JCM Accepts, published online ahead of print on 20 March 2013 J. Clin. Microbiol. doi: /jcm

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1 JCM Accepts, published online ahead of print on 20 March 2013 J. Clin. Microbiol. doi: /jcm Copyright 2013, American Society for Microbiology. All Rights Reserved. A Challenge and an Opportunity to Improve Patient Management and Public Health Surveillance for Foodborne Infections through Culture-Independent Diagnostics Robyn Atkinson 1#, Hugh Maguire 2, Peter Gerner-Smidt 3 1 Utah Unified State Laboratory: Public Health 4431 South 2700 West Taylorsville UT rmatkinson@utah.gov 2 Colorado Department of Public Health and Environment Laboratory Services Division 8100 Lowry Blvd. Denver, CO Centers for Disease Control and Prevention Enteric Diseases Laboratory Branch MS C Clifton Road Atlanta GA

2 The increased use of culture-independent methods in clinical laboratories is threatening to disrupt public health surveillance for bacterial foodborne infections. Our national surveillance systems are an important part of the nation s defense against foodborne 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 foodborne illness. To the clinical microbiology community, culture-independent diagnostic tests (CIDT) are an attractive alternative to standard microbiological culture in that they offer rapid test results, lower cost per positive specimen, decreased turn-around-time, and lower technical complexity than culture methods. As more clinical laboratories embrace these new culture independent diagnostic tests, the challenge emerges as to how 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 foodborne 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 E. 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 profiles, antibiotic sensitivity, and other subtyping information, which is critical for the detection and investigation of many outbreaks of foodborne disease. The main surveillance system, which relies on this public health laboratory information for outbreak detection, is PulseNet, the national subtyping network for foodborne disease surveillance. This system uses pulsed-field gel electrophoresis (PFGE) to subtype foodborne pathogens 2

3 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 foodborne outbreaks occurring in United States since that time. In the fall of 2011, CNN produced a top 10 list of the biggest foodborne outbreaks in the past decade ( - referenced 8/17/2012). The multi-state outbreaks listed in Table 1 include these ten 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 identity 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 ability to detect and investigate outbreaks is threatened. A possible result of this shift in responsibilities could be that our surveillance systems will mirror that of the 1950's, 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 multi-state 3

4 outbreaks or international outbreaks. The surveillance of sporadic infections will also suffer from the effect of CIDTs. For example, without serotype details for Salmonella isolates, it will not be possible 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 or EIA s) 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 (1). 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 onto 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 the 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 stools such as the Luminex xtag Gastrointestinal Pathogen Panel (GPP)(2). In January 2013, Luminex received FDA approval to market their GPP in the US and all other major manufacturers of diagnostic assays are at different stages of developing and commercializing similar assays for use in this country ( Such 4

5 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 the advancement 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 (3). 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 vs. conservative treatment of patients infected with strains of 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 5

6 addition, the delay of detecting outbreaks of foodborne diseases could be reduced from two to four weeks to approximately one week if these advanced test results are reported by the diagnostic laboratories simultaneously to clinicians and public health. 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 sequenced-based information electronically. This would represent a major improvement of the public health response to outbreaks of foodborne 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 industry can ensure the best patient management and the future viability of programs dedicated to surveillance for foodborne 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 true 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 foodborne 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 CIDT 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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8 Table 1. A non-exhaustive list of multi-state outbreaks with bacterial enteric pathogens investigated through culture based surveillance since Year Pathogen Vehicle Comments 2012 Salmonella Sandiego, Salmonella Pomona Salmonella Poona 2012 Salmonella Bareilly and Nchanga 2011 Salmonella I 4,[5],12:i: Listeria monocytogenes Small turtles Raw scrap ground tuna Sprouts Cantaloupe 6 multistate outbreaks Amount product recalled >58,828 lbs Served at a fast food restaurant chain One farm involved 2010 Salmonella Enteritidis Shell eggs >500,000,000 eggs recalled 2010 Salmonella Montevideo Ready-to-eat Italian sausage products/pepper >1,263,754 lbs product recalled 2009 E. coli O157:H7 Cookie dough 300,000 cases of product recalled Salmonella Typhimurium Peanut butter/peanut products >3000 peanut butter/ containing products recalled 2008 Salmonella Agona Toasted oats cereal >3,000,000 lbs product recalled 2008 Salmonella Saintpaul Hot peppers >1400 case patients 2007 E. coli O157:H7 Frozen pizza 5,000,000 pizzas recalled 2007 E. coli O157:H7 Beef patties 21,700,000 lbs of meat recalled Salmonella Tennessee Peanut butter 326,000,000 lbs of product recalled Salmonella Newport Tomatoes Annual recurring outbreak associated with tomatoes grown in VA Salmonella Montevideo Baby chicks From mail-order hatchery Salmonella Enteritidis Raw almonds 13,000,000 lbs 8

