Table 1.

Recommended microbiological tests to support a diagnosis of NTM-PD

Test	Sensitivity	Specificity	Cost	Availability	Comment
Tests to detect NTM in respiratory samples12 22
Microscopy (AFB smear)	Low	Moderate	Low	High	Rapid, but variable sensitivity and cannot distinguish NTM from Mycobacterium tuberculosis
Direct molecular detection on primary sample	Moderate	High	Moderate	Low	NTM-specific: costly and less sensitive than conventional AFB culture. Limited uptake: TB PCR is useful as a rule-out test for NTM on smear-positive samples
Mycobacterial culture	High	High	Low	High	Most sensitive method to detect NTM from respiratory samples. Optimal results require the use of both solid and liquid media. Slow results, taking days to weeks
Tests to speciate and type NTM in respiratory samples12 22
Line probe assays PCR product restriction analysis Partial gene sequencing MALDI-TOF	Moderate	High	Moderate/high	Low/moderate	Enables species identification, including subspecies of M. abscessus. May require phenotypical drug sensitivity testing to determine inducible macrolide resistance
WGS	High	High	Moderate/high	Low/moderate	Improved discrimination of strains enables WGS to be used to investigate possible person-to-person transmission events

AFB, acid-fast bacilli; MALDI-TOF, matrix-assisted laser desorption ionisation-time of flight; NTM, non-tuberculous mycobacteria; NTM-PD, non-tuberculous mycobacterial pulmonary disease; PCR, polymerase chain reaction; TB, tuberculosis; WGS, whole-genome sequencing.