Salmonella


Salmonella is a genus of rod-shaped, Gram-negative bacteria of the family Enterobacteriaceae. The two known species of Salmonella are Salmonella enterica and Salmonella bongori. S. enterica is the type species and is further divided into six subspecies that include over 2,650 serotypes. Salmonella was named after Daniel Elmer Salmon, an American veterinary surgeon.
Salmonella species are non-spore-forming, predominantly motile enterobacteria with cell diameters between about 0.7 and 1.5 μm, lengths from 2 to 5 μm, and peritrichous flagella. They are chemotrophs, obtaining their energy from oxidation and reduction reactions, using organic sources. They are also facultative anaerobes, capable of generating adenosine triphosphate with oxygen when it is available, or using other electron acceptors or fermentation when oxygen is not available.
Salmonella species are intracellular pathogens, of which certain serotypes cause illness such as salmonellosis. Most infections are due to the ingestion of food contaminated by feces. Typhoidal Salmonella serotypes can only be transferred between humans and can cause foodborne illness as well as typhoid and paratyphoid fever. Typhoid fever is caused by typhoidal Salmonella invading the bloodstream, as well as spreading throughout the body, invading organs, and secreting endotoxins. This can lead to life-threatening hypovolemic shock and septic shock, and requires intensive care, including antibiotics.
Nontyphoidal Salmonella serotypes are zoonotic and can be transferred from animals and between humans. They usually invade only the gastrointestinal tract and cause salmonellosis, the symptoms of which can be resolved without antibiotics. However, in sub-Saharan Africa, nontyphoidal Salmonella can be invasive and cause paratyphoid fever, which requires immediate antibiotic treatment.

Taxonomy

The genus Salmonella is part of the family of Enterobacteriaceae. Its taxonomy has been revised and has the potential to confuse. The genus comprises two species, S. bongori and S. enterica, the latter of which is divided into six subspecies: S. e. enterica, S. e. salamae, S. e. arizonae, S. e. diarizonae, S. e. houtenae, and S. e. indica. The taxonomic group contains more than 2500 serotypes defined on the basis of the somatic O and flagellar H antigens. The full name of a serotype is given as, for example, Salmonella enterica subsp. enterica serotype Typhimurium, but can be abbreviated to Salmonella Typhimurium. Further differentiation of strains to assist clinical and epidemiological investigation may be achieved by antibiotic sensitivity testing and by other molecular biology techniques such as pulsed-field gel electrophoresis, multilocus sequence typing, and, increasingly, whole genome sequencing. Historically, salmonellae have been clinically categorized as invasive or non-invasive based on host preference and disease manifestations in humans.

History

Salmonella was first visualized in 1880 by Karl Eberth in the Peyer's patches and spleens of typhoid patients. Four years later, Georg Theodor Gaffky was able to grow the pathogen in pure culture. A year after that, medical research scientist Theobald Smith discovered what would be later known as Salmonella enterica. At the time, Smith was working as a research laboratory assistant in the Veterinary Division of the United States Department of Agriculture. The division was under the administration of Daniel Elmer Salmon, a veterinary pathologist. Initially, Salmonella Choleraesuis was thought to be the causative agent of hog cholera, so Salmon and Smith named it "Hog-cholera bacillus". The name Salmonella was not used until 1900, when Joseph Leon Lignières proposed that the pathogen discovered by Salmon's group be called Salmonella in his honor.
In the late 1930s, Australian bacteriologist Nancy Atkinson established a salmonella typing laboratory – one of only three in the world at the time – at the Government of South Australia's Laboratory of Pathology and Bacteriology in Adelaide. It was here that Atkinson described multiple new strains of salmonella, including Salmonella Adelaide, which was isolated in 1943. Atkinson published her work on salmonellas in 1957.

