How does one refer to an organism in a microbiology report?

Is an organism an entity? Or an observation of an entity (thus, presumably, an observation of an organism)? Can it really be true that, after ten years of HL7 RIM development, the answer to this question is still not clear?

As the useful Resources page of HL7 Australia makes clear:

At first site the RIM is quite simple. The RIM backbone has just five core classes and a number of permitted relationships between them.In HL7 V3, every happening is an Act, which is analogous to a verb in English. Each Act may have any number of Participations, in Roles, played by Entities. These are analogous to nouns. Each Act may also be related to other Acts, via Act-Relationships.Act, Role and Entity classes also have a number of specialisations. For example, Entity has a specialisation called Living Subject, which itself has a specialisation called Person. Person inherits the attributes of both Entity and Living Subject.

Organism, too, is a specialization of Entity, we might reasonably suppose. Thus an organism is not a Role, not a Participation, not a Relationship, and also, we presume, not an Act. That an organism is an Entity is indeed the view embraced by advocates of HL7 in their oral discussions with me over the question whether the RIM can be taken seriously as a representation of the healthcare domain.

Not so for everyone in the world of HL7, however – at least not according to what we can infer from this:

Hi,
I have been working with people at CDC on using V3 messaging to convey microbiology reports among other things. In discussions today, the question came up of where in the Microbiology specification was the observation that identified the organism for which susceptibility results were being passed. I said, well no, the organism was indicated as an entity playing the role of isolate and participating in the "specimen observation cluster". But, I was told, the CDA hospital acquired infection report carried this as an observation, and indeed it does. Is this a problem to be addressed? Or a characteristic of V3 to be managed? It does seem clear that the two specifications have been underway in parallel [*], so it is, if not pointless at least difficult, to say which should be allotted precedence. What ideas do people have?
Mead

*This is exactly the thesis defended here.