An Overview of PulseNet USA Databases
Beth Tolar,Lavin A. Joseph,Morgan N Schroeder,Steven Stroika,Efrain M. Ribot,Kelley Hise,Peter Gerner-Smidt +6 more
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TL;DR: PulseNet USA is the molecular surveillance network for foodborne disease in the United States that consists of state and local public health laboratories that follow PulseNet's standardized protocols to perform pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) and analyze the results using standardized software.
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Abstract: PulseNet USA is the molecular surveillance network for foodborne disease in the United States. The network consists of state and local public health laboratories, as well as food regulator...
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Use of Whole-Genome Sequencing for Food Safety and Public Health in the United States.
TL;DR: The history of WGS technology at the Centers for Disease Control & Prevention, the Food and Drug Administration, and the United States Department of Agriculture's Food Safety and Inspection Service (USDA/FSIS) as it applies to food safety is reported.
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Smart traceability for food safety.
Zhilong Yu,Zhilong Yu,Dongyun Jung,Soyoun Park,Yaxi Hu,Kang Huang,Barbara Rasco,Shuo Wang,Jennifer Ronholm,Xiaonan Lu,Xiaonan Lu,Juhong Chen +11 more
TL;DR: This review focuses on smart food traceability that has the potential to significantly improve food safety in global food supply chains and new digital technologies, such as Internet-of-things (IoTs) and cloud computing, are discussed with the aim of providing readers with an overview of the exciting opportunities in smartfood traceability systems.
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Whole-genome sequencing as part of national and international surveillance programmes for antimicrobial resistance: A roadmap
C. Vegyari,Anthony Underwood,Mihir Kekre,Silvia Argimon,Dawn Muddyman,Monica Abrudan,Celia C. Carlos,Pilar Donado-Godoy,Iruka N. Okeke,K L Ravikumar,Khalil Abudahab,Ayorinde O Afolayan,Alejandra Arevalo,J. Bernal-Morales,Erik C D Osma Castro,June M Gayeta,Vandana Govindan,M.F. Guerrero,Harry Harste,Elmer M Herrera,Jolaade J Ajiboye,P.K. Valdenarro,Marietta L Lagrada,Melissa Ana Masim,Ali Molloy,Geetha Nagaraj,Anderson O Oaikhena,Agnettah M Olorosa,Akshata Prabhu,V. Shammana,M R Shincy,D Sravani,John Stelling,Ben Taylor,Nicole E. Wheeler,A. Schmider,David M. Aanensen +36 more
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens
Ruth Timme,William J. Wolfgang,Maria Balkey,Sai Laxmi Gubbala Venkata,Robyn Randolph,Marc W. Allard,Errol Strain +6 more
- 19 Oct 2020
TL;DR: How microbial pathogen surveillance can be transformed by having an open access database along with Best Practices for contributors to follow is described, thereby advancing the One Health goals of Findable, Accessible, Interoperable and Re-usable (FAIR) data.
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Application of Electrolyzed Water in the Food Industry: A Review
Maksim Rebezov,Kanza Saeed,Adnan Khaliq,Syed Junaid Ur Rahman,Nimra Sameed,Anastasia Semenova,Mars Khayrullin,A.S. Dydykin,YuryViktorovich Abramov,Muthu Thiruvengadam,Mohammad Sharifi,Sneh Punia Bangar,José M. Lorenzo +12 more
TL;DR: In this article , the authors highlight the latest information on the factors responsible for food spoilage and the antimicrobial potential of electrolyzed water in fresh or processed plant and animal products.
References
Microbial genomic taxonomy
Cristiane C. Thompson,Luciane A. Chimetto,Robert Edwards,Jean Swings,Erko Stackebrandt,Fabiano L. Thompson +5 more
TL;DR: The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups.
Implementation of Nationwide Real-Time Whole-Genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation
Brendan R Jackson,Cheryl L. Tarr,Errol Strain,Kelly A. Jackson,Amanda Conrad,Heather A. Carleton,Lee S. Katz,Steven Stroika,L. Hannah Gould,Rajal K. Mody,Benjamin J. Silk,Jennifer Beal,Yi Chen,Ruth Timme,Matthew Doyle,Angela Fields,Matthew E. Wise,Glenn E. Tillman,Stephanie Defibaugh-Chavez,Zuzana Kucerova,Ashley Sabol,Katie Roache,Eija Trees,Mustafa Simmons,Jamie L. Wasilenko,Kristy A. Kubota,Hannes Pouseele,William Klimke,John M. Besser,Eric W. Brown,Marc W. Allard,Peter Gerner-Smidt +31 more
TL;DR: Whole-genome multilocus sequence typing and single nucleotide polymorphism analyses provided equivalent phylogenetic relationships relevant to investigations; results were most useful when interpreted in context of epidemiological data.
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Prospective use of whole genome sequencing (WGS) detected a multi-country outbreak of Salmonella Enteritidis.
Thomas Inns,Philip Ashton,Silvia Herrera-León,J. Lighthill,Sarah Foulkes,Thibaut Jombart,Y. Rehman,A Fox,Timothy J. Dallman,E. de Pinna,L. Browning,J. E. Coia,Obaghe Edeghere,Roberto Vivancos +13 more
TL;DR: This outbreak in the UK was linked with contemporaneous cases in Spain by WGS and it is concluded that UK and Spanish cases were exposed to a common source of Salmonella-contaminated chicken eggs.
Benchmark datasets for phylogenomic pipeline validation, applications for foodborne pathogen surveillance
Ruth Timme,Hugh Rand,Martin Shumway,Eija Trees,Mustafa Simmons,Richa Agarwala,Steven Davis,Glenn E. Tillman,Stephanie Defibaugh-Chavez,Heather A. Carleton,William Klimke,Lee S. Katz,Lee S. Katz +12 more
TL;DR: This work has identified four well-documented foodborne pathogen events in which the epidemiology was concordant with routine phylogenomic analyses (reference-based SNP and wgMLST approaches), and proposed five benchmark datasets to help standardize comparison of current and future phylogenomic pipelines, and facilitate important cross-institutional collaborations.
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Future challenges for tracking foodborne diseases: PulseNet, a 20-year-old US surveillance system for foodborne diseases, is expanding both globally and technologically.
Efrain M. Ribot,Kelley Hise +1 more
TL;DR: PulseNet is a national surveillance network based in Atlanta at the US Centers for Disease Control and Prevention to detect outbreaks of foodborne bacterial pathogens in real time, and its goal is to link information about people who have likely consumed the same contaminated food.
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