Most of us have seen the odd episode, or at least been aware of the popular CSI-Miami or other incarnations of the crime drama TV series. Those of us who are scientists are somewhat cynical about the ease with which samples from crime scenes can be analysed, seemingly within hours, by whizzy machines in gleaming laboratories.
In most cases, this is far from the truth; analysis of DNA samples, for example, requires painstaking care during the collection and processing of the material. You only have to see the real world courtroom challenges to forensic laboratory evidence to realise that the whole process is much more complicated than the TV programmes would have us believe.
However, the detection of pathogenic bacteria in foods, or even the deliberate adulteration of beef burgers with other meats, is now benefiting from these molecular techniques.
The ability to sequence whole genomes of bacteria, coupled with the cheap synthesis of primers (probes) that will bind to specific parts of the bacterial DNA has enabled us to test for the presence of pathogenic bacteria in food samples.
In principle, we extract the bacterial DNA and add our probes to bind to unique sequences in the DNA. If the probe binds to the DNA, then we can use the Polymerase Chain Reaction** to amplify that piece of DNA and then detect it, separating it on a gel to produce a pattern of bands similar to what we see being examined on CSI. If there is no binding, no amplification occurs and no detection, so the bacteria are absent from the food.
In practice, it's a bit more complicated and time-consuming. We normally have to 'selectively enrich' our sample to increase the number of bacteria to a level at which we can detect them. We do this by adding the food to a culture medium that inhibits most other bacteria and encourages our target bacteria to grow. The actual preparation of the media, weighing the sample and putting them together takes only a couple of hours. However, we need to incubate the mixture for up to 48 hours under controlled conditions before we can run the PCR.
Over the past few weeks, I have been working with my research assistant, testing a new PCR-based method of detecting Listeria. It looks as though the method will be quicker and easier than existing methods and we'll publish our results in the near future.
Manufacturers continue to develop new rapid methods, many based on DNA and using automated equipment, making the detection of pathogens in food easier and quicker, allowing products to be checked and released to the market earlier. These methods can also be used to track down sources of contamination, such as in the European E. coli O104:H4 outbreak of 2011.
** For those readers keen to know more about PCR, I'll post a more complete description of the technique, trying to keep it relatively simple.
Showing posts with label molecular technique. Show all posts
Showing posts with label molecular technique. Show all posts
Monday, January 21, 2013
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
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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