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. This includes studying genomes of pathogens which cannot be cultured outside of a host. In the past, researchers and medical professionals found it difficult to study and understand pathogenic traits of infectious organisms. With newer technology, pathogen genomes can be identified and sequenced in a much shorter time and at a lower cost, thus improving the ability to diagnose, treat, and even predict and prevent pathogenic infections and disease. It has also allowed researchers to better understand genome evolution events - gene loss, gain, duplication, rearrangement - and how those events impact pathogen resistance and ability to cause disease. 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, and it has raised ethical questions about the wisdom of reconstructing previously extinct and deadly pathogens in order to better understand virulence.
History.
During the earlier times when genomics was being studied, scientists found it challenging to sequence genetic information. The field began to explode in 1977 when Fred Sanger, PhD, along with his colleagues, sequenced the DNA-based genome of a bacteriophage, using a method now known as the Sanger Method. The Sanger Method for sequencing DNA exponentially advanced molecular biology and directly led to the ability to sequence genomes of other organisms, including the complete human genome.
The Haemophilus influenza genome was one of the first organism genomes sequenced in 1995 by J. Craig Venter and Hamilton Smith using whole genome shotgun sequencing. Since then, newer and more efficient high-throughput sequencing, such as Next Generation Genomic Sequencing (NGS) and Single-Cell Genomic Sequencing, have been developed. While the Sanger method is able to sequence one DNA fragment at a time, NGS technology can sequence thousands of sequences at a time. With the ability to rapidly sequence DNA, new insights developed, such as the discovery that since prokaryotic genomes are more diverse than originally thought, it is necessary to sequence multiple strains in a species rather than only a few. "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. Such knowledge, along with more thorough study of genome gain, loss, and change, is giving researchers valuable insight into how pathogens interact in host environments and how they are able to infect hosts and cause disease.
Pathogen Bioinformatics.
With this high influx of new information, there has arisen a higher demand for bioinformatics so scientists can properly analyze the new data. In response, software and other tools have been developed for this purpose. 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. In response, many publicly accessible databases and other resources have been created, including the NCBI pathogen detection program, the Pathosystems Resource Integration Centre (PATRIC), Pathogenwatch, the Virulence Factor Database (VFDB) of pathogenic bacteria, the Victors database of virulence factors in human and animal pathogens. Until 2022, the most sequenced pathogens are "Salmonella enterica" and "E. coli - Shigella." 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.
Microbe analysis.
Pathogens may be prokaryotic (archaea or bacteria), single-celled eukarya or viruses. Prokaryotic genomes have typically been easier to sequence due to smaller genome size compared to Eukarya. Due to this, there is a bias in reporting pathogenic bacterial behavior. Regardless of this bias in reporting, many of the dynamic genomic events are similar across all the types of pathogen organisms. Genomic evolution occurs via gene gain, gene loss, and genome rearrangement, and these "events" are observed in multiple pathogen genomes, with some bacterial pathogens experiencing all three. Pathogenomics does not focus exclusively on understanding pathogen-host interactions, however. Insight of individual or cooperative pathogen behavior provides knowledge into the development or inheritance of pathogen virulence factors. 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.
Cause and analysis of genomic diversity.
Dynamic genomes with high plasticity are necessary to allow pathogens, especially bacteria, to survive in changing environments. 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. Genomic diversity is important when detecting and treating a pathogen since these events can change the function and structure of the pathogen. There is a need to analyze more than a single genome sequence of a pathogen species to understand pathogen mechanisms. Comparative genomics is a methodology which allows scientists to compare the genomes of different species and strains. There are several examples of successful comparative genomics studies, among them the analysis of "Listeria" and "Escherichia coli". Some studies have attempted to address the difference between pathogenic and non-pathogenic microbes. This inquiry proves to be difficult, however, since a single bacterial species can have many strains, and the genomic content of each of these strains varies.
Evolutionary dynamics.
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.
Gene loss and genome decay.
Gene loss occurs when genes are deleted. The reason why this occurs is still not fully understood, though it most likely involves adaptation to a new environment or ecological niche. Some researchers believe gene loss may actually increase fitness and survival among pathogens. In a new environment, some genes may become unnecessary for survival, and so mutations are eventually "allowed" on those genes until they become inactive "pseudogenes." These pseudogenes are observed in organisms such as "Shigella flexneri, Salmonella enterica," and "Yersinia pestis." 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". These deleted genes are also called Anti-virulence genes (AVG) since it is thought they may have prevented the organism from becoming pathogenic. In order to be more virulent, infect a host and remain alive, the pathogen had to get rid of those AVGs. The reverse process can happen as well, as was seen during analysis of "Listeria" strains, which showed that a reduced genome size led to a non-pathogenic "Listeria" strain from a pathogenic strain. Systems have been developed to detect these pseudogenes/AVGs in a genome sequence.
