Recently, genome sequence has been revolutionalized the field of virology, bacteriology and most importantly infectious diseases outbreaks investigation. The invention of high through output sequencing, computational assembly of sequences and functional inferences give access for gain large amount of information along with genome analysis, which provide an irreplaceable research tools for the different prospective of clinical microbiology. The first genome sequenced was done in 1995, of a free living organism name Homophiles influenza. Now, there are number of bacterial and eukaryotes genomes have been sequenced. Moreover, genome of different bacterial strains from each of 55 species also has been sequenced for the investigation of diseases outbreaks (Pierre-Edouard Fournie et al, 2007). The sequenced genome includes all important human bacterial pathogen, which cover all phylogenetic domains of bacteria. Now, bacterial genome can be easily sequenced in a week or a day instead of month even in a cheapest cost due the microbial genomic advancement (Mark J Pallen 2010). The research for the bacterial genomic sequence has been led to unique advancement in pathogen diagnosis, genotyping virulence detection and antibiotic resistance, which providing significant role to prevent and control the burden of infectious diseases outbreaks. The aim for the review of this article is to evaluate the role of Next generation sequencer for the investigation of different infectious diseases outbreaks and the potential to control and prevent the microbial pathogen.
Structure of the Dissertation:
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After the extensive literature on my dissertation topic, I have selected the following sections to discuss the impact of next generation sequencer in the study of infectious diseases outbreaks.
Background to Genome sequencing:
This is important to provide the background information, not only to the reader but also for the self understanding of the proposed hypotheses. As mentioned in the title of the study, genome sequencing and infectious diseases outbreaks are the two main key terms. These terms were used, in order to find the relevant published articles on our proposed study. Following is the summary of the background with references from the relevant literature.
After the use of genome sequencing, the data on the novel microbial genomic is being produced regularly. The use of genome sequences for this purpose has produced vast information that need to be assessed for its effectiveness. This information has been proving the diversity of the microbial scale and the fact that this microbial gene pool is larger than predicted (Medini et al., 2008). In broad terms, genome sequencing is comprised of four steps. In first step the pathogen is detected in a sample. Secondly, the detected pathogen is then identified and then further tested for drug susceptibility and epidemiological typing (Koser et al., 2012). Needless to say, Whole genome sequencing (WGS) technique promises the transformation of the practice of clinical microbiology. Similarly, the rapid fall in the cost and turnaround time of the test procedure mean, in the near future, this will become a viable assay in diagnostic laboratories
History of genome sequencing:
The next section that I would include in my review is the history of genome sequencing. For instance, since the discovery and knowledge of the sequences of deoxyribonucleic acid (DNA), the whole biology has been revolutionized and has also brought a massive acceleration in medical research. Until recently, one of the most widely used clinical approach for DNA sequence determination has been the chain termination methodology. This was first published by Fredrick Sanger and colleagues in 1977 and then in 1980, Sanger's was awarded his second Nobel prize. for over 30 years, the concept of Sanger's sequencing methodology still remain unchanged. In the next decades, further improvements were made in speed and reaction expediency, such as increased read lengths and dye termination methodologies, capillary electrophoresis and automation. Furthermore, in 1987, the first automated sequencing machines became commercially available by Applied Biosystems, US. The current developed technology (e.g. ABI3730xl) is now considerably offering high-throughput DNA sequence generation with a high quality.
Next generation sequencing:
This is one of the main sections of my review report where I will link the genome sequencing technology with infectious diseases breakpoints. Next-generation sequencing (NGS) technologies have brought tremendous revolution in the era of biodiversity surveillance. This also enables the high-throughput analysis of complex microbial species through short amplicons. Given the scale of sequencing reactions possible in a single run of most NGS platforms. The use of short DNA sequence "barcodes" hundreds to thousands of samples can be analyzed. In this technique, the top 99.9% of the microbiota can be characterized. The comparative ecological analysis has been facilitated by this technology, on a large scale.
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In the past few years, unprecedented efforts have therefore been made to develop and deploy new sequencing strategies (Hall et al., 2007; Schuster et al., 2008). Currently, there are three new methods being commercially used. These techniques are mainly based on amplification strategies, e.g. sequencing by synthesis on DNA that is direct amplification on a glass substrate, sequencing by ligation and high-throughput pyrosequencing on beads30 (Bennett and Solexa, 2004; Bennett et al., 2005). Mainly, PCR is used in these ne methods for the amplifications of individual DNA molecules, immobilized on either a glass surface or beads. However, in parallel, all the present identical molecules can successfully be sequenced using multiplex sequencing. (Medini et al., 2008).
Impact of sequencing on infectious diseases:
This section of my systemic review would describe the role of gene sequencing infectious diseases screening. We now possess at least one complete genomic sequence of virtually all microorganisms and this is due to the application of genetic and molecular methods to the study of microorganisms that cause infection. So far, we can not simply analyze the complete genome of a bacterium on a computer program and also to deduce from the identified sequence, whether or not that organism can cause infectious pathogen. In this section, I would also discuss the answer to the research question that why there is no 'core' set of sequences or genes that defines pathogenicity for a certain infectious viruses? Furthermore, this section would also illustrate what constitutes a pathogen and its pathogenicity? The answers to bacterial species resistant to antibiotics. In addition, the understanding of the host-pathogen dynamic in humans as researched by the work of emerging infectious diseases by Medini et al, 2008. Furthermore, this section will also illustrate current researches which give examples of the many infectious disease outbreaks including mycobacterium tuberculosis outbreaks, Escherichia coli outbreak, meticillin-resistant Staphylococcus aureus outbreaks.
Conclusion and future research:
The conclusion section ill summarize the whole review report and ill also provide some future recommendations for research. For instance, the Whole-genome sequencing can play a crucial role in infectious disease control. Furthermore, this is recommended that the development of a central database for comparison of sequence data will be significant for the implementation of routine whole-genome sequencing for the infectious diseases outbreaks. The whole available data of the isolates from local, national, and global, should also be used for the development of a system for automated interpretation and linking of genome sequence.