The issues with bacteria immunity
Bacterium immunity is caused by the genetic change in the bacteria. This can be through mutations which cause a change in gene sequence which leads to the change in bacterial proteins. Antibiotics bind to receptors in order to kill (bacteriocidal) or to prevent growth (bacteriostatic). If bacterial proteins are changed receptor shapes will differ meaning antibiotics will be unable to bind and interfere with metabolic reactions, this means the bacteria is immune making it harder to treat bacterial infections.
Solution: DNA sequencing
DNA Sequencing is the process of determining the sequence of nucleotide bases (A,T,C,G) section of DNA. Whole Genome sequencing is more complex as it involves breaking the DNA into smaller sections, sequencing them and then assembling them into a long chain.
Whole Genome sequencing is one of the most promising methods for targeting bacteria as the species and strain of bacteria can be identified so the antimicrobial resistant genes can be determined within a shorter time frame than any traditional techniques. DNA sequencing also shows the mutations present in the resistant genes and the locus of them within the genome, this can help determine the origin and the spreading of the gene so more effective action can be taken.
The two most common methods of DNA sequencing are the Sanger or next generation sequencing (deoxy). The Sanger Sequencing Method (chain termination method) was developed in 1977 by Fred Sanger. This method involves the DNA is separated into strands of around 900bp, many copies of the target DNA region are made. The Sanger Sequencing reaction involves chain terminating versions of all the nucleotides (dideoxy) which are labelled with different coloured dyes. Dideoxy nucleotides are similar to deoxy nucleotides however they lack a hydroxyl group on the 3rd carbon atom of the sugar ring, this hydroxyl group would usually act as a hook for the next nucleotide to latch onto. When the dideoxy nucleotide is added no more nucleotides can join so the chain ends and is labelled with the dye that is attached to the nitrogenous base on the dideoxy nucleotide. The section of DNA which need to be sequenced is combined with the primer, DNA polymerase, DNA nucleotides and the dideoxy ribose nucleotides. This mixture is first heated to separate the strands of DNA and then cooled so that the primer can bind to the template strand. The temperature is then raised again to allow the DNA polymerase to synthesise new DNA by adding nucleotides to the chain until one of the dideoxy nucleotides are added. This is repeated a number of times until all of the targeted section of DNA have a dideoxy nucleotide added so that it has been split up into sections with indicator dyes on the final nucleotide. The fragments are then run through a gel matrix (capillary gel electrophoresis), short fragments move quickly and long fragments moves slowly, they all eventually pass through the end where a laser illuminates them and the dye colour can be detected. The original structure of the nucleotide can be built up overtime. The end graph shows peaks in fluorescent readings, the DNA sequence can be read from the peaks.
Next generation sequencing is the collective term for all the modern sequencing technologies, they all share a common features that differentiate them from the Sanger technique. These techniques are highly parallel and performed on a microscale which means that there are lots of reactions taking place at once in a very small space. Unlike the Sanger sequence where 900 base pair are read in the next generation techniques only 50-700 nucleotides are read, more DNA can be sequenced at a faster rate.
Urinary Tract Infections (UTI’s) are one of the most common reason that doctors prescribe antibiotics. UTI’S can be very problematic as once the bacteria has entered the bloodstream patients must be given antibiotics immediately otherwise they are at risk of urosepsis. However it takes a few days for the bacteria to be grown in a lab and tested to see which antibiotic kills it. This leads doctors prescribing a broad range of antibiotic and the targeting the bacteria once the lab results have come through. This has lead to many patients being over-treated, which contributes to the antbiotic resistance. Many patients have bacteria which are resistant to a broad range of antibiotics and go untreated. Researchers have made a new device MinION, which uses DNA sequencing to characterise bacteria from urine samples and detect antibiotic resistance, which means patients can be treated effectively and quickly as this method it four times faster than the traditional culturing methods. It also ensures that antibiotic reserves are not diminished as the antibiotic needed to kill the specific bacteria is identified.
Risks and Limitations DNA sequencing
There are limitations to the sanger sequence as it is inefficient and expensive when trying to sequence an entire genome. Sequencing an entire genome cannot be entirely useful as the role of most of the genes in the genome are still not entirely known or understood therefore the information is unusable in the present day. Also, genomes may contain information that patients do not want to hear such as the discovery of an untreatable terminal disease. In addition, there is also fear of genetic discrimination, that it could have an affect on people’s ability to find jobs and particularly in the USA that it will have an effect in your health insurance.
Benefits of DNA Sequencing
DNA sequencing allows personalised treatment plans to be formed to target the mutant genes in the DNA. Sequencing is important in determining the different nucleotide variations associated with different genetic diseases which can help advance the treatment. DNA sequencing is the pillar in the new scientific field of pharmacogenomics which, analyses how a person’s unique genome variations can have an affect on their response to a drug, this helps determine which drug gives the best outcome. On a large scale it helps pharmaceutical companies determine the right dosage information and who the drug is appropriate for. Individual genetic profiling is a rarer occurrence however it has been very successful in determining what therapies to prescribe to patients with conditions such as, breast cancer, HIV and leukaemia. Future uses will be suitable treatments to target asthma, Alzheimer’s, cancer and depression. Pharmacogenomic data will be used to design drugs which can target specific sub groups of diseases which have specific mutations and genetic profiles. Beyond its uses in medicine DNA sequencing is also used in genetic testing for family relationships and to identify people involved in catastrophic events and crime suspects. As well as detecting organisms which are polluting the air, water, food and soil.