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. 2019 Mar 27;63(4):e02175-18.
doi: 10.1128/AAC.02175-18. Print 2019 Apr.

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

Sebastian M Gygli #  1   2 , Peter M Keller #  3   4 , Marie Ballif  5 , Nicolas Blöchliger  3 , Rico Hömke  3   6 , Miriam Reinhard  1   2 , Chloé Loiseau  1   2 , Claudia Ritter  3   6 , Peter Sander  3   6 , Sonia Borrell  1   2 , Jimena Collantes Loo  7 , Anchalee Avihingsanon  8   9 , Joachim Gnokoro  10 , Marcel Yotebieng  11 , Matthias Egger #  5   12 , Sebastien Gagneux #  13   2 , Erik C Böttger #  14   6
Affiliations

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

Sebastian M Gygli et al. Antimicrob Agents Chemother. .

Abstract

Whole-genome sequencing allows rapid detection of drug-resistant Mycobacterium tuberculosis isolates. 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 clinical M. tuberculosis isolates 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.

Keywords: Mycobacterium tuberculosis; drug resistance; drug resistance level prediction; quantitative phenotypic drug susceptibility testing; whole-genome sequencing.

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Figures

FIG 1
FIG 1
Method agreement between phenotypic DST performed with MGIT 960 and 7H10 agar dilution (agardil.), represented as Bland-Altman plots for all drugs tested in this study.
FIG 2
FIG 2
Maximum likelihood phylogeny of 176 M. tuberculosis strains based on 20,510 variable positions. Reference strains are labeled with green. Main lineages are highlighted with the following color scheme: red, L4; purple, L3; blue, L2; pink, L1; green, L6; brown, L5. Scale bar indicates the number of substitutions per site. Phylogeny is rooted on M. canettii. Colored bars indicate resistance mutations per gene, and within a distinct column (gene) each colored bar represents a distinct mutation. Black bars indicate no mutation, i.e., wt.
FIG 3
FIG 3
Histograms of MICs (7H10 agar dilution) for all drugs assayed in this study.
FIG 4
FIG 4
Correlation between 7H10 agar dilution MICs for rifampin and rifabutin.
See this image and copyright information in PMC

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References

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