P3-67 Whole Genome Sequence Analysis of Salmonella Isolates from Alfalfa Seeds Implicated in Sprout Outbreaks

Wednesday, July 12, 2017
Exhibit Hall (Tampa Convention Center)
Deena Awad , U.S. Food and Drug Administration, Division of Food Processing Science and Technology , Bedford Park , IL
Behzad Imanian , Illinois Institute of Technology, Institute for Food Safety and Health , Bedford Park , IL
Peichen Liu , Illinois Institute of Technology, Institute for Food Safety and Health , Bedford Park , IL
Yizhu Yan , Illinois Institute of Technology, Institute for Food Safety and Health , Bedford Park , IL
Kristin M. Schill , U.S. Food and Drug Administration, Division of Food Processing Science and Technology , Bedford Park , IL
Tong-Jen Fu , U.S. Food and Drug Administration, Division of Food Processing Science and Technology , Bedford Park , IL
Introduction:  Seeds are often linked to sprout outbreaks by epidemiological means, but confirmation through seed testing has not been successful in many cases. Studies are needed to determine whether testing sprouts grown from implicated seeds improves the detection of contamination.

Purpose:  To determine whether testing sprouts permits improved detection of Salmonella in seeds implicated in sprout outbreaks, and evaluate the use of whole genome sequencing (WGS) in linking seed contamination to sprout outbreaks.

Methods:  Alfalfa seeds obtained from two seedlots implicated in previous outbreaks (lot A, linked to 2009 Salmonella Oranienburg outbreak; and lot B, linked to 2016 Salmonella Muenchen/Kentucky outbreak) were analyzed for the presence of Salmonella following FDA BAM. Seeds from each lot were germinated in glass jars for two days at 30°C and germinated sprouts from each jar were analyzed in triplicate for Salmonella. Genomic DNA was isolated using the QIAGEN DNeasy kit. Paired-end sequencing libraries were prepared using Nextera XT and sequenced on an Illumina MiSeq. The sequences were analyzed using NCBI’s Pathogen detection system and submitted to Genome Trakr.

Results:  Salmonella was found in 1 of 10 seed and 1 of 8 sprout samples, or in 3 of 12 seed and 17 of 30 sprout samples from seedlot A or B, respectively. Based on the NCBI SNP tree results, Salmonella isolates IFSH00047-48 collected from sprouts grown from lot A clustered with Salmonella Oranienburg linked to the 2009 outbreak. IFSH00045-46 isolated from sprouts grown from lot B were found within a cluster that also contained a clinical Salmonella Muenchen strain 2016K-0108 collected by the CDC. IFSH00039-44 collected from seeds and sprouts from lot B clustered with clinical and sprout Salmonella Kentucky isolates linked to the 2016 outbreak.

Significance:  Testing sprouts performed better than testing seeds in detecting Salmonella contamination. This is the first report of isolating Salmonella Muenchen in seeds implicated in the 2016 sprout outbreak.