Mycobacterium abscessus Molecular Subspecies Identification and Macrolide Resistance Testing

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M. abscessus
is a rapidly growing mycobacterium that is present in the environment, including water and vegetation. It is a recognized human pathogen that can cause significant disease, particularly in patients with underlying lung disease. Effective therapy for M. abscessus usually includes a macrolide such as clarithromycin, but resistance to macrolides can occur. Knowledge of macrolide resistance is critical to clinical decision making.

Acquired resistance to macrolides will be detected by sequencing for the presence of mutations in rrl (23S rRNA gene).

Inducible macrolide resistance will be performed using sequence-based testing to detect the presence of a functional intact erm(41) gene in M. abscessus spp. abscessus and M. abscessus spp. bolletii. The erm(41) gene in M. abscessus ssp. massiliense contains a deletion rendering it non-functional and will not be subject to sequence analysis.

Testing Indications

Specimen collection is not required for this test.

Effective August 29, 2016, Public Health Ontario’s (PHO) laboratory will identify the subspecies of all new patient isolates of Mycobacterium abscessus (M. abscessus ssp. abscessus, M. abscessus spp. bolletii, and M. abscessus ssp. massilense) using a molecular testing algorithm, and will identify mutations in two targets that are predictive of macrolide resistance. Isolates identified as Mycobacterium abscesses will be used for Mycobacterium abscessus – molecular subspecies identification and macrolide resistance testing.

Test Frequency and Turnaround Time (TAT)

Molecular subspecies identification and macrolide resistance testing is performed once per week on Tuesday.

Culture identification results by line-probe assays (HAIN Lifescience) or MALDI-TOF will be reported in 24 to 36 hours, followed within 7 days by the subspecies identification and presence/absence of a functional erm(41) gene and rrl mutation (acquired resistance). Phenotypic drug susceptibility testing (DST) is performed at the National Reference Centre for Mycobacteriology (NRCM), Winnipeg, Manitoba upon request. Turnaround time is up to 45 days from the submission date of PHO’s laboratory to the NRCM.

Test Methods

Testing will be performed under one or more of the following conditions:

  • All new culture positive for non-tuberculous mycobacteria isolates are identified by line-probe assays (HAIN Lifescience), GenoType Mycobacterium CM or AS, or by MALDI-TOF;
  • Where the isolate cannot be identified by the line-probe assays or MALDI-TOF, 16S rRNA sequencing is used for identification;

Isolates identified as M. abscessus will have further subspecies identification performed by DNA sequencing methods; additional isolates submitted ≥3 months after the initial or previous isolate will be tested whereas more recent isolates will be referred to the first or previous isolate tested result;

M. abscessus isolates will be tested for the presence of an intact erm(41) gene, and erm(41) sequencing will be performed for M. abscessus ssp. abscessus and M. abscessus ssp. bolletii to identify non-functional intact erm(41). All M. abscessus isolates will be tested by sequencing for mutations in the rrl locus known to confer resistance to macrolides. M. abscessus ssp. abscessus and M. abscessus ssp. bolletii isolates where the erm(41) has been identified as non-functional and rrl is not mutated (predictive of macrolide susceptibility) will be sent to the NRCM for confirmation by phenotypic DST, as isolates may still be macrolide resistant due to unknown mechanisms.


Where an isolate is identified as M. abscessus, the reporting for M. abscessus molecular subspecies identification and macrolide resistance testing will be as follows:  

Test Result Comments
M. abscessus subspecies identification M. abscessus spp. (abscessus, bolletii, or massiliense)/Unable to identify to subspecies  
Functional erm(41) gene Functional/Non-functional erm(41) gene sequencing is not performed for M. abscessus spp. massiliense isolates that are identified to have a deletion in the erm(41) gene, rendering it non-functional.
erm(41) gene mutation by sequencing Detected/Not Detected/Not Applicable The presence of a functional erm(41) gene is associated with macrolide resistance (e.g. clarithromycin, azithromycin) with the potential for treatment failure.
rrlgene mutation by sequencing Mutation Detected/Not Detected The presence of rrl gene mutation is associated with macrolide resistance and potential for treatment failure.


Results are reported to the ordering physician, authorized health care provider (General O. Reg 45/22, s.18), or submitter as indicated on the requisition.


  1. Griffith DE et al.  An official ATS/IDSA statement:  Diagnosis, treatment, and prevention of nontuberculous mycobacterial diseases.  Am J Respir Crit Care Med 2007;175:367
  2. Leao SC et al.  Proposal that Mycobacterium massiliense and Mycobacterium bolletii be united and reclassified as Mycobacterium abscessus subsp. Bolletii comb. Nov., designation of Mycobacterium abscessus subsp. abscessus subsp. nov. and emended description of Mycobacterium abscessus.  Int J Syst Evol Microbiol 2011;61:2311
  3. Koh WJ et al.  Clinical significance of differentiation of Mycobacterium massiliense from Mycobacterium abscessus.  Am J Respir Crit Care Med 2011;183:405.
  4. Shallom SJ et al.  New rapid scheme for distinguishing the subspecies of the Mycobacterium abscessus group and identifying Mycobacterium massiliense isolates with inducible clarithromycin resistance.  J Clin Microbiol 2013;51(9):2943
  5.  Bastian S et al.  Assessment of clarithromycin susceptibility in strains belonging to the Mycobacterium abscessus group by erm(41)and rrl sequencing.  Antimicrob Agents Chemother 2013;55(2):775
Mis à jour le 13 mai 2024