In 1884, the first Salmonella species was isolated by veterinary surgeon Daniel E. Salmon from porcine intestines. The isolated species was first referred to as Bacillus choleraesuis, however was renamed Salmonella choleraesuis in 1900 (Ryan). Several years later in 1986, the choleraesuis designation was changed by the Subcommittee of Enterobacteriaceae of the International Committee on Systematic Bacteriology at the XIV International Congress of Microbiology and now the Salmonella type species is recognized as enterica (Ryan).

The genus Salmonella are Gram negative rod-shaped bacteria approximately 2-5 microns in length that belong to the family Enterobacteriaceae. Bacteria belonging to the genus Salmonella are catalase positive, oxidase negative and are not able to form spores (Ryan).  Salmonella are characterized by the possession of peritrichous flagella for mobility. The physiological traits of most of the Salmonella serovars include but are not limited to: the use of citrate as a sole carbon source; fermentation of lactose; production of hydrogen sulfate; and hydrolysis of urea. Salmonella species survival has been reported over a large pH range, from 3.8-9.5 with the optimal growth pH range of 6.5-7.5 (Ryan) (Andino).

Both Salmonella and E. coli are enteric Gram negative bacteria that belong to the family Enterobacteriaceae and possess similar virulence mechanisms such as low pH resistances and the ability to grow on lactose (Windfield). A phylogenetic study conducted by Desai et al. revealed an estimated 140-million-year divergence between Salmonella and E. coli. The divergence of the most recent common ancestor of all Salmonella subspecies resulted in an estimated 657 gene families gained from Escherichia. Of the 657 gene families, 454 gene families were currently present in all of the 29 Salmonella genomes the Desai et al. study sequenced and analyzed. One of the benefits of the genes Salmonella inherently gained from Escherichia allows for Salmonella subspecies to utilize various carbohydrates in anaerobic conditions (Desai).

Approximately 45% of known bacterial genomes have a CRISPR- Cas (clustered regularly interspaced short palindromic repeats and CRISPR associated genes) system to provide immunity protection from invasive genetic elements such as plasmids and bacteriophage. Shariat et al. study performed an extensive sequence analysis on the Salmonella CRISPR-Cas type IE system to acquire a deeper evolutionary perspective of the system. A comparison of CRISPR- Cas sequence data from several different Salmonella enterica serotype isolates (Enteritidis, Typhimurium, Newport and Heidelberg) revealed that leader, operon and array sequences were well conserved among the isolates. CRISPR-Cas systems adapt by obtaining new spacer sequences to combat invading genetic elements however, Salmonella do not acquire new spacers but instead delete or duplicate direct repeat spacer units. Of the isolates sequenced, only 12% of the spacers corresponded with phage and plasmid sequences,  The analysis also determined that Salmonella CRISPR-Cas type IE shared some similarities as well as differences to E. coli CRISPR type I-E. Regulation mechanics of the cas operon is similar in Salmonella and E. coli although the E. coli system has a promoter intergenic region between the cas3 and cse genes while this intergenic region is absent in Salmonella. Collectively, the study concluded that the highly conserved Salmonella CRISPR-Cas system may not be actively involved in immune function but instead may be involved with other processes such as biofilm formation (Shariat).

Salmonella species are typically described as mesophilic organisms but have the ability to thrive at low or high temperatures. The sigma factors of the bacteria sense temperatures changes in the external environment and initiates the activation of rpoH genes to respond to high temperatures. During cold external temperatures Salmonella employs the use of Cold shock proteins to increase the survivability in low temperature environments. Synthesis of these specialized proteins contributes the survivability of Salmonella species in refrigeration conditions (Andino).

The Salmonella genus is categorized into two species: Salmonella enterica and Salmonella bongori (Ryan). Currently, there are six subspecies of Salmonella enterica; of the six, subspecies I is critically recognized as the human disease-causing group while the other subspecies primary reside in cold blooded animals (Desai). A recent phylogenetic study by Desai et al. examined the divergence of subspecies within the species Salmonella enterica using synonymous SNPs. The report concluded that the species separation occurred approximately 27 million years ago and determined that the most recent common ancestor of the subspecies enterica possibly evolved after the emergence of their respective hosts, about 12 million years ago (Desai).

Salmonella bongori is currently recognized by the Judicial Commission of the International Committee for Systematics of Prokaryotes as an entirely separate species from Salmonella enterica. S. bongori is most commonly associated with cold blooded animals such as reptiles, however in extremely rare cases it has been reported to cause disease in humans (Fookes). During the evolutionary divergence of Salmonella from Escherichia, it is proposed that S. bongori lost 63 genes that were present in the most recent common ancestor of Salmonella. Accompanied by the loss of genes, S. bongori does not possess the ability to utilize ethanolamine, catabolize fucose, or perform nitrate and nitrate ammonification (Desai) (Ryan).

