Prediction of Susceptibility to First-Line Tuberculosis Drugs by DNA Sequencing

Abstract

BackgroundThe World Health Organization recommends universal drug susceptibility testing for Mycobacterium tuberculosis complex to guide treatment decisions and improve outcomes. We assessed whether DNA sequencing can accurately predict antibiotic susceptibility profiles for first-line anti-tuberculosis drugs. MethodsWhole-genome sequences and associated phenotypes to isoniazid, rifampicin, ethambutol and pyrazinamide were obtained for isolates from 16 countries across six continents. For each isolate, mutations associated with drug-resistance and drug-susceptibility were identified across nine genes, and individual phenotypes were predicted unless mutations of unknown association were also present. To identify how whole-genome sequencing might direct first-line drug therapy, complete susceptibility profiles were predicted. These were predicted to be pan-susceptible if predicted susceptible to isoniazid and to other drugs, or contained mutations of unknown association in genes affecting these other drugs. We simulated how negative predictive value changed with drug-resistance prevalence.Results10,209 isolates were analysed. The greatest proportion of phenotypes were predicted for rifampicin (9,660/10,130; (95.4%)) and the lowest for ethambutol (8,794/9,794; (89.8%)). Isoniazid, rifampicin, ethambutol and pyrazinamide resistance was correctly predicted with 97.1%, 97.5% 94.6% and 91.3% sensitivity, and susceptibility with 99.0%, 98.8%, 93.6% and 96.8% specificity, respectively. 5,250 (89.5%) drug profiles were correctly predicted for 5,865/7,516 (78.0%) isolates with complete phenotypic profiles. Among these, 3,952/4,037 (97.9%) predictions of pan-susceptibility were correct. The negative predictive value for 97.5% of simulated drug profiles exceeded 95% where the prevalence of drug-resistance was below 47.0%. ConclusionsPhenotypic testing for first-line drugs can be phased down in favour of DNA sequencing to guide anti- tuberculosis drug therapy.

Whole genome sequencing of Mycobacterium tuberculosis isolates and clinical outcomes of patients treated for multidrug-resistant tuberculosis in Tanzania

“…In addition, our analysis revealed a large deletion that involved Rv2044c in [40]. On the other hand, MTBC isolates from DS-TB participants had no mutations in genes encoding for INH, RIF, PZA, SM and EMB, which is in keeping with Cryptic consortium findings that reported susceptibility profiles for all isolates unless uncharacterized mutations or missing key nucleotide calls were present [41]. We found 2 pre-XDR-TB patients possessing R446C and C517Tmutations in the gyrB and rrs genes, in addition S315T, S450L, G406A and C517T mutations in the katG, rpoB, embB and rrs genes respectively.…”

An African origin forMycobacterium bovis

“…The range of host species from which M. bovis was isolated is broad, confirming that M. bovis can cause infection in many different mammalian species (Table S1). Our compilation of M. caprae included genomes from Japan (isolated in Elephants from Borneo) [46], China (isolated in Primates, Table S1) and Peru (host information unavailable but possibly human [47]), suggesting that the host and geographic distribution of this species ranges well beyond Southern- and Central Europe [48, 49]. For all M. bovis, we determined in silico clonal complexes Eu1, Eu2, Af1 and Af2 and spoligotypes, and mapped them on the phylogenetic tree and onto a world map (Fig.…”

Dynamics of within-hostMycobacterium tuberculosisdiversity and heteroresistance during treatment

“…For identification of RAVs, we used a curated list of resistance-conferring mutations adapted from published sources (43,44) as listed in Supplementary Methods 3. We supplemented these mutations lists with more recent published data for new and repurposed drugs (45)(46)(47)(48).…”