Serotyping

Serotyping is done by mixing cells with antibodies for a particular antigen. It can give some idea about risk. A 2014 study showed that S. Reading is very common among young turkey samples, but it is not a significant contributor to human salmonellosis. Serotyping can assist in identifying the source of contamination by matching serotypes in people with serotypes in the suspected source of infection. Appropriate prophylactic treatment can be identified from the known antibiotic resistance of the serotype.
Newer methods of "serotyping" include xMAP and real-time PCR, two methods based on DNA sequences instead of antibody reactions. These methods can be potentially faster, thanks to advances in sequencing technology. These "molecular serotyping" systems actually perform genotyping of the genes that determine surface antigens.

Detection, culture, and growth conditions

Most subspecies of Salmonella produce hydrogen sulfide, which can readily be detected by growing them on media containing ferrous sulfate, such as is used in the triple sugar iron test. Most isolates exist in two phases, a motile phase and a non-motile phase. Cultures that are nonmotile upon primary culture may be switched to the motile phase using a Craigie tube or ditch plate. RVS broth can be used to enrich for Salmonella species for detection in a clinical sample.
Salmonella can also be detected and subtyped using multiplex or real-time polymerase chain reaction from extracted Salmonella DNA.
Mathematical models of Salmonella growth kinetics have been developed for chicken, pork, tomatoes, and melons. Salmonella reproduce asexually with a cell division interval of 40 minutes.
Salmonella species lead predominantly host-associated lifestyles, but the bacteria were found to be able to persist in a bathroom setting for weeks following contamination, and are frequently isolated from water sources, which act as bacterial reservoirs and may help to facilitate transmission between hosts. Salmonella is notorious for its ability to survive desiccation and can persist for years in dry environments and foods.
The bacteria are not destroyed by freezing, but UV light and heat accelerate their destruction. They perish after being heated to for 90 min, or to for 12 min, although if inoculated in high fat, high liquid substances like peanut butter, they gain heat resistance and can survive up to for 30 min. To protect against Salmonella infection, heating food to an internal temperature of is recommended.
Salmonella species can be found in the digestive tracts of humans and animals, especially reptiles. Salmonella on the skin of reptiles or amphibians can be passed to people who handle the animals. Food and water can also be contaminated with the bacteria if they come in contact with the feces of infected people or animals.

Nomenclature

Initially, each Salmonella "species" was named according to clinical consideration, for example Salmonella typhi-murium, S. cholerae-suis. After host specificity was recognized not to exist for many species, new strains received species names according to the location at which the new strain was isolated. These "species" are grouped into "subgenra" using biochemical characteristics by Kauffmann, forming four groups, I through IV.
In 1987, Le Minor and Popoff used molecular findings to argue that Salmonella consisted of only one species, S. enterica, turning former "species" names into serotypes. The species contains seven DNA groups, five of which correponds to Kauffmann's. In 1989, Reeves et al. proposed that the DNA group V should remain its own species, resurrecting the name S. bongori. The current nomenclature has thus taken shape, with six recognised subspecies under S. enterica: enterica, salamae, arizonae, diarizonae, houtenae, and indica.
The serotype or serovar is a classification of Salmonella based on antigens that the organism presents. The Kauffman–White classification scheme differentiates serological varieties from each other, with the serotypes/serovars capitalized but not italicized: an example is Salmonella Typhimurium. This nomenclature can be combined with the species and subspecies, resulting in the full name Salmonella enterica subsp. enterica serovar Typhimurium. More modern approaches for typing and subtyping Salmonella include DNA-based methods such as pulsed field gel electrophoresis, multiple-loci VNTR analysis, multilocus sequence typing, and multiplex-PCR-based methods. They largely agree with the Kauffman-White results, allowing old names to be reused.
Many specialists in infectious disease are unfamiliar with the current Salmonella nomenclature, with journals needing to emphasize the correct taxonomy and orthography.
Notes and legends:
Analysis of whole Salmonella enterica genomes indicated that ancient hybridization has occurred to form some groups. As a result, standard phylogeny trees cannot fully recover the history of their evolution. Gene flux was detected from the node marked ' to VII, from the node marked ' to houtenae A, and from enterica B to houtenae B.
GTDB RS202 reports that S. arizonae, S. diarizonae, and S. houtenae should be classified as species of their own based on the average nucleotide identity metric.