Biology subjects

Dide-Agossou, C.

Publications and source records attributed to Dide-Agossou, C..

6 recordsLinked to original sources

bioRxiv2025

Mind the gap: Understanding discordance between culture- and a non-culture-based measure of bacterial burden in murine tuberculosis treatment models

The standard pharmacodynamic marker in murine tuberculosis drug studies is colony-forming units (CFU). A faster PCR-based marker of bacterial burden is 16S rRNA. For unclear reasons, treatment reduces CFU more than 16S rRNA. We evaluated this CFU-16S gap and estimated the fraction potentially attributable to slow decay of 16S rRNA from dead Mycobacterium tuberculosis (Mtb) versus transition to a viable but not culturable on solid agar (VBNCSA) population. We quantified the CFU-16S gap during and following treatment in six BALB/c mouse studies and one in vitro study. Applying a two-population ordinary differential equation-based model of Mtb death and 16S rRNA decay, we estimated the fraction of the gap potentially attributable to dead Mtb. Using meta-regression, we estimated the association between CFU or 16S rRNA with relapse. For all regimens, CFU fell more than 16S rRNA, ranging from isoniazid-rifampin-pyrazinamide-ethambutol (CFU decreased 39-times more than 16S rRNA at week 4) to bedaquiline-pretomanid-moxifloxacin-pyrazinamide (CFU decreased >500,000-times more). The two-population model suggested that the fraction of the CFU-16S gap attributable to residual 16S rRNA from dead Mtb is modest and decreases over time. After treatment, 16S rRNA often fell while CFU rose. Four-week CFU change explained most variation in relapse (R{superscript 2}=0.90) while four-week 16S rRNA change did not (R{superscript 2}=0.24). CFU-16S gap is only partially explained by slow decay of residual 16S, suggesting development of a VBNCSA population. However, continued decrease in 16S rRNA after treatment cessation and its limited association with relapse suggests VBNCSA may be a transient rather than persistent state.

microbiology↗

bioRxiv2025

Deconvoluting drug interactions based on M. tuberculosis physiologic processes:Transcriptional disaggregation of the BPaL regimen in vivo

Identification of optimal antibiotic combination treatments for tuberculosis (TB) in preclinical studies is impeded by the limited information conventional pharmacodynamic (PD) markers provide about drug interactions. Measurement of individual drug activity based on colony forming units (CFU) does not reliably predict the activity of drug combinations, potentially because one drug may affect the physiology of Mycobacterium tuberculosis (Mtb) in a way that either favors or disfavors the activity of a second drug. SEARCH-TB is a novel candidate PD approach which uses targeted in vivo transcriptional profiling to evaluate the effects of drugs on Mtb physiology. To test the capacity of SEARCH-TB to elucidate drug interactions, we deconstructed the BPaL (bedaquiline, pretomanid, linezolid) regimen in the BALB/c high-dose aerosol mouse infection model, measuring the effect of 2, 7, and 14-day treatment with drugs in monotherapy, pairwise combinations, and as a 3-drug combination. Monotherapy rapidly induced drug-specific Mtb transcriptional responses by day 2 with continued evolution over 14 days. Bedaquiline dominated pairwise combinations with both pretomanid and linezolid. The pretomanid-linezolid combination gave a blended response, inducing transcriptional profiles "intermediate" between either drug. In the 3-drug BPaL regimen, the addition of both pretomanid and linezolid to bedaquiline yielded a greater transcriptional response than expected based on pairwise results. This work demonstrates that physiologic perturbations induced by a single drug may be modified in complex ways when drugs are combined. This establishes proof of concept that SEARCH-TB is a highly granular readout of drug interactions in vivo, providing information distinct from CFU burden and suggesting a future in which regimen selection is informed by in vivo molecular measures of Mtb physiology.

genomics↗

bioRxiv2024

Emergence of antibiotic-specific Mycobacterium tuberculosis phenotypes during prolonged treatment of mice

