Accuracy of whole genome sequencing versus phenotypic (MGIT) and commercial molecular tests for detection of drug-resistant Mycobacterium tuberculosis isolated from patients in Brazil and Mozambique

• Published in: Tuberculosis (Edinburgh, Scotland) Vol. 110; pp. 59 - 67
• Main Authors: Feliciano, Cinara Silva, Namburete, Evangelina Inacio, Rodrigues Plaça, Jéssica, Peronni, Kamila, Dippenaar, Anzaan, Warren, Robin Mark, Silva, Wilson Araújo, Bollela, Valdes Roberto
• Format: Journal Article
• Language: English
• Published: Scotland Elsevier Ltd 01-05-2018; Elsevier Science Ltd
• Subjects: Antimicrobial susceptibility testing; Antitubercular Agents - pharmacology; Bacteria; Cross-Sectional Studies; DNA, Bacterial - genetics; Drug resistance; Drug Resistance, Bacterial - genetics; Drug Resistance, Multiple, Bacterial - genetics; Drug-resistant tuberculosis; Ethambutol; Ethambutol - pharmacology; Gene sequencing; Genomes; Genotypes; Humans; Isoniazid; Isoniazid - pharmacology; Microbial Sensitivity Tests - methods; Mutation; Mycobacterium tuberculosis - drug effects; Mycobacterium tuberculosis - genetics; Next-generation sequencing clinical diagnostics; Patients; Phenotype; Rifampin; Rifampin - pharmacology; RpoB protein; Streptomycin; Streptomycin - pharmacology; Tuberculosis; Tuberculosis, Multidrug-Resistant - drug therapy; Tuberculosis, Multidrug-Resistant - microbiology; Whole Genome Sequencing; Brazil; Mozambique; Drug-resistant tuberculosis; Antimicrobial susceptibility testing; Next-generation sequencing clinical diagnostics; Whole genome sequencing
• ISSN: 1472-9792; 1873-281X
• DOI: 10.1016/j.tube.2018.04.003

The fast and accurate diagnosis of drug-resistant tuberculosis (DR-TB) is critical to reducing the spread of disease. Although commercial genotypic drug-susceptibility tests (DST) are close to the goal, they are still not able to detect all relevant DR-TB related mutations. Whole genome sequencing (WGS) allows better comprehension of DR-TB with a great discriminatory power. We aimed to evaluate WGS in M. tuberculosis isolates compared with phenotypic and genotypic DST.
This cross-sectional study evaluated 30 isolates from patients with detected DR-TB in Brazil and Mozambique. They were evaluated with phenotypic (MGIT-SIRE™) and genotypic (Xpert-MTB/RIF™, Genotype-MTBDRplus™, and MTBDRsl™) DST. Isolates with resistance to at least one first- or second-line drug were submitted to WGS and analyzed with TB profiler database.
WGS had the best performance among the genotypic DST, compared to the phenotypic test. There was a very good concordance with phenotypic DST for rifampicin and streptomycin (89.6%), isoniazid (96.5%) and ethambutol (82.7%). WGS sensitivity and specificity for detection resistance were respectively 87.5 and 92.3% for rifampicin; 95.6 and 100% for isoniazid; 85.7 and 93.3% for streptomycin while 100 and 77.2% for ethambutol. Two isolates from Mozambique showed a Val170Phe rpoB mutation which was neither detected by Xpert-MTB/RIF nor Genotype-MTBDRplus.
WGS was able to provide all the relevant information about M. tuberculosis drug susceptibility in a single test and also detected a mutation in rpoB which is not covered by commercial genotypic DST.