Implementation of Nationwide Real-time Whole-genome Sequencing to Enhance Listeriosis Outbreak Detection and Investigation

Clin Infect Dis. 2016 Aug 1;63(3):380-6. doi: 10.1093/cid/ciw242. Epub 2016 Apr 18.


Listeria monocytogenes (Lm) causes severe foodborne illness (listeriosis). Previous molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE), were critical in detecting outbreaks that led to food safety improvements and declining incidence, but PFGE provides limited genetic resolution. A multiagency collaboration began performing real-time, whole-genome sequencing (WGS) on all US Lm isolates from patients, food, and the environment in September 2013, posting sequencing data into a public repository. Compared with the year before the project began, WGS, combined with epidemiologic and product trace-back data, detected more listeriosis clusters and solved more outbreaks (2 outbreaks in pre-WGS year, 5 in WGS year 1, and 9 in year 2). 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. WGS has transformed listeriosis outbreak surveillance and is being implemented for other foodborne pathogens.

Keywords: DNA sequencing; Listeria monocytogenes; foodborne diseases; outbreaks.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, U.S. Gov't, P.H.S.
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Disease Outbreaks*
  • Food Safety
  • Foodborne Diseases / epidemiology*
  • Foodborne Diseases / microbiology
  • Genome, Bacterial / genetics*
  • High-Throughput Nucleotide Sequencing
  • Humans
  • Listeria monocytogenes / classification*
  • Listeria monocytogenes / genetics
  • Listeria monocytogenes / isolation & purification
  • Listeriosis / epidemiology*
  • Listeriosis / microbiology
  • Multilocus Sequence Typing
  • Phylogeny
  • Sequence Analysis, DNA
  • Whole Genome Sequencing / methods*