Drug regimens identified and optimized by output-driven platform markedly reduce tuberculosis treatment time

Bai-Yu Lee, Daniel L Clemens, Aleidy Silva, Barbara Jane Dillon, Saša Masleša-Galić, Susana Nava, Xianting Ding, Chih-Ming Ho, Marcus A Horwitz, Bai-Yu Lee, Daniel L Clemens, Aleidy Silva, Barbara Jane Dillon, Saša Masleša-Galić, Susana Nava, Xianting Ding, Chih-Ming Ho, Marcus A Horwitz

Abstract

The current drug regimens for treating tuberculosis are lengthy and onerous, and hence complicated by poor adherence leading to drug resistance and disease relapse. Previously, using an output-driven optimization platform and an in vitro macrophage model of Mycobacterium tuberculosis infection, we identified several experimental drug regimens among billions of possible drug-dose combinations that outperform the current standard regimen. Here we use this platform to optimize the in vivo drug doses of two of these regimens in a mouse model of pulmonary tuberculosis. The experimental regimens kill M. tuberculosis much more rapidly than the standard regimen and reduce treatment time to relapse-free cure by 75%. Thus, these regimens have the potential to provide a markedly shorter course of treatment for tuberculosis in humans. As these regimens omit isoniazid, rifampicin, fluoroquinolones and injectable aminoglycosides, they would be suitable for treating many cases of multidrug and extensively drug-resistant tuberculosis.

Conflict of interest statement

The authors are inventors on patents (International Patent Application Serial No. PCT/US2014/012111 and PCT/US2015/058892) covering the technology described herein.

Figures

Figure 1. Short-term efficacy studies of PRS…
Figure 1. Short-term efficacy studies of PRS Regimens I and II.
(a,b) Lung burden of M. tuberculosis in mice that were sham-treated, treated with the Standard Regimen (SR) or treated with PRS Regimens I (a) or II (b) with the drugs administered at high (H), middle (M) or low (L) dose five times per week for 4 weeks. Data are mean±s.e.m. of log10 CFU for n=5 mice per group. All treatment groups had significantly fewer CFU than the sham-treated group (P<0.0001). Differences in treatment efficacy between the Standard Regimen and individual PRS Regimen I or II groups were evaluated by one-way ANOVA with Tukey's correction. *P<0.05, **P<0.01, ***P<0.001, ****P<0.0001. §No M. tuberculosis CFU detected—data plotted as discussed in Methods. (c,d) Heat maps of the drug-dose response surface for PRS Regimens I (c) and II (d). These 3-dimensional graphs show how the projected number of lung CFU changes as the dose of one and/or the other drug is increased or decreased. Drug dose is shown in mg kg−1. In these plots, in addition to CLZ, the third drug is kept at the high dose.
Figure 2. Lung pathology of mice that…
Figure 2. Lung pathology of mice that received sham or Standard Regimen or PRS Regimen I treatment.
Shown are representative gross pathology images of lungs dissected from mice that were sham-treated or treated with the Standard Regimen or PRS Regimen I at high doses of each drug by oral gavage five times (Monday—Friday) a week for 4 weeks.
Figure 3. Lung pathology of mice that…
Figure 3. Lung pathology of mice that received sham or Standard Regimen or PRS Regimen II treatment.
Shown are representative gross pathology images of lungs dissected from mice that were sham-treated or treated with the Standard Regimen or PRS Regimen II at high doses of each drug by oral gavage five times (Monday—Friday) a week for 4 weeks.
Figure 4. Medium-term efficacy and relapse study.
Figure 4. Medium-term efficacy and relapse study.
(a) M. tuberculosis burden in the lung over the course of infection and treatment period, where mice were sham-treated or treated with the Standard Regimen (SR), Enhanced Standard Regimen (ESR) or PRS Regimen I, IIA or IIB starting at Week 0. Data are mean log10 CFU for n=5 mice per group. §CFU at limit of detection. (b) Relapse 3 months after completion of treatment with PRS Regimen IIA for the duration indicated. (c) M. tuberculosis lung burden after treatment 5 days per week for 2, 3, 4, 6 and 8 weeks in sham-treated mice or mice treated with Standard Regimen (SR), Enhanced Standard Regimen (ESR) or PRS Regimen I, IIA or IIB. Data are mean±s.e.m. of log10 CFU for n=5 mice per group. Differences in efficacy between groups were evaluated by one-way ANOVA with Tukey's correction. ***P<0.001, ****P<0.0001. §No M. tuberculosis CFU detected—data plotted as discussed in Methods.
Figure 5. Long-term efficacy and relapse study.
Figure 5. Long-term efficacy and relapse study.
(a) M. tuberculosis burden in the lung over the course of infection and treatment period, where mice were sham-treated or treated with the Standard Regimen, Enhanced Standard Regimen or PRS Regimen I or IIC 5 days (Monday—Friday) a week starting at Week 0. The PRS Regimen IIC (daily) group was treated daily for 14 days. Data transformation as log10 (x+1) with x being the actual CFU was used for graphing purpose. (b) Heatmap for PRS Regimen II with CLZ and EMB dose at 25 and 100 mg kg−1, respectively, indicating that the optimal doses of BDQ and PZA were 30 and 450 mg kg−1, respectively. The white zone around BDQ 30 mg kg−1 at the bottom of the map corresponds to CFU projected to be 0 or below. (c) Relapse in the lung 3 months after completion of treatment with the PRS Regimen I or IIC or control regimens (Standard Regimen or Enhanced Standard Regimen) daily (d) or 5 days per week (wk) for the duration indicated. Differences in time to relapse-free cure between the Standard Regimen and the PRS regimens administered at the same frequency (5 days per week) were statistically significant (P=0.002 versus PRS Regimen I and P<0.0001 versus PRS Regimen IIC, log rank test). Differences between PRS Regimens I and II in time to relapse-free cure (administered at the same frequency (5 days per week)) were also statistically significant (P<0.0001, log rank test).

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