Discordant line probe genotypic testing vs culture-based drug susceptibility phenotypic testing in TB endemic KwaZulu-Natal: Impact on bedside clinical decision making

Abstract

The recommendations for Mycobacterium tuberculosis drug susceptibility testing include both phenotypic and genotypic methods. This concurrent use of differing testing platforms has created an emerging challenge of discordant results, creating a diagnostic dilemma for the laboratorians as well as attending clinicians. We undertook a retrospective study to determine the prevalence of discordant results between the MTBDR plus line probe assay and solid culture-based drug susceptibility testing for rifampicin and isoniazid. The analysis was conducted for the period January 2013 and December 2015 at the Inkosi Albert Luthuli Central Hospital. Rifampicin and isoniazid resistance testing data were “paired” on 8273 isolates for culture-based drug susceptibility testing and line probe assay. The latter method showed high sensitivity and specificity of 93% and 95% respectively for isoniazid testing. For rifampicin testing, sensitivity and specificity were 95% and 75%. Overall, discordance was 14.6% for rifampicin and 7.2% for isoniazid. This report is not intended to determine superiority of one method over another. It is merely to show that discordance does exist between different methods of testing. Given the burden of HIV and Tuberculosis in Sub-Saharan Africa, these findings have clinical significance and huge public health implications. Clinicians should understand the limitations of phenotypic testing methods.

Molecular characterization of genetic mutations with fitness loss in pulmonary tuberculosis patients associated with HIV co-infection in Northwest Amhara, Ethiopia

“… 33 , 40 , 42 The LPA assay may occasionally detect false-positive RIF resistance due to the possibility of silent mutations in the hotspot region that do not result in amino acid changes. Furthermore, our study revealed high sensitivity of 85.0% and 100% specificity for the MTBDRplus assay for identifying INH resistance, which is consistent with other studies from Northwest Ethiopia (94.4% and 100%), 6 South Africa (93% and 95%), 46 Pakistan (90.6% and N/A), 32 and China (82.1% and 94.4%) 37 ; but, our study exhibited higher sensitivity than those from Northeastern Ethiopia (75%) 4 and Pakistan (71.7%) 2 and Iran (71%). 35 The reduced sensitivity of the MTBDRplus assay may be due to the presence of isolates carrying mutations outside the katG and inhA genomic regions causing resistance to INH.…”

“…19 One more finding in our study, the MTBDRplus LPA assay exhibited a high sensitivity of 91.7% and a specificity of 99.3% for detecting RIF resistance, which is comparable with results reported in earlier studies in Northeastern Ethiopia (100% and 98.3%), 4 China (98.7% and 88.9%), 37 Pakistan (98.8% and 92.9%), 32 and Iran (91% and 100%) 35 ; while there was a higher sensitivity than from Northwest Ethiopia (75.0% and 100%) 6 and higher specificity than from South Africa (95% and 75%). 46 This difference in sensitivity might be due to variations in sample size and the presence of strains that carried mutations outside the 81-bp hotspot region or in the amino-terminal end of the rpoB gene that was not detected by LPA strips in detecting RIF resistance. Moreover, some mutations within the hotspot region of the rpoB gene in clinical isolates cause the WT probe to fail to hybridize with MUT strands on a strip, leading to them being misinterpreted as RIF-resistant isolates.…”

Magnitude of Phenotypic and MTBDRplus Line Probe Assay First-Line Anti-Tuberculosis Drug Resistance Among Tuberculosis Patients; Northwest Ethiopia

“…The solid culture-based DST is the current reference standard of diagnosis of drug resistance, providing results in 4-6 weeks. Other diagnosis methods, such as the rapid automated BACTEC MGIT 960 DST SIRE method (MGIT-SIRE) is also used due to a considerable advantage in shorter turnaround time; 17,18 however, its cost is sometimes prohibited in low-income areas. Rapid identification of drug resistance is critical to guide proper choice of anti-mycobacterial drugs and to stop the misuse of drugs and subsequent development of additional drug resistance.…”

“…Delayed detection of active MDR-TB contributes to suboptimal treatment and poor clinical outcomes, disseminating transmission of MDR-TB. 18 Consistent DST for isolates of Mtb complex is critical for selecting effective treatment regimens, interruption of transmission, and prevention of further expansion of resistant forms of TB. 21 Ethiopia is one of the 30 high-TB-burden countries with a current estimated incidence of 140 new TB cases per 100,000 population.…”

Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study

“…In addition, mixed strain infections, where drug-susceptible strains outgrow more resistant strains in culture, may result in discordance ( 29 ). Discordant DST results are relatively common and can be difficult for clinicians to interpret ( 30 ). In this analysis, we employed a conservative approach where any resistance, either detected through routine diagnostic testing or predicted through WGS, was classified as resistance.…”