Whole-Genome Sequencing for Drug Resistance Profile Prediction in Mycobacterium tuberculosis

Abstract

Whole-genome sequencing allows rapid detection of drug-resistantMycobacterium tuberculosisisolates. However, the availability of high-quality data linking quantitative phenotypic drug susceptibility testing (DST) and genomic data have thus far been limited. We determined drug resistance profiles of 176 genetically diverse clinicalM. tuberculosisisolates from the 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 DST results with predicted drug resistance profiles inferred by whole-genome sequencing. Classification of strains by the two phenotypic DST methods into resistotype/wild-type populations was concordant in 73 to 99% of cases, depending on the drug. Our data suggest that the established critical concentration (5 mg/liter) for ethambutol resistance (MGIT 960 system) is too high and misclassifies strains as susceptible, unlike 7H10 agar dilution. Increased minimal inhibitory concentrations were explained by mutations identified by whole-genome sequencing. Using whole-genome sequences, we were able to predict quantitative drug resistance levels for the majority of drug resistance mutations. Predicting quantitative levels of drug resistance by whole-genome sequencing was partially limited due to incompletely understood drug resistance mechanisms. The overall sensitivity and specificity of whole-genome-based DST were 86.8% and 94.5%, respectively. Despite some limitations, whole-genome sequencing has the potential to infer resistance profiles without the need for time-consuming phenotypic methods.

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 secondline 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).…”

Whole Genome Sequencing Results Associated with Minimum Inhibitory Concentrations of 14 Anti-Tuberculosis Drugs among Rifampicin-Resistant Isolates of Mycobacterium Tuberculosis from Iran

“…Unfortunately, quantitative phenotypic DST (MICs) data are often limited and genetic background of resistance for some antibiotics were not clearly understood [11]. Accurate identification of chromosomal mutations is accessible using whole genome sequencing (WGS) and linking with the minimum inhibitory concentrations are necessarily needed to better infer the susceptible strains from the resistant ones [12].…”

Whole-genome sequence analysis and comparisons between drug-resistance mutations and minimum inhibitory concentrations of Mycobacterium tuberculosis isolates causing M/XDR-TB

“…For EMB the agreement between WGS and MYCOTB was low (65%). Possibly the CC (4 μg/ml) used for EMB is too high [24]. When we reduced the CC of EMB to 2 μg/ml, the agreement…”

“…phenotypic tests was even greater for EMB. Similarly, the agreement of EMB between phenotypic and genotypic DST was low [24]. For ETO, we found isolates that had resistance-conferring mutations in the ethA gene and the inhA promotor but had MIC values lower than the CC (5 μg/ml).…”