Remarks

• These recommendations apply to the use of SL-LPA for testing sputum specimens (direct testing) and cultured isolates of M. tuberculosis (indirect testing) from both pulmonary and extrapulmonary sites. Direct testing on sputum specimens allows for the earlier initiation of appropriate treatment.
• These recommendations apply to the direct testing of sputum specimens from MDR/RR-TB, irrespective of the smear status, while acknowledging that the indeterminate rate is higher when testing smear-negative sputum specimens than with smear-positive sputum specimens.
• These recommendations do not eliminate the need for conventional phenotypic DST capacity, which will be necessary to confirm resistance to other drugs and to monitor the emergence of additional drug resistance.
• Conventional phenotypic DST can still be used in the evaluation of patients with negative SL-LPA results, particularly in populations with a high pretest probability for resistance to fluoroquinolones or SLID (or both).
• These recommendations apply to the use of SL-LPA in children with confirmed MDR/RR-TB, based on the generalization of data from adults.
• Resistance-conferring mutations detected by SL-LPA are highly correlated with phenotypic resistance to ofloxacin and levofloxacin.
• Resistance-conferring mutations detected by SL-LPA are highly correlated with phenotypic resistance to SLID.
• Given the high specificity for detecting resistance to fluoroquinolones and SLID, the positive results of SL-LPA could be used to guide the implementation of appropriate infection control precautions.

Implementation considerations The SL-LPA should only be used to test specimens from patients with confirmed MDR/RR-TB. Adoption of SL-LPAs does not eliminate the need for conventional culture and DST capability. Despite good specificity of SL-LPAs for the detection of resistance to fluoroquinolones and the SLIDs, culture and phenotypic DST is required to completely exclude resistance to these drug classes as well as to other second-line drugs. The following implementation considerations apply:

• SL-LPAs cannot determine resistance to individual drugs in the class of fluoroquinolones. Resistance-conferring mutations detected by SL-LPAs are highly correlated with phenotypic resistance to ofloxacin and levofloxacin.
• Mutations in some regions (e.g. the eis promoter region) may be responsible for causing resistance to one drug in a class more than other drugs within that class. For example, the eis C14T mutation is associated with kanamycin resistance in strains from Eastern Europe.
• SL-LPAs should be used in the direct testing of sputum specimens, irrespective of whether samples are smear negative or smear positive.
• SL-LPAs are designed to detect TB and resistance to fluroquinolones and SLIDs from sputum samples. Other respiratory samples (e.g. bronchoalveolar lavage and gastric aspirates) or extrapulmonary samples (tissue samples, CSF or other body fluids) have not been adequately evaluated.
• Culture and phenotypic DST plays a critical role in the monitoring of a patient’s response to treatment, and in detecting additional resistance to second-line drugs during treatment.
• SL-LPAs are suitable for use at the central or national reference laboratory level; they can also be used at the regional level if the appropriate infrastructure can be ensured (three separate rooms are required).
• All patients identified by SL-LPAs should have access to appropriate treatment and ancillary medications.