E. coli is an abbreviation of the species name Escherichia coli, which denotes a bacterium commonly found in the intestines of warm-blooded animals. By convention, species names are always italicized (though many news publications don’t follow this convention with E. coli). The first word (denoting the genus) is capitalized, and the second word (the species) is not capitalized. This is true whether we’re talking about Escherichia coli, Canis lupus, Homo sapiens, or any other species.
Species names are often shortened in the same way as E. coli—for example, C. lupus and H. sapiens—but E. coli is shortened especially often because of Escherichia‘s difficult spelling and pronunciation.
In these examples, E. coli should perhaps be italicized, but otherwise it is used correctly:
Not surprisingly, the deadly E. coli outbreak in Germany has generated a steady stream of comment by American officials and media on similar U.S. vulnerability. [Forbes]
The incubation period for severe illness linked with E. coli is typically three to four days. [Independent]
With all the hoo-ha surrounding the fatal E. coli bug in Europe, maybe the kids are on to something when they don’t eat their greens? [New Zealand Herald]
A row over Russia’s response to the European Union’s E. coli outbreak threatens to overshadow a summit this week. [Wall Street Journal]