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Background The sites of mycobacterial infection in the lungs of tuberculosis (TB) patients have complex structures and poor vascularization, which obstructs drug distribution to these hard-to-reach and hard-to-treat disease sites, further leading to suboptimal drug concentrations, resulting in compromised TB treatment response and resistance development. Quantifying lesion-specific drug uptake and pharmacokinetics (PKs) in TB patients is necessary to optimize treatment regimens at all infection sites, to identify patients at risk, to improve existing regimens, and to advance development of novel regimens. Using drug-level data in plasma and from 9 distinct pulmonary lesion types (vascular, avascular, and mixed) obtained from 15 hard-to-treat TB patients who failed TB treatments and therefore underwent lung resection surgery, we quantified the distribution and the penetration of 7 major TB drugs at these sites, and we provide novel tools for treatment optimization. Methods and findings A total of 329 plasma- and 1,362 tissue-specific drug concentrations from 9 distinct lung lesion types were obtained according to optimal PK sampling schema from 15 patients (10 men, 5 women, aged 23 to 58) undergoing lung resection surgery (clinical study NCT00816426 performed in South Korea between 9 June 2010 and 24 June 2014). Seven major TB drugs (rifampin [RIF], isoniazid [INH], linezolid [LZD], moxifloxacin [MFX], clofazimine [CFZ], pyrazinamide [PZA], and kanamycin [KAN]) were quantified. We developed and evaluated a site-of-action mechanistic PK model using nonlinear mixed effects methodology. We quantified population- and patient-specific lesion/plasma ratios (RPLs), dynamics, and variability of drug uptake into each lesion for each drug. CFZ and MFX had higher drug exposures in lesions compared to plasma (median RPL 2.37, range across lesions 1.26–22.03); RIF, PZA, and LZD showed moderate yet suboptimal lesion penetration (median RPL 0.61, range 0.21–2.4), while INH and KAN showed poor tissue penetration (median RPL 0.4, range 0.03–0.73). Stochastic PK/pharmacodynamic (PD) simulations were carried out to evaluate current regimen combinations and dosing guidelines in distinct patient strata. Patients receiving standard doses of RIF and INH, who are of the lower range of exposure distribution, spent substantial periods (>12 h/d) below effective concentrations in hard-to-treat lesions, such as caseous lesions and cavities. Standard doses of INH (300 mg) and KAN (1,000 mg) did not reach therapeutic thresholds in most lesions for a majority of the population. Drugs and doses that did reach target exposure in most subjects include 400 mg MFX and 100 mg CFZ. Patients with cavitary lesions, irrespective of drug choice, have an increased likelihood of subtherapeutic concentrations, leading to a higher risk of resistance acquisition while on treatment. A limitation of this study was the small sample size of 15 patients, performed in a unique study population of TB patients who failed treatment and underwent lung resection surgery. These results still need further exploration and validation in larger and more diverse cohorts. Conclusions Our results suggest that the ability to reach and maintain therapeutic concentrations is both lesion and drug specific, indicating that stratifying patients based on disease extent, lesion types, and individual drug-susceptibility profiles may eventually be useful for guiding the selection of patient-tailored drug regimens and may lead to improved TB treatment outcomes. We provide a web-based tool to further explore this model and results at http://saviclab.org/tb-lesion/., Using data from resected lung lesions, Radojka Savic and colleagues develop a model to describe the amount and rate of drug penetration for seven major tuberculosis drugs into lung tissue., Author summary Why was this study done? Tuberculosis (TB) remains the number one infectious disease killer, with patients failing treatment despite use of multidrug curative treatment. The potential reason for suboptimal response is reduced drug penetration to the diverse lung lesions formed by the host immune system, in which the bacteria remains in the secluded areas inaccessible to the drug. What did the researchers do and find? We developed a mathematical model for 7 major TB drugs by utilizing actual patient data, which describes the amount and rate of drug penetration into 9 distinct TB lesions in which mycobacteria reside. The majority of TB drugs show poor penetration into the cavitary lesions, leading to inadequate drug levels at the site of the disease. Multidrug-level simulations to identify favorable drug combinations for cure at the site of infection showed that a combination of clofazimine (CFZ) and moxifloxacin (MFX) or CFZ and linezolid (LZD) would be optimal for patients presenting with caseous lesions. What do these findings mean? Drugs do not penetrate equally in different tissues, and considering that a variety of TB patients presented with unique lesion subtypes and lung pathology, the current one regimen to fit all approaches is inadequate to treat every patient. To maximize cure, a patient-focused approach is needed for which clinical phenotype should be used to match the right drug regimen to the right patient.