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Related Concept Videos

Genomics02:02

Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
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Related Experiment Video

Updated: Jun 23, 2025

Characterization of a Pathogenic Escherichia coli Strain Derived from Oreochromis spp. Farms Using Whole-Genome Sequencing
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Genomic perspectives on foodborne illness.

David J Lipman1, Joshua L Cherry2,3, Errol Strain1

  • 1Center for Food Safety and Applied Nutrition, Office of Regulatory Science, College Park, MD, USA.

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|June 21, 2024
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Summary

Whole-genome sequencing reveals foodborne pathogen clusters, showing younger age groups are more susceptible to Salmonella, E. coli, and Campylobacter infections. Many contamination episodes are long-lasting and linked to widespread commercial food distribution.

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Area of Science:

  • Microbiology and Public Health
  • Genomics and Infectious Disease Epidemiology

Background:

  • Whole-genome sequencing (WGS) is crucial for public health to trace foodborne illness outbreaks to their source.
  • Sporadic food poisoning cases are common but often too small to warrant detailed investigation.
  • Understanding the dynamics of pathogen evolution and transmission is key to preventing foodborne diseases.

Purpose of the Study:

  • To analyze clusters of bacterial pathogen genomes (Salmonella, E. coli, Campylobacter, Listeria) with minimal mutations.
  • To gain new insights into the nature and duration of food contamination episodes.
  • To investigate age-related susceptibility and geographic variations in pathogen prevalence.

Main Methods:

  • Analysis of whole-genome sequences from clinical isolates of four key bacterial pathogens.
  • Clustering analysis of isolates differing by a small number of mutations to identify transmission chains.
  • Examination of age distribution, geographic spread, and temporal persistence of identified clusters.

Main Results:

  • Younger age groups exhibit increased susceptibility to Salmonella, E. coli, and Campylobacter infections.
  • Significant regional variations in Salmonella serovar frequencies were observed across the United States.
  • A substantial proportion of contamination episodes, particularly for Salmonella, are long-lasting (up to three years).

Conclusions:

  • WGS-based cluster analysis provides a deeper understanding of foodborne contamination events.
  • Foodborne pathogens frequently cause multi-state outbreaks linked to commercially distributed foods.
  • Salmonella infections in infants under six months are often due to cross-contamination rather than primary formula contamination.