9 2003 E. coli O157:H7 Blade Tenderized Frozen Steak 2002 Listeria Turkey deli-meat monocytogenes almonds recalled 750,000 lbs of meat recalled >30,000,000 lbs of meat recalled 2002 E. coli O157:H7 Ground beef 18,600,000 lbs meat recalled Downloaded from on November 22, 2018 by guest 9

10 Table 2. Threats and opportunities to the implementation of low and high discriminatory cultureindependent diagnostic methods in clinical laboratory practice Threats to public health posed by implementing low discriminatory culture-independent diagnostic methods with low discriminatory power, e.g., EIA and simple molecular diagnostic panels. Subtyped-based laboratory surveillance replaced by crude species identification surveillance, without serotype or subtype information Decreased capacity to detect and respond to foodborne outbreaks Decreased ability to attribute infections to foods and other sources Lack of antibiotic resistance monitoring Decreased ability to track trends and assess progress in prevention Opportunities offered by developing and implementing diagnostic methods with high discriminatory power, e.g., genomics. Improved clinical decision making Rapid and focused foodborne outbreak detection and response Improved ability to attribute infections to foods and other sources Improved antibiotic resistance monitoring Enhanced ability to track trends and assess progress 1. Gould LH, Bopp C, Strockbine N, Atkinson R, Baselski V, Body B, Carey R, Crandall C, Hurd S, Kaplan R, Neil M, Shea S, Somsel P, Tobin-D Angelo M, Griffin PM, Gerner-Smidt P Recommendations for diagnosis of Shiga toxin--producing Escherichia coli infections by clinical laboratories. MMWR Recomm Rep. 58(RR-12): Sparbier K, Weller U, Boogen C, Kostrzewa M Rapid detection of Salmonella sp. by means of a combination of selective enrichment broth and MALDI-TOF MS. Eur J Clin Microbiol Infect Dis. 31(5): Scheutz F, Teel LD, Beutin L, Piérard D, Buvens G, Karch H, Mellmann A, Caprioli A, Tozzoli R, Morabito S, Strockbine NA, Melton-Celsa AR, Sanchez M, Persson S, O'Brien AD A multicenter evaluation of a sequence-based protocol to subtype Shiga toxins and standardize Stx nomenclature. J. Clin. Microbiol. 50:

11 Robyn M Atkinson, PhD, HCLD/ PHLD, is currently the Director of the Public Health Laboratory for the State of Utah. She holds a Bachelor s Degree in Biochemisty from Clemson University in South Carolina. She continued her education by completing a Doctorate of Philosophy Degree in Microbial Pathogenesis at the University of Tennessee Health Sciences Center. Upon graduation, she completed a fellowship in Medical and Public Health Microbiology at Washington University in St Louis School of Medicine. After completion of her fellowship, she joined the New York State Department of Health as the Director of Clinical Bacteriology. While in this position, Dr Atkinson was exposed to the numerous and complex issues regarding food safety as well as standardization of laboratory practices among all state and local public health laboratories. After spending 2 years in New York, she was recruited to Tennessee to serve as the Director of the Knoxville Regional Laboratory. During her 4 years in TN, she continued her focus on food safety by becoming a member of the APHL Food Safety Committee and she is the Committee Chair. Since 2009, she has served as a Member-at-Large to the FDA Coordinating Committee for the Partnership for Food Protection, as well as several sub-committees dedicated to making an integrated food safety system a reality. In addition, her work with APHL has afforded her the opportunity to begin to streamline standards of practice across all state and local public health laboratories by working with subject matter experts to draft Best Practices Guidelines for the isolation and characterization of several infectious organisms of public health significance. The first set of guidelines, Guidance for Public Health Laboratories on the Isolation and Characterization of Shiga toxin-producing Escherichia coli (STEC) from Clinical Specimens, was published in These efforts have led to her familiarity with the implementation of CIDT at the clinical laboratory and how this may impact public health laboratories. Dr. Atkinson received the APHL 2010 Emerging Leader Award for all of her efforts related to food safety and laboratory practice standardization.

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