Phylogenomic Pipeline Validation for Foodborne Pathogen Disease Surveillance
| Autor: | Sandra M. Tallent, Ruth Timme, Maria Sanchez Leon, Steven Davis, Marc W. Allard, Joseph D. Baugher, Narjol Gonzalez-Escalona, Errol Strain, Eric W. Brown, Hugh Rand |
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| Rok vydání: | 2019 |
| Předmět: |
0301 basic medicine
Microbiology (medical) Data Analysis medicine.medical_specialty Computer science 030106 microbiology Harmonization Disease Outbreaks Foodborne Diseases 03 medical and health sciences medicine Humans Phylogeny Disease surveillance Foodborne pathogen Bacteria Whole Genome Sequencing Shotgun sequencing Public health Computational Biology Pipeline (software) Data science United States Electrophoresis Gel Pulsed-Field Identification (information) 030104 developmental biology Workflow Epidemiological Monitoring Public Health Minireview Genome Bacterial |
| Zdroj: | Journal of clinical microbiology. 57(5) |
| ISSN: | 1098-660X |
| Popis: | Foodborne pathogen surveillance in the United States is transitioning from strain identification using restriction digest technology (pulsed-field gel electrophoresis [PFGE]) to shotgun sequencing of the entire genome (whole-genome sequencing [WGS]). WGS requires a new suite of analysis tools, some of which have long histories in academia but are new to the field of public health and regulatory decision making. Although the general workflow is fairly standard for collecting and analyzing WGS data for disease surveillance, there are a number of differences in how the data are collected and analyzed across public health agencies, both nationally and internationally. This impedes collaborative public health efforts, so national and international efforts are underway to enable direct comparison of these different analysis methods. Ultimately, the harmonization efforts will allow the (mutually trusted and understood) production and analysis of WGS data by labs and agencies worldwide, thus improving outbreak response capabilities globally. This review provides a historical perspective on the use of WGS for pathogen tracking and summarizes the efforts underway to ensure the major steps in phylogenomic pipelines used for pathogen disease surveillance can be readily validated. The tools for doing this will ensure that the results produced are sound, reproducible, and comparable across different analytic approaches. |
| Databáze: | OpenAIRE |
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