosed by CIDT and not culture, there is concern that cases would not be reported if alternate definitions are not allowed, leading to inaccurate measures of burden and trends. Without accurate data, it will be difficult to measure the effectiveness of public health control programs and inform policy and the public. CIDTs have varying performance characteristics, and trends may not exactly align with culture data. Further, CIDTs may be used differently from culture (i.e., ordered more or less frequently or for different uses), which may alter the denominator used for detecting and analyzing trends. The Working Group recommended the following:

  • Case definitions should be synchronized with current diagnostic practices, including CIDTs, and not be so complex as to discourage reporting.
  • CDC should continue monitoring the uptake of culture-independent testing by clinical labs and the impact of such testing on the number of isolates available for WGS testing to identify outbreaks.
  • Studies should be conducted to fill knowledge gaps in how results from culture-independent testing and culture compare for tracking disease incidence.
  • In anticipation of further development of CIDT technology (e.g., genotyping), case definitions and reporting of CIDT results should be updated in accordance with their intended use—taking into consideration the different functions and needs of primary care providers and clinical laboratories (diagnosis and treatment) versus health department epidemiologists and reference laboratorians (public health surveillance and response).
Surveillance interpretation issues using CIDT data

CIDT syndromic panels provide information on multiple agents for which practical tests were not previously available. This new data stream provides surveillance opportunities to public health as well as challenges in interpretation. For example, frequent pathogen co-detections are being reported with CIDT use, even in asymptomatic individuals, but current surveillance systems are not designed to effectively track, use, or interpret these data. Also, non-Shiga toxin-producing E. coli infections (e.g., ETEC [enterotoxigenic E. coli], EPEC [enteropathogenic E. coli], EAgEC [enteroaggregative E. coli], and EIEC [enteroinvasive E. coli]) are now being reported to clinicians through the use of CIDTs, but their significance is unknown. The Working Group recommended the following:

  • Additional studies should be conducted to determine pathogen-pathogen interactions and to assess the clinical and public health relevance of co-detections being detected with CIDT panels.
  • Studies should be conducted to assess the public health significance of other non-STEC E. coli infections and the significance of positive CIDT results in asymptomatic individuals.
    • ETEC, in particular, is now frequently being reported among cases without an international travel history. This represents a new surveillance opportunity to better understand the epidemiology of ETEC.
Use of CIDTs for exclusion (and test-of-cure) from sensitive occupations/settings

There are strong incentives for the use of CIDTs to quickly screen persons ill with communicable diseases such as Shiga toxin-producing E. coli disease and salmonellosis who work in sensitive settings (such as healthcare, food service, or daycare) before their return to work. Screening with CIDTs increases the potential for reducing economic hardship to affected individuals due to its quick results. However, this is an “unintended use” for these diagnostics, and the performance characteristics of CIDTs in these circumstances are unknown. The goal of exclusion is to limit transmission, but the tests are designed to measure presence/absence of pathogen nucleic acid, not transmission potential. Nevertheless, CIDTs are already being used for this purpose in some states, and national guidance is urgently needed. The Working Group recommended the following:

  • National standardized guidance for exclusion and return of enteric-positive persons working in high-risk settings should be developed.
    • CSTE offered to form a workgroup with experts from CDC and other stakeholders to develop national model practices for the states, who can then adopt or modify them. CSTE will develop an easily navigable flowchart for detecting and monitoring high-risk cases based on which tests have been ordered for each phase of exclusion.
  • Long-term parallel studies of culture and culture-independent testing of ill workers subject to exclusion should be conducted to fill significant knowledge gaps in this area.
  • The FDA Food Code section on exclusion of food workers, which only addresses culture-confirmed results, should be updated once the CSTE guidelines are developed.

