Outline History of the representation of microbiology data in the SDTMIG Rules for when to use LB vs MB Discussion

How is Microbiology Defined? The science that deals with the study of microorganisms, including algae, archaea, bacteria, fungi, protozoa, and viruses (NCI Thesaurus, C16851).

Microbiology Specimen (MB) Domain The SDTMIG v3.2 definition for the MB domain states that it is "designed to store microbiology findings that include organisms found, gram stain results and organism growth status." All current SDTMIG MB examples are focused on how to represent results from tests performed on bacteria only.  Findings include: Identification (including visual characterization such as shape, color, and growth rate) Quantification

Microbiology Susceptibility (MS) Domain The MS domain is designed to store any findings related to the organisms found and submitted in MB. This will usually consist of susceptibility testing results, but can also be other organism-related findings such as extent of growth of an organism. All current SDTMIG MS examples are focused on how to represent results from tests performed on bacteria only.

Are Microbiology Findings Represented in Domains Outside of MB and MS? Yes! Microscopic examination of tissue samples is represented in the Microscopic Findings (MI) domain (example: tissue stained for the presence of acid-fast bacilli). Viral load is represented in the Laboratory Findings (LB) domain. STD screenings are represented in LB domain. Yeast presence in urine in LB.

Virology v1.0 Virology v1.0 team needed to represent viral resistance and after deciding that the MS structure did not work, instead of modifying MS, they created the Viral Resistance (VR) domain. An identification domain that corresponded to VR was not created. So we had MB/MS and ??/VR. The name of the virus being tested was represented in newly created “species” and “strain” variables.  

Influenza v1.0 and Virology v2.0 Need for a viral identification domain in addition to a viral resistance domain. The structure needed for viral resistance data is not different than the structure needed for other organisms. Decision that MS should be modified to work for any organism. Decision that MB should be used for identification results for all organisms.

Influenza v1.0 and Virology v2.0 The terms “species” and “strain” are problematic because the nomenclature used varies by virus and sometimes there is a need to identify the virus beyond just two levels. Creation of the variable NHOID (non-host organism identifier). The name of the organism is represented in NHOID using whatever granularity is needed. NHOID is used when you are doing test on a known organism.

Influenza v1.0 and Virology v2.0 NHOID is not used in MB because MB is mostly about identification and one can only use NHOID after the organism is identified. NHOID can be used in conjunction with the Non-host Organism Identifiers (OI) domain which is used for storing the levels of taxonomic nomenclature of microbes or parasites that have been either experimentally determined in the course of a study, or are previously known as in the case of lab strains used as reference in the study. MB is used to represent the results of the tests that identify of non-host organisms. OI is used after the non-host organism is identified.

Quantification of Organisms Quantification of viruses is represented in LB with the use of NHOID. Quantification of all other organisms is represented in MB where NHOID is not allowed. This is problematic and makes logically defining when to use LB and when to use MB difficult.

When is LB used? When is MB used? Option 1 LB is used to represent the state of the subject while MB is used to represent the characteristics of the organism. Results regarding viral load, bacterial load, parasite density, and time to detection describe the state of the subject (i.e., how sick they are) and thus would be represented in LB. Results regarding identification and visual characterization would be represented in MB. MS is used to represent drug susceptibility test results from all organisms.

When is LB used? When is MB used? Option 2 MB is used to represent all data regarding organisms including subject state, identification, quantification, and characterization. LB is never used for representing data about organisms. This means moving viral load out of LB and representing it in MB. MS is used to represent drug susceptibility test results from all organisms.

When is LB used? When is MB used? Option 3 Viral load is represented in LB. Quantification of all other organisms is represented in MB. All identification and characterization of all organisms (including viruses) is represented in MB. MS is used to represent drug susceptibility test results from all organisms.

Discussion