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What is the evolutionary process that allows for the increase in host range of food borne pathogens such as Salmonella and its serotypes?

This article divulged the differences in genome sequences of two types of Salmonella enterica isolates. They hypothesized that through study of these genomes, specifically those that contain mutations in the functional homologs of the pseudogenes could potentially lead to discovery of the genetic pathway of host adaptation in S. enterica. They found that some of the representative strains could be a direct descendent of S. enteritidis and that through these findings there is a pathway for the use of genetic approaches through experimentation to determine the genetic basis of host restriction.

This study took a look at different genomes through the lens of phage types. Through this analysis of the 6 different genomes they found that many of the differences were due to SNPs and this could lead to future research. Looked specifically at the Typhurium serovar.

This study approached the evolution of Salmonella from the virulence perspective and how it has the ability to infect many different animal species. Also holds to recent gain of traits.

This study sought to uncover the mechanism of host adaptation through the analysis of the factors that contributed to the divergence of Salmonella into different serotypes according to their corresponding hosts. This required examination of different phases that Salmonella has undergone to evolve. They surmised that further research is needed but that host range increases were the result of multiple horizontal gene transfers and more research needs to be done in order to look at all of the virulent factors that might have contributed to this host adaptation.

This article specifically looked at the possibility of host adaptation and the diversity of the subtypes of S. enterica also from the perspective of the genome. This study was able to separate the different serotypes of S. enterica through observation and experimentation of the genome to find clade-specific genes or operons. The presences of some of the operons suggest that there was an adaptation to a different environment such as a gastrointestinal environment. What they found was that there are at least two subgroups of S. enterica that are different in their "host and tissue tropism, utilization of host specific carbon and nitrogen sources" and therefore likely to have different traits in the areas of ecology and transmission.

This article provides both a definition of host adaptation and surveys the possible mechanisms utilized by Salmonella and its serotypes for host adaptation from the perspective of the host's immune response, in vertebrate animals. This study was pursued through mathematical logic and modeling as well as the study of immune responses in animals such as cows, chickens etc. The study found that O-antigen polymorphism could be a potential mechanism for host transfer but overall the development of a more precise definition of host adaptation might be the first step needed to understand the dynamics of this host-pathogen interaction. Future research will need to be done in order to make sure that the food supply is adequately protected from pathogens with host adaptation potential.

The researchers in this article took a focused at the serotype of S. enterica known as Typhimurium establish some possible ways of differentiating between the different variants. In this way they developed the relationships between the pathogens and their respective hosts or host immune systems. This study allowed for another new opportunity to study increases in host range. Rather than trying to examine the genes and fail they suggest that further research concerning the definition of serotype differences through looking at host immune responses could be more successful.

OCTOBER 1 ASSIGNMENT
This was the site I edited https://en.wikipedia.org/wiki/Salmonella

What about Host Adaptation?
( This was added to the talk section ) I think that this article could use a section devoted to research concerning the evolution of Salmonella and its serotypes in the case of host adaptation. There are several different ways to talk about host adaptation in Salmonella: through genetic sequencing and the study of mutations in pseudogenes, through multiple horizontal gene transfers, and even through an O-antigen polymorphism. See (http://genome.cshlp.org/content/18/10/1624.full.pdf+html), (http://iai.asm.org/content/70/5/2249.short), and (http://iai.asm.org/content/66/10/4579.full.pdf+html) Benson.334 (talk) 02:28, 30 September 2014 (UTC)

Host Adaptation in Salmonella
( This was added to the article ) Salmonella enterica, through some of its serovars, such as Typhimurium and S. Enteriditis, shows signs of not being limited to one host but has the ability to infect several different mammalian host species while other serovars such as, Typhi seem to be restricted to only a few hosts.

