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Once upon a time, I chanced upon an old microbiology book that detailed the rather colorful world of enterobacteria. Salmonella in particular stood out, as it seemed there were a lot of species: typhi / typhosa, paratyphi, gallinarum, typhimurium, choleraesuis, and quite a bunch of others that I have now forgotten.

Flipping through a newer book, it now seems that all of these "species" were collated under choleraesuis (and now more recently enterica), with all those species being demoted to "strains" (or maybe I should use the current term of art, "serovar"). Unfortunately, the book didn't give much in the way of explaining about this merger.

So, why is there now only S. enterica? If "S. typhi" is a mere serovar, how come the species name is still used in the literature?

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up vote 15 down vote accepted

Simply put, old habits die hard; physicians and other medical personnel have grown up with the old species designations so will continue to use them. This is somewhat the reverse of the case with E. coli, where 80-90% of the genome is variable across strains.

Lin-Hui gives a brief history, where strains identified early were given specific names within Salmonella like typhi, typhimurium, panama, etc. In 1966 it was proposed to lump serovars together among three species S. choleraesuis, S. typhosa, and S. kauffmannii. Shortly thereafter in 1972 with the advent of DNA techniques, it was shown they really should be all piled together. There is one exception, Salmonella choleraesuis subsp. bongori, separated in 1989.

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Nice survey article! (Even the switch from choleraesuis to enterica is discussed.) Thanks for this. I believe you intended "typhosa" instead of "thphosa", though. – user132 Dec 15 '11 at 13:58
@J.M.'s misspelled in the review though :/ – Nick T Dec 15 '11 at 14:00

Just open Wikipedia, your question is answered there:

Initially, each Salmonella species was named according to clinical considerations,[15] e.g., Salmonella typhi-murium (mouse typhoid fever), S. cholerae-suis (hog cholera). After it was recognized that host specificity did not exist for many species, new strains (or serovar, short for serological variants) received species names according to the location at which the new strain was isolated. Later, molecular findings led to the hypothesis that Salmonella consisted of only one species,[16] S. enterica, and the serovar were classified into six groups,[17] two of which are medically relevant. But as this now formalized nomenclature[18][19] is not in harmony with the traditional usage familiar to specialists in microbiology and infectologists, the traditional nomenclature is common. Currently, there are two recognized species: S. enterica and S. bongori, with six main subspecies: enterica (I), salamae (II), arizonae (IIIa), diarizonae (IIIb), houtenae (IV), and indica (VI).[20] Historically, serotype (V) was bongori, which is now considered its own species. The serovar classification of Salmonella is based on the Kauffman-White classification scheme that permits serological varieties to be differentiated from each other. Newer methods for Salmonella typing and subtyping include genome-based methods such as pulsed field gel electrophoresis (PFGE), Multiple Loci VNTR Analysis (MLVA), Multilocus sequence typing (MLST) and (multiplex-) PCR-based methods.[21]

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Beautiful. Now, what were these "molecular findings" that were instrumental in collating all those Salmonella "species" (I don't have access to the journal article linked to)? And, why is "S. typhi" still used instead of "S. enterica serovar typhi"? – user132 Dec 15 '11 at 13:56

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