Commentary: A Challenge and an Opportunity To Improve Patient Management and Public Health Surveillance for Food-Borne Infections through Culture-Independent Diagnostics

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The increased use of culture-independent methods in clinical laboratories is threatening to disrupt public health surveillance for bacterial food-borne infections. Our national surveillance systems are an important part of the nation's defense against food-borne infections and consist of a network of public health laboratories. Within this network of laboratories, disease clusters are recognized following detailed characterization of pure culture isolates obtained from patients suffering from food-borne illness. To the clinical microbiology community, culture-independent diagnostic tests (CIDTs) are an attractive alternative to standard microbiological culture in that they offer rapid test results, lower cost per positive specimen, decreased turnaround time, and lower technical complexity than culture methods. As more clinical laboratories embrace these new culture-independent diagnostic tests, the challenge is how do we can reconcile the technology available to clinical microbiologists with the technology used by public health microbiologists to support national surveillance systems.

The public health surveillance systems that are used to track enteric and food-borne bacterial infections are currently based on the characteristics of bacteria isolated in culture from ill patients. The vast majority of our knowledge regarding the epidemiology of Salmonella, Shiga toxin-producing Escherichia coli (STEC) (e.g., O157) and other diarrheagenic E. coli, Listeria monocytogenes, Shigella spp., Yersinia enterocolitica, and Vibrio spp. has been generated by examining and characterizing bacterial isolates from pure cultures. The value derived from the current collegial partnership between clinical and public health laboratories broadly impacts patient management guidelines and the advancement of public health policy. At its foundation is the preservation of culture isolates. These isolates allow public health laboratory scientists to determine the serotype, virulence profile, antibiotic sensitivity, and other subtyping information, which is critical for the detection and investigation of many outbreaks of food-borne disease. The main surveillance system, which relies on this public health laboratory information for outbreak detection, is PulseNet, the national subtyping network for food-borne disease surveillance. This system uses pulsed-field gel electrophoresis (PFGE) to subtype food-borne pathogens with the high discriminatory power needed to differentiate clustered cases from the underlying background of sporadic disease occurring in the community. This network has been in place since 1996 and has been critical in the detection and investigation of virtually all major food-borne outbreaks occurring in the United States since that time. In the fall of 2011, CNN produced a “top 10 list” of the biggest food-borne outbreaks in the past decade (1). The multistate outbreaks listed in Table 1 include these 10 and many others that were brought to light through the workings of the PulseNet system. The value of this system lies in the outbreaks controlled and new hazards identified and also in the sustained partnership of clinical and public health laboratories that make it successful.

For their part of the connection, public health laboratories are responsible not only for the verification of the identities of bacterial isolates but also for determining their serotypes and PFGE profiles. These enhanced characterization activities are dependent on the submission of isolates to public health laboratories via the sustained partnerships with the clinical laboratories within their jurisdictions. An unfavorable cascade of events is set in motion if clinical laboratories stop culturing specimens and switch entirely to CIDTs that do not allow for serotyping and molecular subtyping. The public health laboratories will be forced to take over the task of culturing primary specimens that are positive by a CIDT, since pure cultures are still required for the current surveillance systems. Unfortunately, the current structure of the public health laboratory system is not designed to absorb the routine culture of clinical specimens, and therefore, the abilities to detect and to investigate outbreaks are threatened. A possible result of this shift in responsibilities could be that our surveillance systems will mirror that of the 1950s, before serotyping and PulseNet, when most surveillance was based on genus/pathotype identification and outbreaks were defined by the minimal information available about the etiologic agent and the information obtained from patients who attended well-defined events, e.g., church suppers or weddings (Table 2). We will no longer have the ability to routinely detect multistate outbreaks or international outbreaks. The surveillance of sporadic infections will also suffer from the effects of CIDTs. For example, without serotype details for Salmonella isolates, it will not be possible to explain trends in the incidence of salmonellosis or the persistence of specific serotypes. Upstream in the farm-to-table continuum, it will be very difficult to document the efforts undertaken by public health officials to monitor specific control points in food production, e.g., decreasing the Salmonella prevalence in chickens. The link between patients and between patients and contaminated food products will be broken.