FINAL DRAFT STARTS HERE
Salmonella, a food-borne pathogen that has made headlines time and again, has increased interest over how certain types of bacteria have evolved to infect and persist in different hosts. Food infested with salmonella has led to widespread panic, distrust of the food industry and a generalized fear about the safety of things that can be consumed. While the food industry has taken drastic measures to ensure the quality and “cleanliness” of their food, some bacteria like Salmonella tend to consistently come back. This article is by no means a comprehensive look at every way that Salmonella has adapted to different hosts but is an evaluation of different possibilities and avenues by which Salmonella could have evolved such that host adaptation occurred. Several of the articles reviewed have expressed the presence of genes that are involved in host adaptation and the study of these genes through analysis of barriers to host adaptation, antigens, comparing genomes, and by surmising possible pathways of genetic information transfer.

Host adaptation must be first be defined in the context of the different studies being evaluated. The term of host adaptation is used in two different ways. The first usage is in reference to the “…ability of a pathogen to circulate and cause disease in a particular host population,” which, in the case of Salmonella is the specificity that is expressed in the choice of hosts for each of the many serotypes, or different subspecies [2]. This means that, dependent on the serotype of the Salmonella, different hosts can be infected and can subsequently pass the pathogen on in a viable state. The findings of Thomson et. al. indicated that certain mutations in the, “…cbi, pdu and ttr genes” indicated a relationship with the genome of another serotype known as S. Typhi which could be a signature of more invasive Salmonella types. In the case of the serotype Typhimurium, there is an example of significant host adaptation in pigeons. The resulting infection by this serotype is highly fatal and easily transmitted throughout the population and therefore Typhimurium has been considered a “highly host-adapted” pathogen [4]. The second usage is related to the apparent evolution of Salmonella to adapt to other hosts. Specifically, this second interpretation deals with the ability of certain serotypes to be virulent in several different populations [7]. This means that different serotypes have the ability to infect several hosts and be passed on between these populations and within these populations. Host adaptation will be used below as the ability of Salmonella as a pathogen to infect a host population, being transmitted throughout the population and to other populations with virulent results.

The reality of host adaptation in Salmonella is that there are significant obstacles that have been overcome as Salmonella has adapted to different host species. In mammals and other “higher vertebrates” more developed and effective immune responses have evolved to prevent pathogens such as Salmonella and its serotypes to be virulent and transmit throughout a population [4]. This means that these serotypes have adapted and evolved to bypass and overcome the immune systems of vertebrates. The serotypes, S. Enteritidis and S. Typhimurium, were compared through assessment of their core genes. These two are significant because they represent closely related types of Salmonella that are able to infect several mammalian hosts [7]. By going through the intestinal epithelia of a host, S. enterica can infect and metastasize throughout the tissues of the host by activating different pathways [3]. The similarities between some of the serovars, another name for serotypes, are enough to make predictions about the descent from one serotype to another. These data are indicative of evolution through mutations and loss of genetic material [7]. Some of the ways that these obstacles have been overcome is through mutation and loss of genetic material. The loss of genetic material can make the serotypes less virulent, but through the loss of key features such as flagella or certain antigens, Salmonella can evade immune system antibodies and cell-mediated response [7]. The serotypes that have lost their flagella are able to evade the immune system, because the representative immune systems adapted a way to bind to the flagella of certain serotypes. This binding would allow for macrophages and Membrane Attack Complexes to form which would eliminate the bacteria from that host species. However, due to the loss of genetic material, the Salmonella can evade this highly specified form of immune response.

