Lab Matters Fall 2019 | Page 23

FOOD SAFETY Building the Next Generation of PulseNet by Kristy Kubota, manager, PulseNet and Rhodel Bradshaw, specialist, Food Safety to WGS, while others may not have resources or volume to conduct real-time surveillance as efficiently as with PFGE. During the past year, some laboratories have had to perform PFGE in tandem with WGS in order to validate results. This is costly and requires training personnel to perform both methods. There is also a steep learning curve with WGS technology, and it can be exacerbated at laboratories with limited IT and bioinformatics resources. Addressing turnaround time metrics, automation and upgrading of IT infrastructures to accommodate storage, and upload of massive amounts of data to CDC and NCBI pose additional challenges for public health laboratories. Change is never easy. In fact, it can be daunting, overwhelming and fraught with difficulty. However, at the same time, it can be a refreshing experience. The same can be said for PulseNet’s national transition from pulse-field gel electrophoresis (PFGE) to whole genome sequencing (WGS). PulseNet is the first national laboratory- based surveillance program in the United States to harness the power of WGS, a technology that can change laboratory science practice and transform how outbreaks are detected, investigated and surveilled. Traditional vs. Cutting-edge Traditional subtyping tools like PFGE are organism-dependent, lack discriminatory power and require additional testing to fully identify and characterize pathogens. WGS is a better subtyping tool for bacterial, viral or parasitic surveillance. In addition, with global development of open-sourced tools and databases, WGS allows public health scientists to replace many traditional reference- based methods. Once laboratories fully implement and validate WGS, they can consolidate workflows for identification and characterization of pathogens, and clinical diagnostics can evolve from isolate-based methods to culture- independent testing. Since current US surveillance is dependent on isolates, there is a critical need to develop genomic databases to respond to the changing landscape of clinical diagnostics. Public health laboratories transitioning PulseNet workflows from PFGE to WGS face many challenges. One laboratory may have the capability to easily transition Collaboration Towards Change In early 2019 APHL sponsored Joint PulseNet/OutbreakNet Regional Meetings in Tampa, San Diego and Omaha to discuss implementation of WGS for foodborne surveillance. Roughly 600 laboratory scientists, bioinformaticians, epidemiologists and environmental health specialists involved in foodborne outbreaks and enteric diseases participated. Participants from PulseNet laboratories emphasized quality control and workforce development as priority needs for WGS implementation. Evaluation of current laboratory systems, from the enteric reference bench to the PulseNet subtyping laboratory to the IT infrastructure, were likewise priorities along with identification of areas to improve efficiencies. To prepare attendees to embrace changes in the analysis workflow for cluster detection, the meetings included training in BioNumerics 7.6, Joint Sessions PulseNet Track Sessions • PulseNet and OutbreakNet transition to WGS • Managing New Workflows and Data Integration • Learning from other nations experiences with incorporating WGS into food surveillance • Perspectives fromhigh and low burden states • Outbreak discussions on utility of WGS PublicHealthLabs @APHL • Guidance for Implementing & Conducting PulseNet Surveillance Using WGS • Addressing QA/QC(example: Dry and Wet Lab Sequence Quality Data and • BioNumerics Training APHL.org which provides WGS analysis tools. Attendees discussed examples of how WGS data has supported epidemiological investigations. In one instance, by using WGS, investigators were able to show that the same strain of Salmonella was responsible for a restaurant-associated outbreak that occurred over multiple years. Moving forward, WGS will be useful in demonstrating such long-term harborage of pathogens within the environment as well as trends in the number of prolonged outbreaks. According to an internal survey conducted by APHL and CDC, 93% of attendees rated meeting content and materials as “good” or “excellent.” Particularly valuable were discussions of WGS implementation from different state perspectives. Many attendees mentioned that the diversity of professions represented at the meeting allowed each to observe how others handle and share information on outbreaks. Networking with a range of professions also produced concrete results: improvements in SOPs to guide the transition to WGS. In January 2019, Listeria monocytogenes was the first PulseNet pathogen to fully transition to WGS, and the results are already promising. Nationally, the number of listeriosis clusters detected with WGS has increased, while the number of cases within a cluster has decreased. As national surveillance extends to other PulseNet pathogens, we should expect to observe similar trends. Similar opportunities for professionals in foodborne surveillance to learn from each other will be vital as PulseNet advances with implementation of WGS. n OutbreakNet Track Sessions • Challenges and Successes surrounding Outbreaks • Environmental Health Perspectives on Foodborne Outbreak Investigation • WGS transition at an Epidemiological and Environmental Health Science Perspective and Communication • SEDRIC Training Fall 2019 LAB MATTERS 21