Laboratory activities are a critical component of enteric disease surveillance and cluster and outbreak detection. Identification of the etiologic agent causing illness requires testing of specimens at local hospitals, clinics, and private laboratories. Laboratory-based surveillance identifies confirmed cases of enteric disease infection and can help guide pathogen-specific response activities. Further characterization of pathogens (e.g. subtype, virulence determinants, antimicrobial susceptibility, etc.) at Public Health Laboratories (PHL) enhances the ability to identify patterns and trends, including clusters of disease that may represent unrecognized outbreaks. Additionally, PHLs also provide primary diagnostic functions in event-associated outbreaks of undetermined etiology. This FoodCORE Model Practice summarizes the successful laboratory practices used by PHLs in the FoodCORE centers for improving and maintaining the timeliness and completeness of isolate or specimen submissions to the PHL, the subtyping of enteric pathogens, and the communication of laboratory results and cluster detection reports. The activities described would be applicable for surveillance of various pathogens but are focused on those that are likely transmitted via food. A checklist is provided which may be used to determine if current PHL practices align with the FoodCORE model practices.# Receiving specimens:
FoodCORE centers use various practices and systems to help ensure timely and complete submission of specimens from these external sources. These practices include:
- Rapidly transporting isolates/specimens to the PHL for testing to ensure prompt receipt of all requested or required bacterial, viral or parasitic specimens from clinical and commercial laboratories  Rapid transport can be supported with a variety of services such as the provision of mailing containers, a contract courier service, or other means of specimen transport to the PHL
- Providing guidance for submission of patient, food or environmental isolates/ specimens to the PHL when investigating outbreaks of undetermined etiology
- Providing guidance regarding when and how to submit, for further testing at the PHL, Shiga toxinpositive enrichment broths and other primary clinical specimens that are found positive by culture independent diagnostic tests (CIDT) for STEC or other pathogens that meet submission requirements in your jurisdiction
FoodCORE centers also work closely with the clinical and commercial laboratories that submit specimens so any delays or gaps in submissions can be identified. PHLs should reach out to laboratories to encourage submissions and help eliminate barriers to submission if they are identified.
FoodCORE centers also conduct trainings for local health department (LHD) partners. As part of these trainings, submission protocol documents (manuals, standard operating procedure documents, etc.) and shipping materials can be provided to help ensure all partners know the testing capabilities of the PHL, what type of specimens should be collected, as well as when and how to collect and submit them to the PHL.
To help streamline the receipt and testing of specimens, outreach, resources, and trainings for clinical and commercial laboratories and LHD partners, should include guidance stating that the PHL should to be notified when specimens/samples will be submitted for outbreak investigations.

# Subtyping and testing specimens:
FoodCORE centers work to improve the timeliness and completeness of subtyping for bacterial, viral, and parasitic specimens submitted to the PHL. Depending on jurisdictional resources, attempts should be made to subtype all primary isolates as soon as they are received at the PHL. Subtyping results should be submitted to the appropriate surveillance network in real-time whenever possible. Additionally, PHLs should follow standard CDC isolate submission policies and respond to requests for submitting isolates for additional testing, such as antimicrobial testing through NARMS, MLVA subtyping, or whole genome sequencing. FoodCORE centers use various practices and systems to help enhance subtyping capacity and timeliness. These practices include:
- Cross-training staff in subtyping protocols; this includes having more than one staff member with a specific certification so there is built-in surge capacity and back-up staffing
- Performing real time subtyping of all strains of Salmonella, Shiga toxin-producing E. coli (STEC) and Listeria. Strategies to achieve this goal include:
 Minimizing or eliminating batching so that turnaround times can be improved and then maintained  Initiating subtyping without waiting for pathogen confirmation testing as the proportion of isolates with incorrect primary pathogen identification from diagnostic labs is usually low  Processing Salmonella isolates for simultaneous serotyping and PFGE (i.e., in parallel) rather than waiting for serotyping results before initiating PFGE -Not limiting PFGE to specific serotypes because PFGE of all strains, regardless of serotype, increases the sensitivity of cluster detection and eliminates the need to complete serotying before PFGE  Processing STEC isolates for simultaneous serotyping and PFGE (i.e., in parallel) rather than waiting for serotyping results before initiating PFGE -When shiga toxin-positive broths are received, they are plated on sorbitol-MacConkey (SMAC) agar. Non-sorbitol fermenting isolates are treated as STEC O157 and sorbitol -fermenting isolates are treated as non-O157 STEC strains for PFGE testing.
-Serotype misclassification based on sorbitol fermenting results is usually low and PFGE can be repeated if necessary after full serotyping is completed.
- Incorporating molecular serotyping when available to reduce turn-around times
- Culture-Independent Diagnostic Testing (CIDT)
 Communication with providers/diagnostic laboratories about submission requirements and working together to be sure procedures and samples meet diagnostic and public health needs -Work with APHL and industry initiatives to identify providers and diagnostic laboratories that are implementing CIDT so communications and outreach can be proactive  Identify means for submitting labs to indicate target pathogens based on the CIDT used and the results of their testing to guide PHL processing

# Reporting results and cluster detection:
FoodCORE centers capitalize on the completeness and timeliness of specimen subtyping to quickly identify clusters of illness. All subtyping results should be reported to the appropriate surveillance network in real-time whenever possible, based on jurisdictional resources. To enhance reporting and cluster detection, FoodCORE centers use the following practices:
- Routinely analyzing subtyping data from PHL testing to determine if there is an increase in the identification of a specific subtype or strain
- Routinely comparing subtyping results to centralized databases to determine whether there are additional subtype matches
- Using subtyping results to link pathogens identified from product testing to persons infected with the same subtype or strain
- Using shared data systems that permit routine rapid sharing of laboratory information and results for human, food, and environmental isolate testing to inform and facilitate response activities  Real-time sharing of specimen testing and subtyping information during an investigation
- Routinely exchanging cluster detection reports  At a minimum, weekly reporting with more frequent reporting (i.e., twice-weekly, daily, etc.) if possible  Integrated with the routine data analyses to determine if there is an increase in the number of cases of infection with a specific subtype or strain  Additionally, established methods for exchanging information about potential clusters that are detected between scheduled reports should exist  Combined meetings and trainings that include laboratory and epidemiology staff so staff have a working understanding of the needs and capabilities of each group