Preserving isolate-based surveillance

Until advanced direct-from-specimen pathogen characterization assays are developed, recovery of isolates from patient specimens will be needed to maintain public health functions. Reflex culture (i.e., isolate recovery on CIDT-positive specimens) may be performed at clinical laboratories where the CIDT was used or at public health laboratories, or some combination of the two approaches can be used. For this to occur, the specimen collection methods used by the CIDTs would need to be compatible with methods that will enable culture to be performed, and laboratory resources would need to be identified. Clinical laboratories could potentially be compensated either by reimbursement or workload credit (which affects productivity calculations and allotment of staff). Either approach would require new mechanisms to be put in place and considerable communication between clinical and public health laboratories. Funding would also need to be identified for the public health laboratory option.

Issues with CIDTs and isolate recovery

CIDTs do not require pathogen viability to function, which can result in inconsistent isolate recovery.

Point-of-care testing systems that utilize rectal swabs directly inoculated into the test system also make isolate recovery impossible. The Working Group recommended the following:

  • CDC should work with FDA and manufacturers to develop language that could be included with product inserts to warn users that testing should be compatible with public health reporting mandates and that the CIDT limitations may require additional specimen collection and testing.
  • Modification of laboratory accreditation requirements should be considered to specifically encourage the use of whole stool specimens for isolate recovery.
  • Opportunities should be identified to facilitate collaboration among the medical device industry and clinical and public health laboratories about novel collection devices and isolate recovery issues.
  • More education should be provided to clinical laboratories about reporting laws and approaches to isolate recovery.
Resource and reimbursement

Reimbursement for reflex culture in clinical or reference laboratories currently requires either (a) a test order from the provider or (b) a specific Current Procedural Terminology (CPT) test code (e.g., reflex culture from CIDT for mandated public health requirements). Often, neither of these is included and laboratories must perform reflex cultures at a cost. The Working Group recommended the following:

  • Codes should be developed that allow reflex culture, isolate recovery, and shipment of isolate costs to be reimbursed by third-party payers.
  • Public health laboratories should be informed about potential federal funding (e.g., CDC Epidemiology and Laboratory Capacity for Infectious Diseases [ELC] Cooperative Agreement) for performance of reflex cultures.

Increased communication, education, information sharing, and collaboration with stakeholders such as healthcare institutions, labs, public health, accreditation organizations, insurers, and professional organizations (e.g., the Association of State and Territorial Health Officials [ASTHO], Academy of Health Information Professionals, providers) will be critical to identify and implement solutions to preserve isolate-based surveillance. The Working Group recommended the following:

  • A communication toolkit should be developed to help engage and educate partners and critical stakeholders about the opportunities and challenges associated with CIDTs.
  • Public health case studies and data related to the immediate impacts of CIDTs on foodborne illness and outbreak detection should be published more widely to increase awareness of these challenges among various stakeholders.
  • Economic analysis of the cost-benefits and cost-avoidances associated with maintaining isolate-based surveillance should be conducted to inform decision makers and insurers.

Technological solutions

Characterization of foodborne disease surveillance isolates to the level accomplished by WGS is needed for outbreak detection and to monitor trends in pathogen virulence and antimicrobial resistance. There are a number of intrinsic challenges with developing assays to achieve WGS-type resolution directly from specimens, without the need for a culture step (i.e., culture-independent pathogen characterization). These challenges include (1) the complexity of the stool matrix (large variety of prokaryotic and eukaryotic DNA, including human DNA); (2) the similarity of pathogens to commensal flora, making it difficult to distinguish sequences to the specificity level required; (3) signal-to-noise ratio (especially for pathogens in low abundance); and (4) the need for rapid, low-cost, low-complexity, and potentially high-volume workflows in the resource-constrained public health laboratory environment.

CDC is currently investigating the use of highly multiplexed amplicon sequencing (HMAS, for partial cgMLST) as a short-term solution, along with shotgun metagenomic approaches for the long term. Feedback and additional ideas in this area were solicited from the Forum subject matter experts. The BSC FSMA-SWG members thought that CDC researchers were on the right track, but since few members were experts on this, the Working Group deferred to the BSC/OID Infectious Disease Laboratory Working Group to provide guidance on this topic.

Page last reviewed: February 19, 2019