Appropriate phenotypic susceptibilities for antimicrobial susceptibility testing of Acid Fast Bacilli
Test Code
PHENO
Description
This is the orderable for appropriate phenotypic susceptibility testing only. Selection of this orderable triggers the appropriate phenotypic testing for each type of organism (Table 1), but genotypic drug resistance testing is not performed, even if appropriate. Since genotypic resistance testing can provide a fast turnaround time and important information about treatment and is only performed when relevant, PHENO is typically not the recommended test. Note that testing is not performed, reported, or billed if it is not appropriate for the organism.
PHENO can be ordered on clinical specimens sent for culture. If an organism is grown, the appropriate drugs are automatically added; testing will not be performed if no organism is cultured. PHENO may also be ordered on isolates. Note that if a customized selection of antibiotics are needed, they can be selected individually. See "Menu of Individual Drug Testing for Acid Fast Bacilli" for the full selection of antibiotics that can be ordered.
Table 1. Phenotypic and genotypic susceptibilities performed based on the organism type when APPRO is ordered.
| Organism | Phenotypic testing | |
| Billing code | Drugs | |
| Slowly growing mycobacteria other than certain fastidious mycobacteria | NTM13 | AMK, CIP, CLO, CLR, DOX, LZD, MIN, MXF, RFB, RIF, STR, TMP/SXT |
| Fastidious slowly growing mycobacteria such as M. haemophilum | NTM3 | CLO, LZD |
| M. tuberculosis complex (First line drugs) | MTB2 | INH, PZA, RIF, EMB |
| Drug resistant M. tuberculosis complex (Second line drugs) | MTB1 | AMK, CAP, CS, EMB, ETH, INH, KAN, PAS, RIF, STR |
| Rapidly growing mycobacteria | NTM6, NTM6V (vet) |
AMK, CLR, CIP, CLO, DOX, FOX, IPM, LZD, MXF, TGC, TOB, TMP/SXT Nonvalidated, research use only: AUG, FEP, AXO KAN, GEN, FOT, AZM, MIN, CLO/AMK |
| Partial acid fast bacteria (e.g. Nocardia sp., Gordonia sp., Tskuamurella sp.) | NTM4, NTM4V (vet) |
AMK, AUG, AXO, CIP, CLR, DOX, IPM, LZD, MIN, MXF, TOB, TMP/SXT Nonvalidated, research use only: AZM, CLO, FEP, FOT, GEN, KAN, FOX |
Table 2. Drug abbreviations (used on the requisition)
| Abbreviation | Drug | Abbreviation cont'd | Drug cont'd |
| AMK | Amikacin | INH | Isoniazid |
| AUG | Augmentin | IPM | Imipenem |
| AXO | Ceftriaxone | KAN | Kanamycin |
| AZM | Azithromycin | LZD | Linezolid |
| CIP | Ciprofloxacin | MIN | Minocycline |
| CLO | Clofazimine | MXF | Moxifloxacin |
| CLO/AMK | Clofazimine & Amikacin synergy | OFX | Ofloxacin |
| CLR | Clarithromycin | OMC | Omadacycline |
| CAP | Capreomycin | PAS | p-Aminosalicyclic acid |
| CS | Cycloserine | PZA | Pyrazinamide |
| DOX | Doxycycline | RFB | Rifabutin |
| EMB | Ethambutol | RIF | Rifampin |
| ETH | Ethionamide | RIF/EMB | Rifampin & Ethambutol synergy |
| FEP | Cefepime | STR | Streptomycin |
| FOT | Cefotaxime | TGC | Tigecycline |
| FOX | Cefoxitin | TMP/SXT | Trimethoprim/sulfamethoxazole |
| GEN | Gentamicin | TOB | Tobramycin |
Collect
An identified isolate is required for testing (does not necessarily apply to veterinary rapidly growing isolates).
- This test can be ordered on a clinical specimen that has been sent to our laboratory for isolation and identification of mycobacteria. See specimen requirements for culture of mycobacteria from a clinical specimen (AFB1, AFB3 or AFB7)
- This test can also be ordered on organisms identified elsewhere. Pure mycobacterial isolates should be sent in solid media such as a Middlebrook slant (7H10 or 7H11), Lowenstein-Jensen (LJ) slant, or in broth (7H9, MGIT, MP BACT/Alert, VersaTrek).
- Specimen Volume: Laboratory must receive visible growth of an isolate on solid media or an isolate in broth media (≥3 mL).
Unacceptable Conditions
- Cultures received with incomplete identifiers.
- Mixed cultures; Note that prior to rejection, attempts will be made to isolate organisms. A re-isolation charge will be applied in these cases.
- Cultures containing mold.
- Solid media with insufficient growth.
- Cultures submitted on agar plates.
- Liquid media with < 2 mL.
- Leaking specimens.
Storage Transport Temp
Transport or mail isolates at ambient temperature. For nontuberculous mycobacteria (NTM), follow IATA/ DOT category B and for M. tuberculosis complex isolates, follow IATA/DOT category A requirements for shipping biological materials.
Stability
Isolate at ambient temperature
Performed
Typically all days
Methodology
Phenotypic susceptibilities are performed using agar proportion, broth microdilution, or broth macrodilution methods.
Turnaround Time
- MIC's for M. tuberculosis complex and other slowly growing mycobacteria are reported 4 to 6 weeks after a pure culture is achieved.
- MIC's for rapidly growing mycobacteria and aerobic actinomycetes are reported 2 to 3 weeks after a pure culture is achieved.
Department
Infectious Disease Laboratory, Mycobacteriology
Study Offerings
RUO
CAP/CLIA
Related Tests
NTM13, AFB6, MTB1, MTB2, NTM4, NTM4V, NTM6, NTM6V, NTM15
Interpretation
For MIC methods, an MIC will be provided. Susceptible, intermediate, or resistant (S, I, R) interpretations will be included whenever CLSI interpretations are available for a drug-organism combination, or NI will be reported if no interpretation is available.
CPT Code
| Test code performed within APPRO | CPT Code | Billing Code |
| MTB1 | 87190 x10 | MTBP1 |
| MTB2 | 87188 x5 | MTBP2 |
| NTM4 | 87186 | NTMP4 |
| NTM4V | 87186 | NTP4V |
| NTM6 | 87186 | NTMP6 |
| NTM6V | 87186 | NTMPV |
| NTM13 | 87186 | NTM13 |
New York Approved
Standard
FDA
Standard Method