Biology subjects

Aubry, A.

Publications and source records attributed to Aubry, A..

12 recordsLinked to original sources

bioRxiv2026

Assessing Corynebacterium glutamicum as a surrogate of Mycobacterium tuberculosis for DNA gyrase inhibitor design.

DNA gyrase is an essential bacterial enzyme and a clinically validated target for the treatment of tuberculosis. However, the discovery of new inhibitors remains limited by the many challenges regarding the manipulation on pathogenic mycobacteria. This study validates Corynebacterium glutamicum (Cglu) as a safe, non-pathogenic surrogate for Mycobacterium tuberculosis (Mtb) to investigate DNA gyrase and facilitate the identification of new inhibitors. Using Cglu as a target allows for fast whole-cell screening under safe conditions while ensuring efficient drug uptake. Cglu shares key physiological features with Mtb, including genome size, complex cell wall structure, and a single type I and type II topoisomerase. Structural and functional comparisons emphasize the similarity of Cglu and Mtb gyrases, which share 70% sequence identity and show comparable catalytic properties and responsiveness to known inhibitors. Thus, the cryo-EM structure of the Cglu gyrase-DNA complex at 3.2 [A] resolution reveals highly conserved drug-binding pockets for known anti-gyrase inhibitors and the genetic depletion of gyrA or gyrB in Cglu causes severe growth and morphological defects, mirroring the effects of chemical inhibition and allowing to link gyrase function to cellular phenotypes. Comparative imaging of different inhibitor classes (fluoroquinolones, aminocoumarins, NBTIs) uncovers distinct morphological signatures that reflect each compounds mode of action. Finally, cross-species complementation confirms functional conservation but also highlights subtle structural differences affecting efficiency. Together, these findings establish Cglu as a robust and biosafe model for dissecting gyrase function, visualizing DNA topology dynamics, and accelerating the discovery of gyrase-targeting antimicrobials. More generally, our studies demonstrate the feasibility of using Cglu as a cell-based screening platform to discover new anti-tuberculous compounds targeting conserved mechanisms, not only for validated TB drug targets such as DNA gyrase but also for new, yet to be identified, targets.

microbiology↗

bioRxiv2026

Minimal effective dose of telacebec administered orally in a murine model of leprosy

Leprosy treatment requires prolonged therapy with challenging patient follow-up. New regimens are needed to simplify current treatments. A recent clinical trial evaluating bedaquiline has shown promising results; however, to prevent the emergence of drug resistance, additional therapeutic options are required. Telacebec (TCB), an imidazopyridine amide targeting the Mycobacterium leprae electron transport chain, represents a promising candidate. In this study, we determined the minimal effective dose (MED) of TCB against M. leprae in vivo by using the proportional bactericidal method in the mouse footpad model. Results were analyzed by using microscopy, RLEP qPCR and molecular viability. The MED obtained was 20 mg/kg. TCB doses [≥]20 mg/kg achieved complete bacterial clearance, similar to bedaquiline 25mg/kg. Molecular enumeration confirmed these findings whereas molecular viability assessment had limited applicability due to insufficient bacterial burden. These findings provide a strong foundation for clinical trial design and the development of combination therapies.

microbiology↗

bioRxiv2026

A Murine Model of Mycobacterium abscessus Encapsulated in Alginate-Beads: Advancing Toward a Chronic Infection Model

BackgroundThe increasing incidence of Mycobacterium abscessus (M. abscessus) lung infections, together with its intrinsic multidrug resistance, highlights the need for new therapeutic regimens. However, the lack of a reliable chronic infection model in immunocompetent mice limits preclinical evaluation. MethodsTo mimic the bronchial environment of infected patients, we evaluated the effect of encapsulating M. abscessus in alginate beads on infection progression in BALB/cJRJ mice following intratracheal inoculation, compared with intranasal infection using non-encapsulated bacteria. The impact of dexamethasone treatment (DEX) was also assessed. Bacterial loads in lungs, spleen, liver, and kidneys were quantified over time in untreated and antibiotic-treated mice. Lung inflammation was evaluated by measuring IFN-{gamma} and TNF- levels. In vitro, the activity of imipenem and bedaquiline was assessed against free or alginate-encapsulated M. abscessus. ResultsCompared with intranasal infection, intratracheal infection with alginate-encapsulated bacteria resulted in slower pulmonary clearance and greater extrapulmonary dissemination. DEX further enhanced these features, reducing lung clearance, increasing dissemination, and amplifying lung inflammation. Bedaquiline showed no effect, whereas imipenem efficacy depended on treatment timing. For both drugs, alginate encapsulation reduced in vitro antibacterial activity. ConclusionThis model represents a step toward a chronic M. abscessus infection model characterized by moderate lungs clearance, extrapulmonary dissemination, and pronounced inflammatory responses. Reduced antibiotic activity against alginate-encapsulated bacteria may more accurately predict treatment efficacy in humans than activity measured against free bacteria.

microbiology↗

bioRxiv2026

Does Infection Progression of Mycobacterium abscessus Depend on Sex, Age, and Mouse strain?

