Although based on that book, with which I agree here, the plural seems unambiguously the preferred term for this article's context, I'm not convinced of the book's examples of incorrect use of the singular form. It seems like in the given examples, the word "bacteria" is treated as singular when referring to a specific strain of bacteria. It seems unwieldy in referring to one particular strain, IMHO, to say "the bacterium that causes <x>", since one typically gets infected by a vast quantity of the individual entities, not just one. Thus I think "the [strain of] bacteria that causes ..." [for one strain] sounds just as natural as "bacteria that cause <x> include <a>, <b>, <c> ..." [referring to multiple strains].
