The US PulseNet and GenomeTrakr laboratory networks work together within the Genomics for Food Safety (Gen-FS) consortium to collect and analyze genomic data for foodborne pathogen surveillance (species include Salmonella enterica, Listeria monocytogenes, Escherichia coli (STECs), and Campylobactor). In 2017 these two laboratory networks started harmonizing their respective proficiency test exercises, agreeing on distributing a single strain-set and following the same standard operating procedure (SOP) for genomic data collection, running a jointly coordinated annual proficiency test exercise. In this data release we are publishing the reference genomes and raw data submissions for the 2017 and 2018 proficiency test exercises.

Vibrio parahaemolyticus is an aquatic halophilic bacterium that occupies estuarine and coastal marine environments, and is a leading cause of seafood-borne food poisoning cases. To investigate the environmental reservoir and potential gene flow that occurs among V. parahaemolyticus isolates, the virulence-associated gene content and genome diversity of a collection of 133 V. parahaemolyticus isolates were analyzed. Phylogenetic analysis of housekeeping genes, and pulsed-field gel electrophoresis, demonstrated that there is genetic similarity among V. parahaemolyticus clinical and environmental isolates. Whole-genome sequencing and comparative analysis of six representative V. parahaemolyticus isolates was used to identify genes that are unique to the clinical and environmental isolates examined. Comparative genomics demonstrated an O3:K6 environmental isolate, AF91, which was cultured from sediment collected in Florida in 2006, has significant genomic similarity to the post-1995 O3:K6 isolates. However, AF91 lacks the majority of the virulence-associated genes and genomic islands associated with these highly virulent post-1995 O3:K6 genomes. These findings demonstrate that although they do not contain most of the known virulence-associated regions, some V. parahaemolyticus environmental isolates exhibit significant genetic similarity to clinical isolates. This highlights the dynamic nature of the V. parahaemolyticus genome allowing them to transition between aquatic and host-pathogen states.

We investigated an outbreak of 396 Salmonella enterica serotype I 4,5,12:i:- infections to determine the source. After 7 weeks of extensive hypothesis-generation interviews, no refined hypothesis was formed. Nevertheless, a case-control study was initiated. Subsequently, an iterative hypothesis-generation approach used by a single interviewing team identified brand A not-ready-to-eat frozen pot pies as a likely vehicle. The case-control study, modified to assess this new hypothesis, along with product testing indicated that the turkey variety of pot pies was responsible. Review of product labels identified inconsistent language regarding preparation, and the cooking instructions included undefined microwave wattage categories. Surveys found that most patients did not follow the product's cooking instructions and did not know their oven's wattage. The manufacturer voluntarily recalled pot pies and improved the product's cooking instructions. This investigation highlights the value of careful hypothesis-generation and the risks posed by frozen not-ready-to-eat microwavable foods.

OBJECTIVE: Although amphibians are known Salmonella carriers, no such outbreaks have been reported. We investigated a nationwide outbreak of human Salmonella Typhimurium infections occurring predominantly among children from 2008 to 2011. METHODS: We conducted a matched case-control study. Cases were defined as persons with Salmonella Typhimurium infection yielding an isolate indistinguishable from the outbreak strain. Controls were persons with recent infection with Salmonella strains other than the outbreak strain and matched to cases by age and geography. Environmental samples were obtained from patients' homes; traceback investigations were conducted. RESULTS: We identified 376 cases from 44 states from January 1, 2008, to December 31, 2011; 29% (56/193) of patients were hospitalized and none died. Median patient age was 5 years (range <1-86 years); 69% were children <10 years old (253/367). Among 114 patients interviewed, 69 (61%) reported frog exposure. Of patients who knew frog type, 79% (44/56) reported African dwarf frogs (ADF), a type of aquatic frog. Among 18 cases and 29 controls, illness was significantly associated with frog exposure (67% cases versus 3% controls, matched odds ratio 12.4, 95% confidence interval 1.9-infinity). Environmental samples from aquariums containing ADFs in 8 patients' homes, 2 ADF distributors, and a day care center yielded isolates indistinguishable from the outbreak strain. Traceback investigations of ADFs from patient purchases converged to a common ADF breeding facility. Environmental samples from the breeding facility yielded the outbreak strain. CONCLUSIONS: ADFs were the source of this nationwide pediatric predominant outbreak. Pediatricians should routinely inquire about pet ownership and advise families about illness risks associated with animals.

Vibrio parahaemolyticus is a pathogenic marine bacterium that is the main causative agent of bacterial seafood borne gastroenteritis in the United States. An increase in the frequency of V. parahaemolyticus-related infections during the last decade has been attributed to the emergence of an O3:K6 pandemic clone in 1995. The diversity of the O3:K6 pandemic clone and serovariants has been examined using multiple molecular techniques including multilocus sequence analysis (MLSA), pulsed-field gel electrophoresis (PFGE), and group-specific PCR (GS-PCR) analysis. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has become a powerful tool for rapidly distinguishing between related bacterial species. In the current study we demonstrate the development of a whole-cell MALDI-TOF MS method for the identification of V. parahaemolyticus from other Vibrio spp. We identified 30 peaks that were present only in the spectra of the V. parahaemolyticus strains examined in this study that may be developed as MALDI-TOF MS biomarkers for identification of V. parahaemolyticus. We detected variation in the MALDI-TOF spectra of V. parahaemolyticus strains isolated from different geographical locations and at different times. The MALDI-TOF MS spectra of the V. parahaemolyticus strains examined were distinct from the other Vibrios examined including the closely related V. alginolyticus, V. harveyi, and V. campbellii. The results of this study demonstrate the first use of whole-cell MALDI-TOF MS analysis for the rapid identification of V. parahaemolyticus.