Editing Salmonella (section)

== Nomenclature ==
{{See also|Salmonella enterica|Salmonella enterica subsp. enterica}}
Initially, each ''Salmonella'' "species" was named according to clinical consideration, for example ''Salmonella typhi-murium'' (mouse-typhoid), ''S. cholerae-suis'' (pig-cholera). 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.<ref>{{cite book |first=F. |last=Kauffmann |title=Die Bakteriologie der Salmonella-Gruppe |publisher=Munksgaard |location=Kopenhagen |year=1941 |oclc=3198699 }}</ref>

In 1987, Le Minor and Popoff used molecular findings to argue that ''Salmonella'' consisted of only one species, ''[[Salmonella enterica|S. enterica]]'', turning former "species" names into [[serotypes]].<ref>{{cite journal | vauthors = Le Minor L, Popoff MY | year = 1987 | title = Request for an Opinion: Designation of ''Salmonella enterica'' sp. nov., nom. rev., as the type and only species of the genus ''Salmonella'' | journal = Int. J. Syst. Bacteriol. | volume = 37 | issue = 4| pages = 465–468 | doi=10.1099/00207713-37-4-465| doi-access = free }}</ref> In 1989, Reeves ''et al.'' proposed that the serotype V should remain its own species, resurrecting the name ''[[Salmonella bongori|S. bongori]]''.<ref>{{cite journal | vauthors = Reeves MW, Evins GM, Heiba AA, Plikaytis BD, Farmer JJ | title = Clonal nature of Salmonella typhi and its genetic relatedness to other salmonellae as shown by multilocus enzyme electrophoresis, and proposal of Salmonella bongori comb. nov | journal = Journal of Clinical Microbiology | volume = 27 | issue = 2 | pages = 313–320 | date = February 1989 | pmid = 2915026 | pmc = 267299 | doi = 10.1128/JCM.27.2.313-320.1989 }}</ref> The current (by 2005) nomenclature has thus taken shape, with six recognised subspecies under ''S. enterica'': ''enterica'' (serotype I), ''salamae'' (serotype II), ''arizonae'' (IIIa), ''diarizonae'' (IIIb), ''houtenae'' (IV), and ''indica'' (VI).<ref name=":3" /><ref>Janda JM, Abbott SL (2006). "The Enterobacteria", ASM Press.</ref><ref>{{cite journal | title = The type species of the genus Salmonella Lignieres 1900 is Salmonella enterica (ex Kauffmann and Edwards 1952) Le Minor and Popoff 1987, with the type strain LT2T, and conservation of the epithet enterica in Salmonella enterica over all earlier epithets that may be applied to this species. Opinion 80 | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 55 | issue = Pt 1 | pages = 519–520 | date = January 2005 | pmid = 15653929 | doi = 10.1099/ijs.0.63579-0 | doi-access = free | author1 = Judicial Commission Of The International Committee On Systematics Of Prokaryotes }}</ref><ref>{{cite journal | vauthors = Tindall BJ, Grimont PA, Garrity GM, Euzéby JP | title = Nomenclature and taxonomy of the genus Salmonella | journal = International Journal of Systematic and Evolutionary Microbiology | volume = 55 | issue = Pt 1 | pages = 521–524 | date = January 2005 | pmid = 15653930 | doi = 10.1099/ijs.0.63580-0 | doi-access = free }}</ref> As specialists in infectious disease are not familiar with the new nomenclature, the traditional nomenclature remains common.{{cn|date=November 2023}}

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. Serotypes are usually put into subspecies groups after the genus and species, with the serotypes/serovars capitalized, but not italicized:  An example is ''Salmonella 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|multiple-loci VNTR analysis]], [[multilocus sequence typing]], and multiplex-[[Polymerase chain reaction|PCR]]-based methods.<ref name= PorwollikS>{{cite book | veditors = Porwollik S | year=2011 | title=Salmonella: From Genome to Function | publisher=[[Caister Academic Press]] | isbn= 978-1-904455-73-8}}</ref><ref name=Achtman2012>{{cite journal | vauthors = Achtman M, Wain J, Weill FX, Nair S, Zhou Z, Sangal V, Krauland MG, Hale JL, Harbottle H, Uesbeck A, Dougan G, Harrison LH, Brisse S | title = Multilocus sequence typing as a replacement for serotyping in Salmonella enterica | journal = PLOS Pathogens | volume = 8 | issue = 6 | pages = e1002776 | year = 2012 | pmid = 22737074 | pmc = 3380943 | doi = 10.1371/journal.ppat.1002776 | author-link11 = Gordon Dougan | author-link1 = Mark Achtman | doi-access = free }} {{open access}}</ref>

In 2005, a third species, ''Salmonella subterranea'', was proposed, but according to the [[World Health Organization]], the bacterium reported does not belong in the genus ''Salmonella''.<ref name=Pasteur>{{cite book |  vauthors = Grimont PA, Xavier Weill F |title=Antigenic Formulae of the Salmonella Serovars|date=2007|publisher=WHO Collaborating Centre for Reference and Research on Salmonella|location=Institut Pasteur, Paris, France|page=7|edition=9th|url=http://www.scacm.org/free/Antigenic%20Formulae%20of%20the%20Salmonella%20Serovars%202007%209th%20edition.pdf |archive-url=https://ghostarchive.org/archive/20221009/http://www.scacm.org/free/Antigenic%20Formulae%20of%20the%20Salmonella%20Serovars%202007%209th%20edition.pdf |archive-date=2022-10-09 |url-status=live|access-date=26 August 2015}}</ref> In 2016, ''S. subterranea'' was proposed to be assigned to ''[[Atlantibacter subterranea]]'',<ref>{{cite journal | vauthors = Hata H, Natori T, Mizuno T, Kanazawa I, Eldesouky I, Hayashi M, Miyata M, Fukunaga H, Ohji S, Hosoyama A, Aono E, Yamazoe A, Tsuchikane K, Fujita N, Ezaki T | title = Phylogenetics of family Enterobacteriaceae and proposal to reclassify Escherichia hermannii and Salmonella subterranea as Atlantibacter hermannii and Atlantibacter subterranea gen. nov., comb. nov | journal = Microbiology and Immunology | volume = 60 | issue = 5 | pages = 303–311 | date = May 2016 | pmid = 26970508 | doi = 10.1111/1348-0421.12374 | s2cid = 32594451 | doi-access = free }}</ref> but LPSN rejects it as an [[valid publication|invalid publication]], as it was made outside of IJSB and IJSEM.<ref>{{cite web |title=Species: Atlantibacter subterranea |url=https://lpsn.dsmz.de/species/atlantibacter-subterranea |website=lpsn.dsmz.de |language=en}}</ref> [[GTDB]] and NCBI agree with the 2016 reassignment.<ref>{{cite web |title=GTDB - Tree at g__Atlantibacter |url=https://gtdb.ecogenomic.org/tree?r=g__Atlantibacter |website=gtdb.ecogenomic.org}}</ref><ref>{{cite web |title=Taxonomy browser (Atlantibacter) |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Undef&id=1903434&lvl=3&lin=f&keep=1&srchmode=1&unlock |website=www.ncbi.nlm.nih.gov}}</ref>

[[GTDB]] RS202 reports that ''S. arizonae'', ''S. diarizonae'', and ''S. houtenae'' should be species of their own.<ref>{{cite web |title=GTDB - Tree at g__Salmonella |url=https://gtdb.ecogenomic.org/tree?r=g__Salmonella |website=gtdb.ecogenomic.org}}</ref>