While studying Salmonella and comparing the genomes, there is still the question of how Salmonella evolved. Bäumler et. al. postulated that, “in the genus Salmonella virulence evolved in three phases.” The first phase involved gaining a pathogenicity island through the transfer of a plasmid or horizontal gene transfer. The transfer of a plasmid is also known as conjugation, where a bacterium can pass a plasmid to another bacterium. Pathogenicity islands are involved in evolutionary qualities and could aid in the continued evolution of Salmonella. The second phase could be postulated as the formation of different serotypes which are supported by the presence of additional pathogenicity islands. The third phase is an estimation of the ancestry of Salmonella [1]. What this means, is that Salmonella has been able to adapt to different types of hosts by the horizontal transfer of pathogenic, or disease-like, genetic information. This article looked specifically at the serotypes of S. enterica and so far, many serotypes exist from Gallinarum, Choleraesuis to Typhi which are host adapted to fowl, pigs and humans respectively [8]. If this were true, it could explain the similarities between the different serotypes and provide a mechanism for host adaptation in other species. However in Bakker et. al. genome sequencing found very few similarities between distinct serotypes of Salmonella enterica and that the virulent factors had arisen more recently rather than been passed along [2]. This article proffered a counter point to the idea of horizontal gene transfer and instead implied that the disease-like effects of Salmonella came into effect sooner rather than long ago. Some of the mechanisms that could have been utilized for host adaptation are adhesion to mucosal surfaces, and loss of gene function [6]. This means that serotypes are so specific that they bind to receptors in the walls of the intestines of their hosts resulting in an immune response from the host. Other types have lost gene functions due to possible selection against a trait, while this makes the serotype more likely to survive; it also reduces its potential virulence as traits such as motility are often lost [1]. While there is an advantage to losing genetic information in the short run, in grand scheme of host adaptation, the loss of genetic information leads to more detrimental effects for the bacterium, like loss of movement and therefore ability to evade the immune system by entering other tissues.

Salmonella is a complex genus of bacteria. For example, the serotype Typhimurium has over six different strains, and when compared against each other, their differences were due to evolution through mutation. The distinct variations of ¬¬Typhimurium arose due to accumulation of SNPs or single nucleotide polymorphisms [6]. This diversity, driven by factors such as selection by immune systems and other defensive barriers has led to an arms race between the higher vertebrate mammals with complex immune systems and the serotypes of Salmonella. S. typhi in chronic typhoid fever carriers, is harbored in large concentrations in the gall bladder where it is not exposed to the immune system [4]. Another mechanism that Salmonella serotypes have evolved is the ability to replicate within macrophages and have the ability to express just the right proteins in order to adapt to their host environments [3]. These mechanisms and the genetic information associated with them have to be studied thoroughly to understand them, but many are difficult to fully illustrate or describe. Studies of the variants of Typhimurium confer narrow host ranges to different species in efforts to determine the genes that are involved with host adaptation have not been successful [8]. It will be difficult to determine the genes involved in host adaptation because it is difficult to transfer a virulent variance to another species without knowing the genes involved. Through mutations, human intervention and evolutionary arms races, Salmonella continues to be selected against and continues to adapt to new environments and different hosts.

In addition to horizontal gene transfer, single amino acid replacement seems to also play a significant role in the evolution of Salmonella. The study by Kisiela et. al. found that this replacement will play such a significant role to create a variety of results from increased virulence to inactivity [5]. This idea of inactivation due to a change in amino acid sequence continues the theme of mutation as one of the main driving forces for the evolution of host adaptation in Salmonella [7]. Mutations have the potential to be deleterious to the continued survival and propagation of the Salmonella but also have the potential to create more virulent strains of bacteria which could be fatal to the host. In highly pathogenic strains of S. enterica serotypes it has been found that certain adhesins are common and that this adaptation has developed from convergent evolution [5]. This is just another example of the ways that the evolutionary arms races continues to play out between species as more virulent strains and more adaptive immune systems encounter different serotypes.

In conclusion, host adaptation in Salmonella and its serotypes has emerged from several significant evolutionary forces. Mutations, the resulting SNPs, amino acid changes and genomic differences have resulted in a vast range of genetic diversity that is expressed in the virulence, and amount of host adaptation exhibited by each of the serotypes. Selection due to changing environmental conditions, immune systems, and antibiotics have all affected and lent to the evolution of host adaptation in Salmonella. In the evolutionary arms race, Salmonella, has adapted to immune system antibodies and pathogen specific responses. Through its many serotypes, Salmonella is a genus that has a rich history of evolutionary change and will continue to adapt as germs are spread.