A major challenge in tuberculosis (TB) therapeutics is that antibiotic exposure leads to changes in the physiologic state of M. tuberculosis (Mtb) which may enable the pathogen to withstand treatment. While antibiotic-treated Mtb have been evaluated in short-term in vitro experiments, it is unclear if and how long-term in vivo treatment with diverse antibiotics with varying treatment-shortening activity (sterilizing activity) affect Mtb physiologic states differently. Here, we used SEARCH-TB, a pathogen-targeted RNA-sequencing platform, to characterize the Mtb transcriptome in the BALB/c high-dose aerosol infection mouse model following 4-week treatment with three sterilizing and three non-sterilizing antibiotics. Certain transcriptional changes were concordant among most antibiotics, including decreased expression of genes associated with protein synthesis and metabolism, and the induction of certain genes associated with stress responses. However, the magnitude of this concordant response differed between antibiotics. Sterilizing antibiotics rifampin, pyrazinamide, and bedaquiline generated a more quiescent Mtb state than did non-sterilizing antibiotics isoniazid, ethambutol, and streptomycin, as indicated by decreased expression of genes associated with translation, transcription, secretion of immunogenic proteins, metabolism, and cell wall synthesis. Additionally, we identified distinguishing transcriptional effects specific to each antibiotic, indicating that different mechanisms of action induce distinct patterns of cellular injury. In addition to elucidating Mtb physiologic changes associated with antibiotic stress, this study demonstrates the value of SEARCH-TB as a highly granular pharmacodynamic assay that reveals antibiotic effects that are not apparent based on culture alone.

genomics↗

bioRxiv2023

Transcriptional adaptation of drug-tolerant Mycobacterium tuberculosis in mice

Transcriptome evaluation of Mycobacterium tuberculosis in the lungs of laboratory animals during long-term treatment has been limited by extremely low abundance of bacterial mRNA relative to eukaryotic RNA. Here we report a targeted amplification RNA sequencing method called SEARCH-TB. After confirming that SEARCH-TB recapitulates conventional RNA-seq in vitro, we applied SEARCH-TB to Mycobacterium tuberculosis-infected BALB/c mice treated for up to 28 days with the global standard isoniazid, rifampin, pyrazinamide, and ethambutol regimen. We compared results in mice with 8-day exposure to the same regimen in vitro. After treatment of mice for 28 days, SEARCH-TB suggested broad suppression of genes associated with bacterial growth, transcription, translation, synthesis of rRNA proteins and immunogenic secretory peptides. Adaptation of drug-stressed Mycobacterium tuberculosis appeared to include a metabolic transition from ATP-maximizing respiration towards lower-efficiency pathways, modification and recycling of cell wall components, large-scale regulatory reprogramming, and reconfiguration of efflux pumps expression. Despite markedly different expression at pre-treatment baseline, murine and in vitro samples had broadly similar transcriptional change during treatment. The differences observed likely indicate the importance of immunity and pharmacokinetics in the mouse. By elucidating the long-term effect of tuberculosis treatment on bacterial cellular processes in vivo, SEARCH-TB represents a highly granular pharmacodynamic monitoring tool with potential to enhance evaluation of new regimens and thereby accelerate progress towards a new generation of more effective tuberculosis treatment.

microbiology↗

bioRxiv2023

Lung microenvironments harbor Mycobacterium tuberculosis phenotypes with distinct treatment responses

Tuberculosis lung lesions are complex and harbor heterogeneous microenvironments that influence antibiotic effectiveness. Major strides have been made recently in understanding drug pharmacokinetics in pulmonary lesions, but the bacterial phenotypes that arise under these conditions and their contribution to drug tolerance is poorly understood. A pharmacodynamic marker called the RS ratio quantifies ongoing rRNA synthesis based on the abundance of newly-synthesized precursor rRNA relative to mature structural rRNA. Application of the RS ratio in the C3HeB/FeJ mouse model demonstrated that Mycobacterium tuberculosis populations residing in different tissue microenvironments are phenotypically distinct and respond differently to drug treatment with rifampin, isoniazid or bedaquiline. This work provides a foundational basis required to address how anatomic and pathologic microenvironmental niches may contribute to the long treatment duration and drug tolerance during treatment of human tuberculosis.

microbiology↗

bioRxiv2021

Combination of Mycobacterium tuberculosis RS ratio and CFU improves the ability of murine efficacy experiments to distinguish between drug treatments

Murine tuberculosis drug efficacy studies have historically monitored bacterial burden based on colony forming units of M. tuberculosis in lung homogenate. In an alternative approach, a recently described molecular pharmacodynamic marker called the RS ratio quantifies drug effect on a fundamental cellular process: ongoing ribosomal RNA synthesis. Here we evaluated the ability of different pharmacodynamic markers to distinguish between treatments in three BALB/c mouse experiments at two institutions. We confirmed that different pharmacodynamic markers measure distinct biological responses. We found that a combination of pharmacodynamic markers distinguishes between treatments better than any single marker. The combination of the RS ratio with colony forming units showed the greatest ability to recapitulate the rank order of regimen treatment-shortening activity, providing proof of concept that simultaneous assessment of pharmacodynamic markers measuring different properties will enhance insight gained from animal models and accelerate development of new combination regimens. These results suggest potential for a new era in which antimicrobial therapies are evaluated not only on culture-based measures of bacterial burden but also on molecular assays that indicate how drugs impact the physiological state of the pathogen.

microbiology↗