Tuesday, November 8, 2011

Those dreadful scientists - do they ever do any good?

 If you read the popular press, you could be excused for thinking that scientists, particularly the genetic engineers, are a pretty bad bunch.  Wandering round spooky laboratories wearing white coats, these bearded boffins invented preservatives that are now widely used in processed foods, they developed milk pasteurisation and homogenisation, and the genetic engineers made corn with built-in insecticide.  Food technologists are employed by food manufacturers to make food keep forever and fool the consumers.

My perhaps somewhat biased view is that this is absolute rubbish.  To name just a few good things, we have safe food and effective vaccines, a whole range of new fruit cultivars and wonderful test kits that can quickly diagnose all kinds of disease.  All these things were developed by scientists, technologists and engineers.

A recent report from Cornell University describes a new test to trace and identify outbreaks of foodborne disease.  So far this is applied only to a common Salmonella subspecies, but the principle can be applied to many other foodborne disease bacteria.

One way of recognising a specific bacterial strain, such as one suspected of causing a food poisoning outbreak, is to chop up the DNA into bits with enzymes and to amplify the bits, followed by separation of the fragments by gel electrophoresis, which is a way of creating a band pattern or fingerprint.  Alternatively, parts of the DNA can be amplified with random primers, or starting sequences, that will also produce a fingerprint.  You will have seen DNA fingerprints used for crime detection in various television series.  However, it is never as quick and simple as portrayed in these cop shows.  Unfortunately, closely related bacteria may produce band patterns that can't be distinguished, making it impossible to differentiate one strain from another.

With the development of very rapid sequencing techniques, it is now possible to determine the nucleotide sequence of the full bacterial genome.  In other words, we can read the whole genetic code of the bacterium.  Very closely related strains may differ by only a few nucleotides, or code letters.  By looking at these very small differences, we can tell if a particular strain was responsible for apparently linked illnesses in Germany, United Kingdom, New York, and France.  The technique is called Single Nucleotide Polymorphism (SNP) test.

The technique is still quite expensive, but as rapid sequencing is developed further, the cost is likely to decrease.  Being able to track an infecting bacterium, such as the Escherichia coli that caused so much disease and death in Europe earlier this year, is a valuable tool in fighting such outbreaks.  In the face of such devastating outbreaks of foodborne disease, the cost of full sequencing is insignificant.

The researchers, led by Martin Wiedmann, who developed the technique intend to continue perfecting the method and to apply it to other bacteria.


Of course, the description above is a gross simplification of the SNP test.  Wiedmann's original paper is highly technical.  You can read it in:
Applied and Environmental Microbiology, 2011; DOI: 10.1128/AEM.06538-11

Alternatively, you can read a press release from Cornell University at:
http://www.sciencedaily.com/releases/2011/10/111025113540.htm#.TqoxsV5BB1U.email

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