The lack of a reliable chronic murine model limits drugs evaluation against Mycobacterium abscessus. Models show discrepancies, especially regarding host factors (mouse strain, sex and age). Using beads-model, we compared BALB/cJRJ and C57BL/6NCrl across sexes and ages. BALB/cJRJ showed more sustained infection and lower variability, with no significant sex- or age-related differences. Considering these results and the higher prevalence of NTM pulmonary infections in female patients, 5-6 weeks-old female BALB/cJRJ are appropriate for M. abscessus beads-model.

microbiology↗

bioRxiv2026

Deep learning extracts MoA-specific signatures from high-throughput images of chemically and genetically perturbed Corynebacteria

Tuberculosis (TB) is the worldwide leading infectious killer due to a single pathogen and increasing antimicrobial resistance (AMR) makes it imperative to discover and develop new drugs with novel modes of action (MoAs) to treat TB infections. Phenotypic screening of chemical libraries has proven effective at identifying new compounds against bacterial pathogens. However, a major limitation of standard screens is their inability to uncover the MoA of hits thereby preventing targeted selection of compounds with novel MoAs. Linking drug perturbations to mutants from images could potentially enable to predict the targets of compounds that act through novel MoAs. Here, we develop a deep learning (DL)-based method to screen drug-treated Corynebacterium glutamicum (Cglu), a surrogate model for Mycobacterium tuberculosis (Mtb). Our DL model is based on a convolutional neural network architecture that takes high throughput images as input and is trained to distinguish between different MoAs. We show that our approach can robustly differentiate between the MoAs of established antibiotics and correctly recognise the MoA of antibiotics that were not previously seen by the DL model. We also show that inhibitors with the same and previously unseen MoA cluster together and apart from all other reference drugs, allowing for new MoA discovery. Importantly, we show that our model links images of chemical (drugs) and genetic (mutants) perturbations targeting similar pathways, thus paving the way towards mutant-based target prediction of compounds that act through novel MoAs, directly from high-content images. Finally, we explore the phenotypes induced by genetic disruption of pathways and demonstrate that features extracted with our DL model recover known biological relationships from high-throughput images alone using the cell cycle of Cglu as a case study, a finding with promising potential for fundamental mechanistic studies.

microbiology↗

bioRxiv2025

Evaluation of the role of whiB6 and kdpDE in the dominant multidrug resistant clone Mycobacterium tuberculosis B0/W148

Multidrug resistant (MDR) strains of Mycobacterium tuberculosis represent an obstacle to eradicating tuberculosis (TB) due to the low treatment success rate of MDR TB. Among them, the MDR B0/W148 clone has recently evolved from the M. tuberculosis Beijing lineage 2 and widely disseminated in Russia and Europe. To get more insights into the genetic factors underlying the evolutionary success of the MDR M. tuberculosis B0/W148 clone in addition to environmental and patient-related features, we focused on two mutations specific from this clone that are found in the transcriptional regulators WhiB6 and KdpDE and investigated in a H37Rv strain background the transcriptional profile associated with these mutations and their impact on the in vitro and in vivo growth characteristics. Through the construction and use of H37Rv{Delta}whiB6, H37Rv{Delta}kdpDE, and complemented strains, we found that both mutations did not impair the in vitro growth of M. tuberculosis in standard mycobacterial growth media. The mutation T51P in whiB6 prevented the upregulation of 9 genes in the esx-1 core region and 44 genes elsewhere in the genome, while the deletion of two nucleotides in kdpD leads to a fusion protein of KdpD with KdpE that inhibits the transcriptional activity of KdpE. Both mutations did not lead to hypervirulence in a mouse infection model. These results point to the role of other MDR B0/W148 specific mutations in the wide geographic diffusion of this clone, and/or put in question a hypothesized hypervirulence as driving factor for this large dissemination. ImportanceHuman tuberculosis (TB), caused by the bacterium Mycobacterium tuberculosis, remains a global public health issue estimated to have been responsible for 1.25 million deaths in 2023. Multidrug resistant (MDR) strains of M. tuberculosis, resistant to rifampicin and isoniazid, lead to lower treatment success. Among them, the MDR B0/W148 clone has widely disseminated in Russia and Europe. To get more insights into the genetic factors underlying the evolutionary success of this clone, we investigated two strain-specific mutations found in the transcriptional regulators WhiB6 and KdpDE. By constructing and analysing laboratory M. tuberculosis strains carrying these specific mutations, we found numerous changes in their transcriptional profiles, whereas we observed only little impact of these mutations on virulence of M. tuberculosis in a mouse infection model. Our study provides new insights into the transcriptional landscape of the selected MDR strains, although no direct connection to virulence could be established.

microbiology↗

bioRxiv2024

Chronic Social Defeat Stress Gives Rise to Social Avoidance Through Fear Learning

