title: Predicting extensively drug-resistant Mycobacterium tuberculosis phenotypes with genetic mutations.
abstract: Molecular diagnostic methods based on the detection of mutations conferring drug resistance are promising technologies for rapidly detecting multidrug-/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 Mycobacterium tuberculosis isolates from multinational sites with a high prevalence of drug resistance to determine the sensitivities and specificities of mutations associated with M/XDR TB to inform the development of rapid diagnostic methods. We collected M/XDR TB isolates from regions of high TB burden in India, Moldova, the Philippines, and South Africa. The 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. Eight genes (katG, inhA, rpoB, gyrA, gyrB, rrs, eis, and tlyA) were sequenced using Sanger sequencing. Three hundred seventy isolates were INHr, 356 were RIFr, 292 were MOXr/OFXr, 230 were AMKr, 219 were CAPr, and 286 were KANr. Four single nucleotide polymorphisms (SNPs) in katG/inhA had a combined sensitivity of 96% and specificities of 97 to 100% for the detection of INHr. Eleven SNPs in rpoB had a combined sensitivity of 98% for RIFr. Eight SNPs in gyrA codons 88 to 94 had sensitivities of 90% for MOXr/OFXr. The rrs 1401/1484 SNPs had 89 to 90% sensitivity for detecting AMKr/CAPr but 71% sensitivity for KANr. Adding eis promoter SNPs increased the sensitivity to 93% for detecting AMKr and to 91% for detecting KANr. Approximately 30 SNPs in six genes predicted clinically relevant XDR-TB phenotypes with 90 to 98% sensitivity and almost 100% specificity.
authors.affiliation: Department of Medicine, University of California San Diego, San Diego, California, USA.
authors.forename: Timothy C
authors.initials: TC
authors.lastname: Rodwell
authors.forename: Faramarz
authors.initials: F
authors.lastname: Valafar
authors.forename: James
authors.initials: J
authors.lastname: Douglas
authors.forename: Lishi
authors.initials: L
authors.lastname: Qian
authors.forename: Richard S
authors.initials: RS
authors.lastname: Garfein
authors.forename: Ashu
authors.initials: A
authors.lastname: Chawla
authors.forename: Jessica
authors.initials: J
authors.lastname: Torres
authors.forename: Victoria
authors.initials: V
authors.lastname: Zadorozhny
authors.forename: Min Soo
authors.initials: MS
authors.lastname: Kim
authors.forename: Matt
authors.initials: M
authors.lastname: Hoshide
authors.forename: Donald
authors.initials: D
authors.lastname: Catanzaro
authors.forename: Lynn
authors.initials: L
authors.lastname: Jackson
authors.forename: Grace
authors.initials: G
authors.lastname: Lin
authors.forename: Edward
authors.initials: E
authors.lastname: Desmond
authors.forename: Camilla
authors.initials: C
authors.lastname: Rodrigues
authors.forename: Kathy
authors.initials: K
authors.lastname: Eisenach
authors.forename: Thomas C
authors.initials: TC
authors.lastname: Victor
authors.forename: Nazir
authors.initials: N
authors.lastname: Ismail
authors.forename: Valeru
authors.initials: V
authors.lastname: Crudu
authors.forename: Maria Tarcela
authors.initials: MT
authors.lastname: Gler
authors.forename: Antonino
authors.initials: A
authors.lastname: Catanzaro
mesh_terms: D000995:Antitubercular Agents / Q000494:pharmacology* / Q000627:therapeutic use; D001426:Bacterial Proteins / Q000235:genetics; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics; D024901:Drug Resistance, Multiple, Bacterial; D054908:Extensively Drug-Resistant Tuberculosis / Q000175:diagnosis* / Q000382:microbiology; D005838:Genotype; D006801:Humans; D007194:India; D008826:Microbial Sensitivity Tests / Q000379:methods; D008966:Moldova; D025202:Molecular Diagnostic Techniques / Q000379:methods*; D009169:Mycobacterium tuberculosis / Q000235:genetics* / Q000302:isolation & purification; D010641:Phenotype; D010679:Philippines; D017354:Point Mutation; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity; D017422:Sequence Analysis, DNA; D013019:South Africa
chemical_list: D000995:Antitubercular Agents; D001426:Bacterial Proteins; D004269:DNA, Bacterial