Whole genome sequencing for drug resistance profile prediction inMycobacterium tuberculosis

Abstract

Whole genome sequencing allows rapid detection of drug-resistant M. tuberculosis isolates. However, high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been lacking.We determined drug resistance profiles of 176 genetically diverse clinical M. tuberculosis isolates from Democratic Republic of the Congo, Ivory Coast, Peru, Thailand and Switzerland by quantitative phenotypic DST for 11 antituberculous drugs using the BD BACTEC MGIT 960 system and 7H10 agar dilution to generate a cross-validated phenotypic DST readout. We compared phenotypic drug susceptibility results with predicted drug resistance profiles inferred by whole genome sequencing.Both phenotypic DST methods identically classified the strains into resistant/susceptible in 73-99% of the cases, depending on the drug. Changes in minimal inhibitory concentrations were readily explained by mutations identified by whole genome sequencing. Using the whole genome sequences we were able to predict quantitative drug resistance levels where wild type and mutant MIC distributions did not overlap. The utility of genome sequences to predict quantitative levels of drug resistance was partially limited due to incompletely understood mechanisms influencing the expression of phenotypic drug resistance. The overall sensitivity and specificity of whole genome-based DST were 86.8% and 94.5%, respectively.Despite some limitations, whole genome sequencing has high predictive power to infer resistance profiles without the need for time-consuming phenotypic methods.One sentence summaryWhole genome sequencing of clinical M. tuberculosis isolates accurately predicts drug resistance profiles and may replace culture-based drug susceptibility testing in the future.

Wild-Type MIC Distribution for Re-evaluating the Critical Concentration of Anti-TB Drugs and Pharmacodynamics Among Tuberculosis Patients From South India

“…Similarly, discrepancies between genotypic and phenotypic resistance have been reported in ETH, MXF (Chen et al, 2019 ), and STR (Chaidir et al, 2019 ). The drug resistance mechanisms are not well-studied (Gygli et al, 2019 ) especially for second-line anti-TB drugs, and thus, the specificity of the reported genetic mutations to confer phenotypic resistance is low. Apart from genetic mutations, there are also other mechanisms like efflux pumps that confer phenotypic resistance (Satta et al, 2017 ).…”

Natural Polymorphisms in Mycobacterium tuberculosis Conferring Resistance to Delamanid in Drug-Naive Patients

“…We identified putative delamanid resistance-conferring mutations in M. tuberculosis strains from TB patients living with HIV (PLWH) and delamanid-naive, HIV-negative TB patients by whole-genome sequencing (WGS) and MIC determination. We collected information on the demographic and clinical characteristics of patients who were recruited between 2013 and 2016 in Peru, Thailand, Côte d’Ivoire, the Democratic Republic of the Congo (DRC), Kenya, and South Africa ( 24 , 25 ). The Cantonal Ethics Committee in Bern, Switzerland, and local institutional review boards approved the study.…”

“…The sequencing pipeline has been described previously ( 25 ). In brief, M. tuberculosis DNA was extracted and sequenced using the Illumina HiSeq 2500 system (Illumina, San Diego, CA, USA).…”

“…All patients infected with either of these strains were naive to delamanid. We selected strains fulfilling the following criteria: (i) mutations in a part of the gene encoding regions of catalytic or structural importance predicted by ARIBA and then the PhyResSE pipeline ( 32 , 33 ), (ii) availability of a culture of the strain, and (iii) bacterial growth amenable to microdilution ( 25 ). MICs were determined for 10 isolates with mutations in the F 420 genes.…”

Improving Multidrug-Resistance Tuberculosis Papua’s Management Using Whole Genome Sequencing

“…The accumulation of WGS data allows us to assess the genetic diversity across the genome, seeking signatures of selective pressure [5]. Many countries apply WGS for detecting MDR and XDR Tuberculosis [6][7][8][9][10][11][12][13]. Whole-genome sequencing of bacteria has been shown to provide comprehensive data like as prediction of drug susceptibility and resistance, epidemiological analysis and research [14][15][16].…”