During the early 1950’s the serotyping of Salmonella species was conducted by the Kauffman-White scheme using the identification of somatic O and flagellar H surface antigens. The O antigen is found on the outer surface of the lipopolysaccharide of the bacterial membrane, consisting of a heat stable polysaccharide arrangement. The H antigen is located on the filamentous region of the Salmonella flagella which are composed of flagellin subunits (Ryan).  In accordance with the standard identification procedures, the O antigen signifies the group that the Salmonella isolate will be categorized into while the H antigen determines the serovar assignment of the isolate (Ryan). Although horizontal gene transfer events of the O and H antigen genes can cause inaccuracies regarding identification (Desai). Currently, more than 2500 serotypes of Salmonella have been identified with S. enterica Typhimurium , S. enterica Enteritidis , S.enterica Newport, and S. enterica Javiana as the most prevalent isolated serotypes in the United States (Braden).

Salmonella species are enteric organisms that initially invade the host intestinal epithelium by activation of invasion genes (SPI-1). The addition of organic acids was predicted to alter the expression of SPI-1 and as a result interfere with Salmonella virulence. S. Typhimurium exhibited lower epithelial cell invasion when grown in media modified with butyrate and propionate; it was determined that the acids decreased the expression of SPI-1 activators (hilA and invF). Acetate modified media produced a different response; acetate led to an increased expression of hilA and invF activators resulting in greater Salmonella virulence (Van Immerseel).

As Salmonella species takes up residence in a host organism, the host defenses are activated. The pathogens begin their existence intracellularly as they are consumed by macrophage cells and epithelial cells. The pathogens first penetrate the intestinal epithelium by the promotion of early invasion genes (SPI-1); then they can disseminate to other tissues causing gastroenteritis, enteric fever and septicemia (Van Immerseel). Defense mechanisms such as the two- component signal transduction PhoP/PhoQ system comprised of a senor kinase and response regulator is required for Salmonella pathogens to tolerate the harsh acidic environment of phagocytic cells. The PhoP and PhoQ is a highly conserved regulon of Salmonella responsible for the induction of five pag genes that allow for the production of nuclear envelope proteins to improve survival and activate virulence properties (White) (Ren). PhoQ is activated by autophosphorylation in response to external environmental changes such as low concentrations of essential metal ions or changes in pH. The phosphorylated PhoQ then leads to the activation the PhoP which then facilitates the transcription of phoP and other genes contributing to enhanced virulence and production of acid shock proteins. (Ren). PhoP is also involved in the downregulation of the invasion genes SPI-1 master regulator, HilA. During early invasion, the PhoQ/PhoQ system is repressed in order to allow for expression of SPI-1 genes required for initial infection (Ren).

Virulence attributes of Salmonella are also activated by the hilA gene regulated by increased environmental acetic acid concentration (Andino). Overall, the activation of virulence genes is upregulated by external environmental stresses indicating that Salmonella species could exhibit greater infectivity potential and resilience in unfavorable acidic and temperature conditions (Ren, White, Andino).

Salmonellae are facultative anaerobic pathogens whose growth is supported by the environmental conditions of the intestinal tract of humans and animals. Salmonella organisms thriving in the digestive system of a host are often excreted from the host in the feces. Insects and other creatures contact the feces and collect the excreted organisms transmitting Salmonella to other locations such as a water source or food product. Consumption of a contaminated source by a human or animal will introduce Salmonella to the digestive tract, continuing the cycle of Salmonella contamination. The amount of organisms inoculated into the host as well as the host immunity will determine salmonellosis disease progression (Andino).

Salmonella species strategically exploit the host immune system by evading the host’s nutritional immunity. Nutritional immunity of a host is described as a process by which the host restricts the availability of essential transition metals in an effort to prevent the proliferation of pathogenic microbes. Specific genes of the Salmonella species allow the bacterium to acquire the necessary transition metals in the digestive tract of a host organism (Allard) (Hood). A study by Lui et al.  indicated that during a bacterial infection the host upregulates the production of calprotectin, a zinc- and magnesium-dependent antimicrobial protein required to combat microbial growth. Consequently, the presence of the calprotectin provides an ideal environment for S. Typhimurium by the inhibition of the growth of invading microbes while enhancing the growth of S. Typhimurium (Lui).

