Pathogenomics
Pathogenomics is a field which uses high-throughput screening technology and bioinformatics to study encoded microbe resistance, as well as virulence factors (VFs), which enable a microorganism to infect a host and possibly cause disease.
[5] In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms.
[8] This influx of information has created a need for bioinformatics tools and databases to analyze and make the vast amounts of data accessible to researchers,[10][11] and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
[19] E.coli was an example of why this is important, with genes encoding virulence factors in two strains of the species differing by at least thirty percent.
[19][13] With this high influx of new information, there has arisen a higher demand for bioinformatics so scientists can properly analyze the new data.
[10][20] Also, as of 2008, the amount of stored sequences was doubling every 18 months, making urgent the need for better ways to organize data and aid research.
[10] The sequencing technologies, the bioinformatics tools, the databases, statistics related to pathogen genomes and the applications in forensics, epidemiology, clinical practice and food safety have been extensively reviewed.
[13] Through a deeper understanding of the small sub-units that cause infection, it may be possible to develop novel therapeutics that are efficient and cost-effective.
[26] Dynamic genomes with high plasticity are necessary to allow pathogens, especially bacteria, to survive in changing environments.
[19] With the assistance of high throughput sequencing methods and in silico technologies, it is possible to detect, compare and catalogue many of these dynamic genomic events.
[31] Varying microbe strains and genomic content are caused by different forces, including three specific evolutionary events which have an impact on pathogen resistance and ability to cause disease, a: gene gain, gene loss, and genome rearrangement.
[33] Over time, the pseudogenes are deleted, and the organisms become fully dependent on their host as either endosymbionts or obligate intracellular pathogens, as is seen in Buchnera, Myobacterium leprae, and Chlamydia trachomatis.
[36] It is of particular interest in microbial studies because these mobile genetic elements may introduce virulence factors into a new genome.
[42] Pathogens that do not live in an isolated environment have been found to contain a large number of insertion sequence elements and various repetitive segments of DNA.
[19] At this time, no studies demonstrate genome-wide rearrangement events directly giving rise to pathogenic behavior in a microbe.
[19] Single Nucleotide Polymorphisms, or SNPs, allow for a wide array of genetic variation among humans as well as pathogens.
They allow researchers to estimate a variety of factors: the effects of environmental toxins, how different treatment methods affect the body, and what causes someone's predisposition to illnesses.
[46] It has been thought that the total number of genes associated with a single pathogen species may be unlimited,[46] although some groups are attempting to derive a more empirical value.
For example, Streptococcus agalactiae, which exists in diverse biological niches, has a broader pan-genome when compared with the more environmentally isolated Bacillus anthracis.
This allows for the bacteria to have a wider range in genetic traits and can cause a potential threat to humans from which there is more resistance towards antibiotics.
[54] These genes and also surface proteins may be characterized through in silico methods to form an expression profile of biofilm-interacting bacteria.
[58] The sequence of commensal Escherichia coli strain SE11, for example, has already been determined from the faecal matter of a healthy human and promises to be the first of many studies.
[62] Understanding how these strain changes occur from being low or non-pathogenic to being highly pathogenic and vice versa may aid in developing novel therapeutics for microbial infections.
Accompanied with phylogenetic analysis, it was possible to supply a detailed account of the virus' evolution and behavior, in particular its adaptation to humans.
[68] Using technologies and insight gained from reconstruction of the Spanish influenza, it may be possible to prevent future deadly planted outbreaks of disease.
An addition to this measure would be to monitor natural water reservoirs as a basis to prevent an attack or outbreak.
