Lab Matters - Fall 2014

HHS Innovates Award Paves Way for the Future of Food Safety and PulseNet

Kristy Kubota, MPH, senior specialist, PulseNet Program and Jennifer Adams, lead specialist, PulseNet Quality Assurance 2014-11-12 12:29:59

What do a suicide prevention, a breast cancer challenge, analytics for reviewing drug approvals and whole genome sequencing (WGS) for public health all have in common? These projects won the 2014 Health and Human Services (HHS) Innovates award competition. This competition fosters innovation among HHS agencies to address the most critical challenges facing the 21st century. To date, nearly 500 HHS staff-driven innovations and over 60,000 votes have been cast since the program’s inception. This year, CDC’s Enteric Diseases Laboratory and Epidemiology Branches, USDA’s Food Safety and inspection Service, FDA’s Center for Food Safety and Applied Nutrition, NIH’s National Center for Biotechnology Information (NCBI) and APHL submitted a proof-of-concept study, “Whole Genome Sequencing: Future of Food Safety.” This project demonstrated WGS technology as a real-time national surveillance tool. Since 2013, CDC has sequenced over 900 clinical isolates with over 900 food isolates sequenced by GenomeTrakr laboratories. To date, 13 clusters have been identified by pulsed-field gel electrophoresis (PFGE) and WGS and five clusters have been identified by WGS alone. The power of this technology for cluster detection was observed in an investigation of five listeriosis cases with differing PFGE patterns in three states. Using WGS, cases clustered together suggesting a possible epidemiological association whereas PFGE did not. All cases had origins from the former USSR or Poland suggesting a possible common source. In 2014, the Canadian Food Inspection Agency recalled pre-packaged lettuce from a US supplier after several listeriosis cases were reported in Canada. PulseNet USA surveillance found a match, as defined by high quality single nucleotide polymorphisms (hqSNPs) and whole genome multi locus sequence typing (wgMLST), between a sporadic case in the US and the lettuce isolate from Canada. This case reported consumption of lettuce within the same time frame suggesting that this case could have involved the recalled product. Lessons learned from the WGS project demonstrated that real-time surveillance of Listeria monocytogenes is possible and this technology provides better discrimination of clusters than PFGE. However, it is still essential that epidemiological data is collected to obtain exposure information. Additionally, WGS technology within a public health setting has the potential to replace many traditional reference methods used to characterize enteric pathogens using a single method. The technology is gradually being transferred to local levels so that individual laboratories can sequence their isolates and send real-time results to NCBI. Having this information publically available is a paradigm shift to the traditional flow and storage of data within current surveillance systems. On September 22-23, 2014, state and federal agencies convened a meeting at NIH to attain a vision on how to advance real-time surveillance for foodborne pathogens using WGS. The goal of this meeting was to develop consensus with regard to establishing analytical standards, data sharing policies, determining roles and responsibilities and prioritizing future activities. Prospective activities include agencies to review existing data sets to examine cluster algorithms; creating a glossary of common terminology for WGS; publishing SNP and whole genome wgMLST pipelines for public health; and sequencing other enteric genomes. A summary of priorities will be finalized by the group leadership and information will be disseminated by CDC, FDA and APHL in the coming months. PulseNet’s vision to migrate subtyping methods to WGS is one way to respond to the impact of culture-independent diagnostics within clinical and public health laboratory settings. Currently, WGS utilizes isolates as the primary source of DNA; however, the PulseNet network needs to work towards innovating subtyping methodologies to address the changing field of clinical diagnostics. Establishing WGS libraries now will pave the way for the next generation of sequencing methodologies for foodborne surveillance.

Published by Association of Public Health Laboratories. View All Articles.

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