Beef is one of the top five most common food products susceptible to Salmonella contamination. S. Typhimurium, S. Dublin, and S. Montevideo are three of the most common serotypes infective in cattle causing fever, reduced milk production, and potential miscarriages. In accordance with the 2014 USDA inspection, Salmonella isolates were recovered from 1.6% of the 7,320 ground beef samples. S. Dublin accounted for 12.4 % of the positive samples while S. Montevideo made up 22.4 %. Consumption of contaminated beef products generally results in gastroenteritis (Andino) (USDA/FSIS).

Two of the most medically important serotypes of Salmonella are Salmonella enterica serovars Typhi and Paratyphi, which are the primary causative agents of enteric fevers. These serotypes are distinct from other Salmonella species in that they are strictly human pathogens and do not possess the ability to ferment lactose (Andino) (Braden).

Enteric fever is a progressed salmonellosis disease in humans primarily endemic in Southeast and Central Asian countries and is manifested by typhoidal Salmonella enterica serovars S. enterica Typhi and S. enterica Paratyphi. Symptoms indicative of typhoid fever are fever, rose colored spots on the chest, and bradycardia. Similarly, both typhoidal and non-typhoidal serotypes spread via the fecal oral route. Non-typhoidal serovars (NTS) include S. enterica Typhimurium, S. enterica Enteriditis, S. enterica Newport and S. enterica Heidelberg. NTS are more frequently associated with morbidity and hospitalizations from food contamination, shifting the prevention focus to NTS. Symptoms of NTS salmonellosis are generally self-limiting including nausea, vomiting, fever, chills, abdominal pain, and myalgia (Andino).

S. choleraesuis is one of the most prevalent serotypes (along with S. Typhimurium and S. derby) that infects swine products. Salmonella IV formally referred to as Salmonella marina is associated with reptilian creatures (Braden).

Many Salmonella serovars commonly are found in poultry and poultry processing equipment (Van Immerseel). The most prevalent subspecies of Salmonella involved in food related outbreaks is enterica. The most frequently occurring serovar are S. enterica Enteriditis and S. enterica Typhimurium (Allard). In the United States, S. Enteriditis, is the most frequently reported serovar of Salmonella most commonly associated with poultry products.  In relation to other Salmonella serovars, S. enterica Enteriditis does not produce any symptoms of infection in a chicken host; however if a mother hen is infected with this unique strain then she will transfer bacteria directly to the egg through vertical transmission or horizontal transmission (Andino) (Gantois). Horizontal transmission occurs when Salmonella from contaminated feces or from the colonized gut of the hen infiltrates the egg shell during or after oviposition. Infected reproductive organs of the hen can lead to contamination of the developing egg before oviposition known as a vertical transmission process.  Salmonella contamination inside of eggs is most likely a consequence of infected reproductive organs of the mother hens which results in egg contamination during egg formation (Gantois).

Poultry host specific serovars S. enterica Pullorum and S. enterica Gallinarum cause Pullorum disease and fowl typhoid in poultry but are not usually a risk to humans. Pullorum disease and fowl typhoid are associated with high mortality rates and can affect the national poultry livestock and product supply if untreated. Since 1975 these poultry Salmonella serovars have been eradicated commercially in most of the developing world. The elimination of some species in a niche will reduce the resource competition and allow for a new organism to thrive; it has been proposed that the eradication of these poultry-affecting Salmonella serotypes has allowed for S. Enteriditis to inhabit the vacant niche (Andino).

In 2014, the USDA inspection report revealed that Salmonella was present in 325 broiler chicken carcass samples out of 8816 total sampled. S. kentucky, a serotype not associated with human infection, accounted for 60.8% of the positive samples while S. enterica Enteriditis composed 13.6% of the positive samples (USDA/FSIS).

Over 70% of salmonellosis cases are the result of the consumption of contaminated poultry products such as eggs (Andino). Salmonella species survive with great success in farm environments. Contamination of chickens and eggs is often unnoticed since major pathogenic serotypes such as S. enterica Enteritidis do not produce any signs of disease in the poultry (Braden). Egg shells are considered one of the major sources of contamination. Between 1986 and 1987 65 outbreaks of Salmonella were the cause of 257 hospitalizations and 11 deaths in the United States. Of the 65 cases 77% of 35 of the outbreaks were egg and egg product associated. From 1985-2003 the United States alone reported 997 S. enterica serovar Enteritidis resulting in 33687 illnesses, 3281 hospitalizations and 82 deaths; 75% of the outbreaks were egg and egg product associat