Metagenomic Approaches for Public Health Surveillance of Foodborne Infections: Opportunities and Challenges

Details

• Alternative Title:
  Foodborne Pathog Dis
• Personal Author:
  Carleton, Heather A. ; Besser, John ; Williams-Newkirk, Amanda J. ; Huang, Andrew ; Trees, Eija ; Gerner-Smidt, Peter
• Description:
  Foodborne disease surveillance in the United States is at a critical point. Clinical and diagnostic laboratories are using culture-independent diagnostic tests (CIDTs) to identify the pathogen causing foodborne illness from patient specimens. CIDTs are molecular tests that allow doctors to rapidly identify the bacteria causing illness within hours. CIDTs, unlike previous gold standard methods such as bacterial culture, do not produce an isolate that can be subtyped as part of the national molecular subtyping network for foodborne disease surveillance, PulseNet. Without subtype information, cases can no longer be linked using molecular data to identify potentially related cases that are part of an outbreak. In this review, we discuss the public health needs for a molecular subtyping approach directly from patient specimen and highlight different approaches, including amplicon and shotgun metagenomic sequencing.
• Subjects:
  Foodborne Disease Surveillance Metagenomics Review/Overview Articles Whole-genome Sequencing
• Source:
  Foodborne Pathog Dis. 2019; 16(7):474-479
• Pubmed ID:
  31170005
• Pubmed Central ID:
  PMC6653786
• Document Type:
  Journal Article
• Volume:
  16
• Issue:
  7
• Collection(s):
  CDC Public Access
• Main Document Checksum:
  urn:sha256:d3f0f9c2250111d61fe07c315d19e68dccef41fdf04f44211cb052c0dcd28395
• Download URL:
  https://stacks.cdc.gov/view/cdc/81028/cdc_81028_DS1.pdf
• File Type:
  [PDF - 338.95 KB ]