Download When is LB used?

Outline
• History of the representation of microbiology data
in the SDTMIG
• Rules for when to use LB vs MB
• Discussion
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How is Microbiology Defined?
• The science that deals with the study of microorganisms,
including algae, archaea, bacteria, fungi, protozoa, and
viruses (NCI Thesaurus, C16851).
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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
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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Discussion
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