Are WHO approved nucleic acid amplification tests causing large-scale “false identification” of rifampicin-resistant tuberculosis?: Programmatic experience from south india

Abstract

Introduction: The nucleic acid amplification tests (NAATs): Line probe assay and GeneXpert (Xpert) have evolved as the primary tool for identification of rifampicin (RIF)-resistant (RR) tuberculosis (TB) worldwide, primarily because of the ease and speed. We rechecked RR isolates identified by NAATs from presumptive RR TB cases belonging to South India by the Revised National TB Control Program, India using multiple RIF concentrations on Bactec MGIT system and compared the mutation patterns with the resistance levels. Methodology: Standard protocol for Bactec MGIT system as given by the manufacturer modified for the multiple RIF concentrations was used. All the retests were done in a certified BSL3 laboratory. Results: We found that there is a mismatch of up to 20% (RIF breakpoint 0.5 mg/L); the NAATs probably overidentifying RR TB. Half of the cases with mismatch showed a sub-breakpoint rise in resistance level (0.125 mg/L to 0.5 mg/L RIF). Discussion and Conclusion: The probable reasons for the mismatch are “sub-breakpoint low-level resistance mutants,” hetero-resistant bacterial populations, and other inherent test limitations along with the low RR TB prevalence in South India (<5%) among “presumptive multidrug-resistants.” This could be due to the incomplete selection pressure by an inadequate RIF exposure caused by various factors including a low-RIF dosage being used widely and poor Directly observed treatment. To prevent the false diagnosis of RR TB in a massive scale when using NAATs, we may need to enforce a carefully targeted testing approach and a phenotypic susceptibility testing with multiple RIF concentrations for confirmatory purposes.

Keywords

• GeneXpert
• Line probe assay
• MGIT 960
• positive predictive value
• rpoB Resistance Determining Region