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. 2020 Dec 31;15(12):e0244829.
doi: 10.1371/journal.pone.0244829. eCollection 2020.

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

Ditthawat Nonghanphithak  1   2 , Orawee Kaewprasert  1   2 , Pratchakan Chaiyachat  1   2 , Wipa Reechaipichitkul  2   3 , Angkana Chaiprasert  4 , Kiatichai Faksri  1   2
Affiliations

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

Ditthawat Nonghanphithak et al. PLoS One. .

Abstract

Drug resistance (DR) remains a major challenge for tuberculosis (TB) control. Whole-genome sequencing (WGS) provides the highest genetic resolution for genotypic drug-susceptibility tests (DST). We compared DST profiles of 60 Mycobacterium tuberculosis isolates which were drug resistant according to agar proportion tests (one poly DR-TB, 34 multidrug-resistant TB and 25 extensively drug-resistant TB). We additionally performed minimum inhibitory concentration (MIC) tests using Sensititre MYCOTBI plates (MYCOTB) and a WGS-based DST. Agreement between WGS-based DST and MYCOTB was high for all drugs except ethambutol (65%) and ethionamide (62%). Isolates harboring the -15 c/t inhA promoter mutation had a significantly lower MIC for isoniazid than did isolates with the katG Ser315Thr mutation (p < 0.001). Similar patterns were seen for ethambutol (embB Gly406Asp vs. embB Met306Ile), streptomycin (gid Gly73Ala vs. rpsL Lys43Arg), moxifloxacin (gyrA Ala90Val vs. gyrA Asp94Gly) and rifabutin (rpoB Asp435Phe/Tyr/Val vs. rpoB Ser450Leu). For genotypic heteroresistance, isolates with lower proportion of mapped read tended to has lower MIC of anti-TB drugs than those with higher proportion. These results emphasize the high applicability of WGS for determination of DR-TB and the association of particular mutations with MIC levels.

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Conflict of interest statement

The authors have declared that no competing interests exist.

Figures

Fig 1
Fig 1. Distributions of drug resistance-conferring mutations with corresponding MIC values.
Each stacked column represents a collection of isolates colored by different genetic background. The dashed lines indicate the critical concentrations used for MYCOTB. The H37Rv control strain was susceptible to all anti-tuberculosis drugs and represents the wild-type.
Fig 2
Fig 2. Comparisons between resistance-conferring mutations and MIC values of anti-TB drugs.
Only those anti-TB drugs are shown for which common mutations are associated with significant differences in MIC levels. The dashed lines indicate the critical concentrations used for MYCOTB. The size of each circle is proportional to the number of isolates. The color of circles indicate the MIC level from low (blue-green) to high (red).
Fig 3
Fig 3. Comparison between heteroresistance (inferred from read frequencies of relevant SNPs) and MIC levels of Mtb.
Comparisons between heteroresistance (inferred from read frequencies of relevant SNPs) and MIC levels for each anti-TB drug. The dashed line indicates the critical concentrations used for MYCOTB. Only anti-TB drugs against which heteroresistance was inferred based on read frequencies are shown. The size of each circle is proportional to the number of isolates.
See this image and copyright information in PMC

References

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