Your question ventures deep into the territory of style issues—where choices are a matter of preference, not of objective right and wrong. Nevertheless, I think it's an interesting question.
If you're running the title in all-uppercase letters, it seems to me, you have already adopted a rather unorthodox title style. That being the case, you are operating outside the ambit of most style guides and are free to deal with the scientific name Escherichia coli as you see fit.
My preference, if the rest of the title is to appear in roman all-caps, would be to render it in italic all-caps. I can't think of any rationale for suddenly switching from all-caps to standard in-text genus-and-species form for a scientific name—just as it would seem odd to switch from all-caps to upper and lower case for Democratic Republic of the Congo in the midst of a bunch of all-cap BLAH BLAH BLAHS. So I would recommend following your option A above in this case:
BLAH BLAH BLAH BLAH ESCHERICHIA COLI BLAH BLAH
If you are working in normal title case, where articles (definite and indefinite) and short prepositions are lowercased, I would be inclined to follow scientific style rather than word-based uppercasing conventions in the title (that is, I would favor Escherichia coli over Escherichia Coli in the title). That would yield this result:
Blah Blah Blah Blah Escherichia coli Blah Blah
In scientific journals, it is quite common to render titles of articles and papers in sentence style, which gives you a third option and a third issue to resolve: cap Escherichia or lowercase it? Since the genus name appears in scientific names as if it were a proper noun, it makes sense to me to capitalize it even in a sentence-case setting:
Blah blah blah blah Escherichia coli blah blah
Regrettably, I couldn't dig up a discussion of this particular issue in the style guides I consulted, although it must come up now and then. The closest thing to a relevant suggestion that I could find was this tangentially related item from The Chicago Manual of Style, fifteenth edition (2003):
17.157 Italics and quotation marks within article titles. Book titles and other normally italicized terms remain italicized within an article title. ...
[Relevant example:] Connell, A. D., and D. D. Alrey. 1982. The chronic effects of fluoride on the estuarine amphipods Grandidierella lutosa and G. lignorum. Water Research 16: 1313–17.
This example (which appears in a discussion of how to present a journal article in documentation) makes clear that, under Chicago style, scientific names are italicized in otherwise nonitalicized titles, and that the genus name remains initial-capped in a sentence-style title. In other respects, however, the example doesn't help much with the particular questions you raise.