Currently, the most prevalent culture-independent diagnostic assays (enzyme immunoassays [EIAs]) are used for the detection of STEC and Campylobacter. In guidelines published in 2009, clinical laboratories were requested to forward any specimens with a positive finding for Shiga toxin to the public health laboratory in their jurisdiction, where an attempt could be made to isolate the causative organism and subtype it for inclusion in the surveillance system (2). Campylobacter is not routinely submitted to the public health system unless an outbreak is suspected. These practices are currently not an overwhelming burden to the system, and both partners continue to benefit from the sharing of information. However, the emergence of FDA-approved CIDTs targeting single or multiple enteric pathogens in the U.S. market may quickly alter this partnership. It was recently shown that it is possible to detect Salmonella in a mixed culture without isolating it in pure culture through the use of mass spectroscopy of an enrichment broth, but more worrisome for public health (with regard to isolate preservation) is the current introduction of molecular diagnostic enteric panels for the simultaneous detection of bacterial, viral, and parasitic enteric pathogens directly in stool samples, such as the Luminex xTAG gastrointestinal pathogen panel (GPP) (3). In January 2013, Luminex received FDA approval to market their Luminex xTAG GPP in the United States (Luminex, Austin, TX), and all other major manufacturers of diagnostic assays are at different stages of developing and commercializing similar assays for use in this country. Such expanded pathogen detection at the clinical level will support a more accurate calculation of the burden of illness in this country, but without culture isolates the ability of public health laboratories to detect outbreaks will suffer because these methods lack the ability to differentiate between different strains of the same species/pathotype.

With all the changes outlined above, we are also faced with the reality that the way we define a pathogen may be changing, which will require public health laboratory surveillance systems to change as well. We now know that not all strains belonging to the same species or pathotype are equally virulent, and thanks to advancements in biotechnology, we are gradually acquiring knowledge about different virulence genes/factors and their clinical importance, e.g., certain subtypes of the Shiga toxin of Shiga toxin-producing Escherichia coli are strongly associated with bloody diarrhea and hemolytic-uremic syndrome (HUS), whereas others are less virulent or even not associated with disease (4). As this type of knowledge becomes available, we will see a paradigm shift in what defines a pathogen. With information about the virulence characteristics, clinicians will be better able to prioritize the treatment options for individual patients, e.g., aggressive rehydration therapy for patients infected with hypervirulent STEC strains versus conservative treatment of patients infected with strains with low virulence.

However, rapid detection of pathogens based on their virulence profile without culture is currently not feasible. The rapid technological evolution of biotechnology and bioinformatics, more advanced sequencing, and DNA array diagnostic methods that could satisfy both clinical and public health needs could become possible very soon. Such advanced tests would be extremely useful to clinicians, especially if the detection of some common antimicrobial resistance traits were included. At the same time, by adding genetic subtyping targets to the tests, these tests would satisfy the public health need for discriminating among strains of the same species for outbreak detection and investigation, attributing illnesses to their sources, tracking trends, and other surveillance purposes (Table 2). In addition, the delay of detecting outbreaks of food-borne diseases could be reduced from 2 to 4 weeks to approximately 1 week if these advanced test results are reported by the diagnostic laboratories simultaneously to clinicians and public health laboratorians. With this type of technology, the need to forward the isolates or specimens to the public health laboratories for subtyping would be replaced by forwarding the sequence-based information electronically. This would represent a major improvement of the public health response to outbreaks of food-borne infections.

In order to expedite and optimize this evolution, a major collaborative effort is needed. Only a tight collaborative effort between clinicians, clinical laboratories, public health institutions, regulatory agencies, and the biotechnology and diagnostics industries can ensure the best patient management and the future viability of programs dedicated to surveillance for food-borne infections. Public health laboratories are beginning the transition to methods that allow for the characterization of pathogens that are complementary to clinically valuable culture-independent diagnostics. However, before these technologies evolve to move us toward truly culture-independent diagnostics, cultures are still needed for public health purposes. An interim solution will involve reflex culture of all CIDT-positive specimens in the clinical laboratories or a transfer of clinical material to the public health laboratory for primary culture isolation of the suspected pathogen. This interim solution will require infusion of additional resources to the clinical and/or public health laboratories, but it is critical for the continuation of the current efficient response to food-borne infections in this country. Clinical and public health laboratories have always fulfilled their respective roles and will continue to evolve cooperatively to support their mutual interests. The current challenges created by the application of CIDTs represent an opportunity to develop and implement enhanced yet compatible testing capabilities that ensure the safety of the food sold and served to the American people.

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