Monday, July 27, 2015
Exhibit Hall (Oregon Convention Center)
Laura Ewing
, U.S. Food and Drug Administration
, Laurel
, MD
Nicole Addy
, Oak Ridge Institute for Science and Technology
, Oak Ridge
, TN
Gopal Gopinath
, U.S. Food and Drug Administration
, Laurel
, MD
Christopher Grim
, U.S. Food and Drug Administration
, Laurel
, MD
Karen Jarvis
, U.S. Food and Drug Administration
, Laurel
, MD
Marie-Laure Flamer
, JIFSAN
, College Park
, MD
Darcy Hanes
, U.S. Food and Drug Administration
, Laurel
, MD
Junia Jean-Gilles Beaubrun
, U.S. Food and Drug Administration
, Laurel
, MD
Introduction: Recently, spices have been implicated in at least fourteen illness outbreaks worldwide, including the United States, resulting in 1946 human illnesses, 128 hospitalizations, and two deaths. It is necessary to identify potential foodborne pathogens associated with spices such as oregano, white pepper, and cloves and improve methods for mitigation and rapid outbreak response. Shotgun metagenomic sequencing is a useful tool for meeting these goals by: (1) simultaneously identifying pathogens of interest present in each spice, (2) evaluating the efficacy of enrichment methods and microbiome shifts throughout the process, and (3) establishing variations between the natural flora found in spices. Spices are difficult to analyze because of their essential oils and chromophores; therefore, specific method optimization is often necessary.
Purpose: The purpose of this study was to optimize a protocol for shotgun metagenomic sequencing and assess its utility to identify the microbiome of spices.
Methods: Oregano, white pepper and cloves were enriched following a modification of the BAM method using Tryptic Soy Broth (TSB), and modified Buffered Peptone Water (mBPW). Samples were collected throughout the enrichment process. DNA was extracted using the Qiacube and shotgun metagenomic sequencing was performed on the MiSeq using the Nextera kit with modifications. The data was analyzed using Metaphlan.
Results: Analysis shows that the three spices tested have different metagenomic profiles; however, they contain many similar bacteria, including members of Salmonella, Cronobacter, Shigella, Yersinia, Escherichia coli and Bacillus cereus. Results also show that profiles shift throughout the enrichment process and differ depending on the growth media.
Significance: Shotgun metagenomic sequencing revealed the microbiomes of oregano, white pepper, and cloves and the presence of potential foodborne pathogens. This and the ability to trace shifts in microbial communities during enrichment can help the FDA improve our pathogen identification methods during outbreaks.
