Genome Advance of the Month - David Testing.
Protecting the food supply and human health with genomics
By Jonathan Gitlin, Ph.D.
Science Policy Analyst
Across the Atlantic, a new strain of the E. coli bacteria has caused an epidemic of food poisoning in Germany. As of June 7, 2011, more than 2,500 people have been sickened, 23 people have died and public health officials still do not know the source of the food contamination, though they suspect raw vegetables.
The rate of deaths and serious illness mystified physicians. Certainly many strains of E. coli can kill, but this particular strain releases a toxin that attacks the kidneys and blood vessels. According to The Robert Koch Institut in Berlin, nearly 650 patients who were stricken now suffer kidney failure (See: Investigation Update: Outbreak of Shiga toxin-producing E. coli O104 Infections Associated with Travel to Germany [cdc.gov]).
The scale of this public health crisis gave some urgency to knowing which strain of E. coli caused the epidemic. Many strains of E. coli are harmless to humans and commonly found in the intestines; others are less benign. Most serious E. coli infections result in gastrointestinal bleeding; these pathogenic strains are known as enterohemorrhagic E. coli, or EHEC. The most common strain of EHEC is E. coli 0157 (See: Escherichia coli O157:H7 and other Shiga toxin-producing Escherichia coli [cdc.gov] ). The German epidemic is causing gut hemorrhaging, but it has also been affecting patients' kidneys as bacterial toxins leave the gut and enter the bloodstream (known as hemolytic-uremic syndrome), which suggested that it might be a result of a strain other than E. coli 0157.
The Beijing Genome Institute (BGI), in conjunction with University Medical Center Hamburg-Eppendorf, used some of the newest sequencing platforms available to rapidly sequence the entire genome of the bug causing the German outbreak, and their findings suggest that the cause is a much less common strain of E. coli called 0104:H4. E coli 0104 has been occasionally found in humans but in the past has not caused illness.
BGI produced a preliminary sequence of the E. coli in just three hours by using the Ion Personal Genome Machine from Life Technologies of Carlsbad, Calif. Earlier generation sequencers can take days to produce the same data. Previously called Ion Torrent, the sequencing machine is well suited to this type of work of sequencing bacterial genomes very quickly and at low cost.
BGI's sequences results shows that 0104:H4 has acquired genes that make it resistant to many antibiotics as well as genes that are similar to other strains of E. coli that can cause hemolytic-uremic syndrome. Knowing the bacteria's sequence should help German public health officials track down the source for the food-borne contaminant, figure out how best to treat it and track future strains as they evolve.
DNA sequencing is also working its way into other public health approaches to protecting the food supply. The European Commission published Deterring Illegal Activities in the Fisheries Sector [publications.jrc.ec.europa.eu], which advocates the adoption of genomic technologies to fight the problem of fake fish. Cheaper fish like tilapia or catfish is often, and increasingly, passed off as a more expensive type of fish. In New York City, a high school science project (See: Fish Tale Has DNA Hook: Students Find Bad Labels [nytimes.com]) found that a quarter of the fish tested was mislabeled. The students determined this by looking for specific DNA sequences — known as DNA barcodes — in the fish. By properly identifying the fish being sold, it should be possible to reduce fraud and find out about illegal fishing.
Other Recent Developments
In May, the Battelle Technology Partnership Practice, funded by Life Technologies, published a report that calculated the economic impact of the Human Genome Project (HGP) and the federal investment in genomics research. The report found that every dollar invested in HGP generated $141 in economic activity, an amazing return on investment. You can read more about the study here: Calculating the economic impact of the Human Genome Project, as well as the report: Economic Impact of the Human Genome Project
And finally, several more organisms have had their genomes sequenced, including:
- Thinopyrum intermedium, or intermediate wheatgrass: On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae). BMC Evol. Biol., May 18, 2011. [PubMed]
- Eucalyptus grandis, or the eucalyptus tree: The Eucalyptus grandis (Eucalyptus) genome sequence on Phytozome [phytozome.net]
- Barley: Unlocking the Barley Genome by Chromosomal and Comparative Genomics. Plant Cell, 23(4):1249-63. 2011. [PubMed]
- Lyngbya majuscula 3L, a marine cyanobacteria, one oldest forms of life on the planet: Genomic insights into the physiology and ecology of the marine filamentous cyanobacterium Lyngbya majuscula Proc. Nat. Acad. Sci. U.S.A., May 9, 2011. [PubMed]
- Melampsora larici-populina, a fungal pathogen that causes poplar leaf rust, and Puccinia graminis f. sp. Tritici, which causes wheat and barley stem rust, a plant disease that is threatening the global wheat supply: Obligate biotrophy features unraveled by the genomic analysis of rust fungi Proc. Nat. Acad. Sci. U.S.A., May 2, 2011. [PubMed]
Posted: June 8, 2011