From UCSD: Predicting Extensively Drug-resistant Tuberculosis (XDR-TB) Phenotypes with Genetic Mutations

J Clin Microbiol. 2013 Dec 18. [Epub ahead of print]

Predicting Extensively Drug-resistant Tuberculosis (XDR-TB) Phenotypes with Genetic Mutations.

Rodwell TC, Valafar F, Douglas J, Qian L, Garfein RS, Chawla A, Torres J, Zadorozhny V, Soo Kim M, Hoshide M, Catanzaro D, Jackson L, Lin G, Desmond E,Rodrigues C, Eisenach K, Victor TC, Ismail N, Crudu V, Gle MT, Catanzaro A.

Author information

• Department of Medicine, University of California, San Diego, San Diego, US.

Abstract

Molecular diagnostics, based on detection of mutations conferring resistance are promising technologies for rapidly detecting multi/extensively drug resistant tuberculosis (M/XDR-TB), but large studies of mutations as markers of resistance are rare. The Global Consortium for Drug-resistant TB Diagnostics analyzed 417 Mtb isolates from multinational sites with high prevalence of drug resistance to determine sensitivity and specificity of mutations associated with M/XDR-TB and inform development of rapid diagnostics. We collected M/XDR-TB isolates from regions of high TB burden in India, Moldova, Philippines and South Africa. Isolates underwent standardized phenotypic drug susceptibility testing (DST) to isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN) and capreomycin (CAP) using MGIT 960 and WHO recommended critical concentrations. Seven genes (katG, inhA, rpoB, gyrA, gyrB, rrs, eis and tlyA) were sequenced using Sanger sequencing. Three hundred seventy isolates were INH^R, 356 RIF^R, 292 MOX^R/OFX^R, 230 AMK^R, 219 CAP^R and 286 KAN^R. Four SNPs in katG/inhA had combined sensitivity of 96% and specificity of 97-100% for detection of INH^R. Eleven SNPs in rpoB had combined sensitivity of 98% for RIF^R. Eight SNPs in gyrA88-94 had sensitivity of 90% for MOX^R/OFX^R. The rrs 1401/1484 SNPs had 89-90% sensitivity for detecting AMK^R/CAP^R, but 71% sensitivity for KAN^R. Adding eis promoter SNPs increased sensitivity for detecting AMK^R to 93% and KAN^R to 91%. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90-98% sensitivity and almost 100% specificity.