The example below shows how to represent HCV study data using the MB domain.
Row 1:
Shows the identification of Hepatitis C virus during SCREENING. This is a non-targeted assessment with the intent of the following query: “What microorganism(s) are there in the subject’s sample?" Therefore the MBTEST = Microbial Organism Identification, is used.
Row 2:
Shows the further "sub-species specification" of the previously identified Hepatitis C Virus, and the result indicates that the HCV strain isolated from the subject is of "genotype 1". This test is still performed during the SCREENING visit.
Row 3:
Shows the viral load measurement of Hepatitis C Virus Genotype 1 RNA during SCREENING. Note that "VIRAL LOAD" is represented by MBTSTDTL.
Rows 4-5:
Show the detection of Hepatitis C Virus Genotype 1 and its viral load measurements at WEEK 2 visit. The result shows a reduction in HCV viral load after treatment, in comparison to the record in row 3. The targeted, microorganism-specific MBTEST of "Hepatitis C Virus Genotype 1" is used for the treatment cycle instead of "MBTEST=Microbial Organism Identification" because Hepatitis C Virus Genotype 1 infection had been confirmed during screening (Rows 1-3). Therefore, in this instance, the targeted, microorganism pre-coordinated MBTEST should be used.
Rows 6-7:
Show the detection of Hepatitis C Virus Genotype 1 and its viral load measurements at WEEK 4 visit. The result shows continued reduction in HCV viral load after further treatment, in comparison to the record in row 5.
Row 8:
Shows an absence of Hepatitis C Virus Genotype 1 in the subject after 6 weeks of treatment.
A particular species of bacteria may have hundreds of strains with taxonomic naming conventions, including the year and region of identification and genotype information of the said bacteria strain (e.g., influenza B virus (B/Acre/128560-IEC/2014), influenza B virus (B/Ann Arbor/1/1966 [cold-adapted and wild-type]).
Due to the naming complexity of microbial taxonomy below the species level, the NCI C-code will be used as the MBTESTCD if the corresponding MBTEST represents a specific microorganism at the strain level. NCI C-codes convey uniqueness in 8 characters or fewer without the additional resource required to create unique alphanumeric TESTCDs. This is why, in the preceding MB dataset, the MBTESTCD value in Rows 3-8 are populated with "C_CODE".
For antibody and antigen testing, frequently both detection and quantification measurements are performed of the same TEST. The values "DETECTION" and "CONCENTRATION" therefore will populate the --TSTDTL variable. However, for clarity and consistency, even if only the detection of antibody test is performed and there is only one row of record, the value "DETECTION" should also populate the --TSTDTL variable.
Example 2: Bacterial Studies
Non-specific microorganism identification test
For bacterial studies, to identify what bacteria is present in a sample, culturing must be performed. One can identify a bacterial species by observing the physical appearance/properties of the bacterial colony growing in or on the culture (such as the color, size, number, smell of the bacterial colonies, etc.). In this example the Middlebrook 7H10 Agar is used to cultivate bacterial growth from the lavage fluid. Middlebrook 7H10 agar allows the "selective" enrichment and growth of various Mycobacterial species (i.e. not limited to Mycobacterium tuberculosis cultivation). Therefore this medium is not for targeted use to grow M. tuberculosis.
In the example below, MBTEST = Microbial Organism Identification, is used to show that a non-specificmicroorganism identification test has been performed to identify the specific species of bacteria present in the sample.
Row 1:
During the screening process, subject ABC-008 who was suspected to have contracted tuberculosis had undergone a microbial identification test to verify whether Mycobacterium tuberculosis was present in the subject's lavage fluid sample. The lavage fluid sample was cultured on the MIDDLEBROOK 7H10 AGAR, which is a selective medium that supports the growth of M. tuberculosis and is represented by the MBMEDTYP NSV. However, other Mycobacterium species can also grow on this medium. Row 1 record shows the growth and thus presumptive identification of M. tuberculosis in the subject's sample.The MBTEST of "Microbial Organism Identification" is used here (row 1) in the screening process because while there was suspicion that the subject may have been infected with M. tuberculosis until agar testing was performed to confirm the existence of M. tuberculosis, this was a non-targeted assessment with the intent of the following query: “what microorganism(s) are there in the subject’s sample?"
Rows 2-3:
Show the quantitative and ordinal colony count for Mycobacterium tuberculosis. From the same "colony count" test there are two results, one is quantitative (row 2) and one is ordinal (row 3), in order to distinguish the two records, the NSV MBRRSTYP is used to house "QUANTITATIVE" and "ORDINAL".
Row 4:
Shows that after two weeks of treatment, the same subject was tested again for the presence of M. tuberculosis in his lavage fluid sample. The targeted, microorganism-specific MBTEST of "Mycobacterium Tuberculosis" is used for the treatment cycle instead of the "MBTEST = Microbial Organism Identification" because M. tuberculosis infection had been confirmed during screening (rows 1-4). Therefore in this instance, the targeted, microorganism pre-coordinated MBTEST should be used.
Rows 5-6:
Show the quantitative and ordinal colony count of M. tuberculosis growing on the agar. Rows 6-7 show the reduction of colony numbers after treatment, in comparison to the records in rows 2-3.
mb.xpt
mb.xpt
Row
STUDYID
DOMAIN
USUBJID
MBSEQ
MBGRPID
MBTESTCD
MBTEST
MBTSTDTL
MBORRES
MBORRESU
MBSTRESC
MBSTRESN
MBSTRESU
MBSPEC
MBMETHOD
VISITNUM
VISIT
MBDTC
MBMEDTYP
MBRRSTYP
1
ABC
MB
ABC-008
1
1
MCORGIDN
Microbial Organism Identification
Mycobacterium Tuberculosis
Mycobacterium Tuberculosis
Mycobacterium Tuberculosis
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
1
SCRENING
2017-08-21
MIDDLEBROOK 7H10 AGAR
2
ABC
MB
ABC-008
2
1
MTB
Mycobacterium Tuberculosis
COLONY COUNT
369
CFU
369
369
CFU
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
1
SCREENING
2017-08-21
MIDDLEBROOK 7H10 AGAR
QUANTITATIVE
3
ABC
MB
ABC-008
3
1
MTB
Mycobacterium Tuberculosis
COLONY COUNT
3+
3+
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
1
SCREENING
2017-08-21
MIDDLEBROOK 7H10 AGAR
ORDINAL
4
ABC
MB
ABC-008
1
2
MTB
Mycobacterium Tuberculosis
DETECTION
PRESENT
PRESENT
PRESENT
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
2
WEEK 2
2017-09-09
MIDDLEBROOK 7H10 AGAR
5
ABC
MB
ABC-008
2
2
MTB
Mycobacterium Tuberculosis
COLONY COUNT
147
CFU
147
147
CFU
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
2
WEEK 2
2017-09-09
MIDDLEBROOK 7H10 AGAR
QUANTITATIVE
6
ABC
MB
ABC-008
3
2
MTBAB
Mycobacterium Tuberculosis
COLONY COUNT
1+
1+
LAVAGE FLUID
MICROBIAL CULTURE, SOLID
2
WEEK 2
2017-09-09
MIDDLEBROOK 7H10 AGAR
ORDINAL
Dataset Debug Message
There are 11 leading, trailing, or non-breaking spaces in the dataset.