Bibliography for Paper
1. Bäumler, Andreas J., Tsolis, Renée M., Ficht, Thomas A., and Adams, L. Garry. Evolution of Host Adaptation in Salmonella enterica. Infect. Immun. October 1998 66:10 4579-4587

2. den Bakker, Henk C., Switt, Andrea I. Moreno, Govoni, Gregory, Cummings, Craig A., Ranieri, Matthew L., Degoricija, Lovorka, Hoelzer, Kari, Rodriguez-Rivera, Lorraine D., Brown, Stephanie, Bolchacova, Elena, Furtado, Manohar R., Wiedmann, Martin. Genome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica. BMC Genomics 2011, 12:425 doi:10.1186/1471-2164-12-425

3. Ellermeier, Jeremy R., Slauch, James M. Adaptation to the host environment: regulation of the SPI1 type III secretion system in Salmonella enterica serovar Typhimurium. Current Opinion in Microbiology 2007, 10:24–29 DOI 10.1016/j.mib.2006.12.002

4. Kingsley, R. A. and Bäumler, A. J. Host adaptation and the emergence of infectious disease: the Salmonella paradigm. (2000), Molecular Microbiology, 36: 1006–1014. doi: 10.1046/j.1365-2958.2000.01907.x

5. Kisiela D. I., Chattopadhyay S., Libby S. J., Karlinsey J. E., Fang F. C., et al. Evolution of Salmonella enterica Virulence via Point Mutations in the Fimbrial Adhesin. (2012) PLoS Pathog 8(6): e1002733. doi: 10.1371/journal.ppat.1002733

6. Thomson, Nicholas R., Clayton, Debra J., Windhorst, Daniel, et al. Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways. Genome Res. Jun 2008 18: 1624-1637; doi:10.1101/gr.077404.108

7. Pang, Stanley. Octavia, Sophie. Feng, Lu. Liu, Bin. Reeves, Peter R. Lan, Ruiting. Wang, Lei. Genomic diversity and adaptation of Salmonella enterica serovar Typhimurium from analysis of six genomes of different phage types. BMC Genomics 2011, 12:425 doi:10.1186/1471-2164-12-425

8. Wolfgang Rabsch, Helene L. Andrews, Robert A. Kingsley, Rita Prager, Helmut Tschäpe, L. Garry Adams, and Andreas J. Bäumler. Salmonella enterica Serotype Typhimurium and Its Host-Adapted Variants. Infect. Immun. May 2002 70:5 2249-2255; doi:10.1128/IAI.70.5.2249-2255.2002

Contributions to Wikipedia
Created new page: Host Adaptation url: https://en.wikipedia.org/wiki/Host_adaptation

-Host adaptation, when considering pathogens, has some varying descriptions. For example, in the case of Salmonella, host adaptation is used to describe the "ability of a pathogen to circulate and cause disease in a particular host population.

-Another usage of host adaptation, still considering the case of Salmonella, refers to the evolution of a pathogen such that it can infect, cause disease, and circulate in another host.

-While there might be pathogens that can infect other hosts and cause disease, the inability to pervade, or spread, throughout the infected host species indicates that the pathogen is not host adapted to that species.

Made edits to Salmonella page: http://en.wikipedia.org/wiki/Salmonella

In Host Adaptation in Salmonella section:

-Some of the ways that Salmonella, through its serovars, has adapted to its hosts is through the loss of genetic material and mutations. In more complex mammalian species, immune systems, which include pathogen specific immune responses, target serotypes of Salmonella through binding of antibodies to structures like flagella. Through the loss of the genetic material that codes for a flagellum to form, Salmonella can evade a host's immune system.

-In the study by Kisela et. al., more pathogenic serovars of S. enterica were found to have certain adhesins in common that have developed out of convergent evolution. This means that, as these strains of Salmonella have been exposed to similar conditions such as immune systems, similar structures evolved to complement these more advanced defenses in hosts.

-There are still many questions about the way that Salmonella has evolved into so many different types but it has been suggested that Salmonella evolved through several phases. As Baumler et. al. have proffered, Salmonella most likely evolved through horizontal gene transfer, formation of new serovars due to additional pathogenicity islands and through an approximation of its ancestry. So, Salmonella could have evolved into its many different serovars through gaining genetic information from different pathogenic bacteria, and through this, different serovars emerged. The presence of several pathogenicity islands in the genome of different serovars have lent credence to viability of this postulation.