Gene gain and duplication.
One of the key forces driving gene gain is thought to be horizontal (lateral) gene transfer (LGT). It is of particular interest in microbial studies because these mobile genetic elements may introduce virulence factors into a new genome. A comparative study conducted by Gill et al. in 2005 postulated that LGT may have been the cause for pathogen variations between Staphylococcus epidermidis and Staphylococcus aureus. There still, however, remains skepticism about the frequency of LGT, its identification, and its impact. New and improved methodologies have been engaged, especially in the study of phylogenetics, to validate the presence and effect of LGT. Gene gain and gene duplication events are balanced by gene loss, such that despite their dynamic nature, the genome of a bacterial species remains approximately the same size.
Genome rearrangement.
Mobile genetic insertion sequences can play a role in genome rearrangement activities. 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. The combination of these two genetic elements is thought help mediate homologous recombination. There are pathogens, such as "Burkholderia mallei," and "Burkholderia pseudomallei" which have been shown to exhibit genome-wide rearrangements due to insertion sequences and repetitive DNA segments. At this time, no studies demonstrate genome-wide rearrangement events directly giving rise to pathogenic behavior in a microbe. This does not mean it is not possible. Genome-wide rearrangements do, however, contribute to the plasticity of bacterial genome, which may prime the conditions for other factors to introduce, or lose, virulence factors.
Single-nucleotide polymorphisms.
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. SNPs play a key role in understanding how and why mutations occur. SNPs also allows for scientists to map genomes and analyze genetic information.
Pan and core genomes.
Pan-genome overview The most recent definition of a bacterial species comes from the pre-genomic era. In 1987, it was proposed that bacterial strains showing ;70% DNA·DNA re-association and sharing characteristic phenotypic traits should be considered to be strains of the same species. The diversity within pathogen genomes makes it difficult to identify the total number of genes that are associated within all strains of a pathogen species. It has been thought that the total number of genes associated with a single pathogen species may be unlimited, although some groups are attempting to derive a more empirical value. For this reason, it was necessary to introduce the concept of pan-genomes and core genomes. Pan-genome and core genome literature also tends to have a bias towards reporting on prokaryotic pathogenic organisms. Caution may need to be exercised when extending the definition of a pan-genome or a core-genome to the other pathogenic organisms because there is no formal evidence of the properties of these pan-genomes.
A core genome is the set of genes found across all strains of a pathogen species. A pan-genome is the entire gene pool for that pathogen species, and includes genes that are not shared by all strains. Pan-genomes may be open or closed depending on whether comparative analysis of multiple strains reveals no new genes (closed) or many new genes (open) compared to the core genome for that pathogen species. In the open pan-genome, genes may be further characterized as dispensable or strain specific. Dispensable genes are those found in more than one strain, but not in all strains, of a pathogen species. Strain specific genes are those found only in one strain of a pathogen species. The differences in pan-genomes are reflections of the life style of the organism. For example, "Streptococcus agalactiae", which exists in diverse biological niches, has a broader pan-genome when compared with the more environmentally isolated "Bacillus anthracis". Comparative genomics approaches are also being used to understand more about the pan-genome. Recent discoveries show that the number of new species continue to grow with an estimated 1031 bacteriophages on the planet with those bacteriophages infecting 1024 others per second, the continuous flow of genetic material being exchanged is difficult to imagine.
Virulence factors.
Multiple genetic elements of human-affecting pathogens contribute to the transfer of virulence factors: plasmids, pathogenicity island, prophages, bacteriophages, transposons, and integrative and conjugative elements. Pathogenicity islands and their detection are the focus of several bioinformatics efforts involved in pathogenomics. It is a common belief that "environmental bacterial strains" lack the capacity to harm or do damage to humans. However, recent studies show that bacteria from aquatic environments have acquired pathogenic strains through evolution. 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.
Microbe-microbe interactions.
Microbe-host interactions tend to overshadow the consideration of microbe-microbe interactions. Microbe-microbe interactions though can lead to chronic states of infirmity that are difficult to understand and treat.
Biofilms.
Biofilms are an example of microbe-microbe interactions and are thought to be associated with up to 80% of human infections. Recently it has been shown that there are specific genes and cell surface proteins involved in the formation of biofilm. These genes and also surface proteins may be characterized through in silico methods to form an expression profile of biofilm-interacting bacteria. This expression profile may be used in subsequent analysis of other microbes to predict biofilm microbe behaviour, or to understand how to dismantle biofilm formation.
Host microbe analysis.
Pathogens have the ability to adapt and manipulate host cells, taking full advantage of a