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HelpTest Code MISC2MAYOCTBID Culture Referred for Identification, Mycobacterium and Nocardia, Varies
Infectious
Reporting Name
Culture Refer for ID, MycobacteriumUseful For
Rapid identification to the species level for Mycobacterium species, Nocardia species, and other aerobic actinomycete genera and species from pure culture isolates
Performing Laboratory
Mayo Clinic Laboratories in Rochester
Specimen Type
VariesShipping Instructions
1. See Infectious Specimen Shipping Guidelines.
2. Place specimen in a large infectious container (T146) and label as an etiologic agent/infectious substance.
Necessary Information
1. Specimen source is required.
2. Isolate description is required: Gram stain reaction, morphology, tests performed.
Specimen Required
Specimen Type: Mycobacterium species or aerobic actinomycetes organism in pure culture
Supplies: Infectious Container, Large (T146)
Container/Tube: Middlebrook (7H10 or 7H11) or Lowenstein-Jensen medium slant or in broth (eg, Mycobacteria Growth Indicator Tube [7H9] broth)
Specimen Volume:
Solid media: Visible growth of isolate
Isolate in broth media: ≥3 mL
Collection Instructions: Organism must be in pure culture, actively growing. Do not submit mixed cultures.
Additional Information: A minimum volume of 3 mL is recommended to perform all initial testing, this may include: stains, sub-culture media, nucleic acid probes, and any additional testing that may be required to determine the identification. If the broth sample volume is less than 3 mL, initial testing may be limited, and increased turnaround time is likely.
Specimen Stability Information
| Specimen Type | Temperature | Time |
|---|---|---|
| Varies | Ambient (preferred) | |
| Refrigerated | ||
Special Instructions
Reference Values
Not applicable
Day(s) Performed
Monday through Sunday
Test Classification
This test has been cleared, approved, or is exempt by the US Food and Drug Administration and is used per manufacturer's instructions. Performance characteristics were verified by Mayo Clinic in a manner consistent with CLIA requirements.LOINC Code Information
| Test ID | Test Order Name | Order LOINC Value |
|---|---|---|
| CTBID | Culture Refer for ID, Mycobacterium | 543-9 |
| Result ID | Test Result Name | Result LOINC Value |
|---|---|---|
| CTBID | Culture Refer for ID, Mycobacterium | In Process |
Testing Algorithm
Reflex tests may be performed at an additional charge. All mycobacteria and Nocardia (including aerobic actinomycetes) submitted will be identified and billed as appropriate.
See Culture Referred for Identification Mycobacterium and Nocardia Algorithm.
Clinical Information
Approximately 200 recognized species of mycobacteria and more than 100 Nocardia species exist. Many of these species are human pathogens and, therefore, identification to the species level is important to help guide patient care. In addition, other aerobic actinomycete genera can be human pathogens including, but not limited to, Tsukamurella, Rhodococcus, and Gordonia species.
Mycobacteria species, Nocardia species and other aerobic actinomycete genera are identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry or nucleic acid sequencing of a 500-base pair region of the 16S ribosomal RNA gene.
Interpretation
Organisms growing in pure culture are identified to the species level where indicated.
Method Description
DNA sequence analysis utilizes a 500 base pair region of the 16S rRNA gene as the target for identification of mycobacteria and is performed using the MicroSeq kit from Applied Biosystems. Sequence data generated is compared to several different databases of known mycobacterial and aerobic actinomycete sequences to obtain organism identification. These include MicroSeq, NCBI GenBank, and Mayo Clinic Mycobacteria database. A 100% or greater agreement with a database strain is needed for an acceptable identification to the species level.(Hall L, Doerr KA, Wohlfiel SL, Roberts GD. Evaluation of the MicroSeq system for identification of mycobacteria by 16S ribosomal DNA sequencing and its integration into a routine clinical mycobacteriology laboratory. J Clin Microbiol. 2003;41[4]:1447-1453)
Matrix-assisted laser desorption ionization time-of-flight mass spectrometry analysis is done using the Bruker BioTyper platform and the Bruker BDAL library, Bruker Mycobacterial Library and the Mayo Clinic Library. A spectral score of 2.0 or more is required for identification to the species level.(Buckwalter SP, Olson SL, Connelly BJ, et al. Evaluation of matrix-assisted laser desorption ionization-time of flight mass spectrometry for identification of Mycobacterium species, Nocardia species, and other aerobic actinomycetes. J Clin Microbiol. 2016;54[2]:376-384)
Rapid polymerase chain reaction (PCR) is performed following specimen digestion and decontamination using N-acetyl cysteine and sodium hydroxide. Genomic DNA is extracted using the MagNA Pure (Roche Applied Sciences) extraction platform. The purified genomic DNA is placed on the LightCycler instrument, which amplifies and monitors, by fluorescence, the development of target nucleotide sequences after each PCR cycle. A specific target sequence from a portion of the katG gene from Mycobacterium tuberculosis complex is amplified and the resulting segment is detected by melt-curve analysis using sequence-specific fluorescence resonance energy transfer hybridization probes. The LightCycler PCR assay is a closed PCR system that greatly reduces the potential for false-positive results due to specimen cross-contamination as compared with traditional open-system PCR or other amplification methods like transcription-mediated amplification.(Buckwalter SP, Connelly BJ, Louison LK, et al. Description, validation, and review of a decade of experience with a laboratory-developed PCR test for detection of Mycobacterium tuberculosis complex in pulmonary and extrapulmonary specimens. J Clin Tuberc Other Mycobact Dis. 2022;29:100340. doi:10.1016/j.jctube.2022.100340)
Reject Due To
| Agar plate | Reject |
| Isolates other than Mycobacterium species or aerobic actinomycetes | Reject |
Report Available
60 to 70 daysReflex Tests
| Test ID | Reporting Name | Available Separately | Always Performed |
|---|---|---|---|
| RMALM | Id MALDI-TOF Mass Spec AFB | No, (Bill Only) | No |
| RTBSP | Id, Mtb Speciation, PCR | No, (Bill Only) | No |
| ISMY | ID by 16S Sequencing | No, (Bill Only) | No |
| LCTB | Id, MTB complex Rapid PCR | No, (Bill Only) | No |
CPT Code Information
Culture Referred for Identification, Mycobacterium
87118-Identification of mycobacteria
87158-Identification of mycobacteria by other methods (if appropriate)
87118 -Id MALDI-TOF Mass Spec AFB (if appropriate)
87153-Mycobacteria Identification by Sequencing (if appropriate)
87150-Id, Mtb Speciation, PCR (if appropriate)
87150- Id, MTB complex Rapid PCR (if appropriate)
Method Name
Matrix-Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS)/16S rDNA Sequencing/Rapid Polymerase Chain Reaction (PCR)
Forms
If not ordering electronically, complete, print, and send a Microbiology Test Request (T244) with the specimen.
Secondary ID
80278Specimen Minimum Volume
See Specimen Required