Chronic social defeat stress (CSDS), a widely used rodent model of stress, reliably leads to decreased social interaction in stress susceptible animals. Here, we investigate a role for fear learning in this response using 129Sv/Ev mice, a strain that is more vulnerable to CSDS than the commonly used C57BL/6 strain. We first demonstrate that defeated 129Sv/Ev mice avoid a CD-1 mouse, but not a conspecific, indicating that motivation to socialize is intact in this strain. CD-1 avoidance is characterized by approach behavior that results in running in the opposite direction, activity that is consistent with a threat response. We next test whether CD-1 avoidance is subject to the same behavioral changes found in traditional models of Pavlovian fear conditioning. We find that associative learning occurs across 10 days CSDS, with defeated mice learning to associate the color of the CD-1 coat with threat. This leads to the gradual acquisition of avoidance behavior, a conditioned response that can be extinguished with 7 days of repeated social interaction testing (5 tests/day). Pairing a CD-1 with a tone leads to second-order conditioning, resulting in avoidance of an enclosure without a social target. Finally, we show that social interaction with a conspecific is a highly variable response in defeated mice that may reflect individual differences in generalization of fear to other social targets. Our data indicate that fear conditioning to a social target is a key component of CSDS, implicating the involvement of fear circuits in social avoidance.

animal behavior and cognition↗

bioRxiv2023

Chemokine receptor 5 signaling in PFC mediates stress susceptibility in female mice

Chronic stress induces changes in the periphery and the central nervous system (CNS) that contribute to neuropathology and behavioral abnormalities associated with psychiatric disorders. In this study, we examined the impact of peripheral and central inflammation during chronic social defeat stress (CSDS) in female mice. Compared to male mice, we found that female mice exhibited heightened peripheral inflammatory response and identified C-C motif chemokine ligand 5 (CCL5), as a stress-susceptibility marker in females. Blocking CCL5 signaling in the periphery promoted resilience to CSDS. In the brain, stress-susceptible mice displayed increased expression of C-C chemokine receptor 5 (CCR5), a receptor for CCL5, in microglia in the prefrontal cortex (PFC). This upregulation was associated with microglia morphological changes, their increased migration to the blood vessels, and enhanced phagocytosis of synaptic components and vascular material. These changes coincided with neurophysiological alterations and impaired blood-brain barrier (BBB) integrity. By blocking CCR5 signaling specifically in the PFC were able to prevent stress-induced physiological changes and rescue social avoidance behavior. Our findings are the first to demonstrate that stress-mediated dysregulation of the CCL5-CCR5 axis triggers excessive phagocytosis of synaptic materials and neurovascular components by microglia, resulting in disruptions in neurotransmission, reduced BBB integrity, and increased stress susceptibility. Our study provides new insights into the role of cortical microglia in female stress susceptibility and suggests that the CCL5-CCR5 axis may serve as a novel sex-specific therapeutic target for treating psychiatric disorders in females.

animal behavior and cognition↗

bioRxiv2023

Minimal effective dose of oral bedaquiline and activity of a long acting formulation of bedaquiline in the murine model of leprosy

BackgroundBedaquiline (BDQ), by targeting the electron transport chain and having a long half-life, is a good candidate to simplify leprosy treatment. Our objectives were to (i) determine the minimal effective dose (MED) of oral BDQ, (ii) evaluate the benefit of adding another inhibitor of the respiratory chain to oral BDQ (i.e. clofazimine (CFZ)) and (iii) evaluate the benefit of an intramuscular injectable long-acting formulation of BDQ (intramuscular BDQ; BDQ-LA IM), in a murine model of leprosy. Methodology/ Principal FindingsTo determine the MED of oral BDQ and the benefit of adding CFZ, 100 four-week-old female nude mice were inoculated in the footpads with 5.103 bacilli of M. leprae strain THAI53. Mice were randomly allocated into: 1 untreated group, 5 groups treated with oral BDQ (0.10 to 25 mg/kg), 3 groups treated with CFZ 20 mg/kg alone or combined with oral BDQ 0.10 or 0.33 mg/kg, and 1 group treated with rifampicin (RIF) 10 mg/kg. Mice were treated 5 days a week during 24 weeks. To evaluate the benefit of the BDQ-LA IM, 340 four-week-old female Swiss mice were inoculated in the footpads with 5.103 to 5.101 bacilli (or 5.100 for the untreated control group) of M. leprae strain THAI53. Mice were randomly allocated into the following 11 groups treated with a single dose (SD) or 3 doses (3D) 24h after the inoculation: 1 untreated group, 2 treated with RIF 10 mg/kg SD or 3D, 8 treated with oral BDQ or BDQ-LA IM 2 or 20 mg/kg, SD or 3D. Twelve months later, mice were sacrificed and M. leprae bacilli enumerated in the footpad. All the footpads became negative with BDQ at 3.3 mg/kg. The MED of oral BDQ against M. leprae in this model is therefore 3.3 mg/kg. The addition of CFZ to a dose of BDQ 10-fold lower than this MED increased the bactericidal activity of BDQ suggesting synergies between both drugs. The BDQ-LA IM displayed similar or lower bactericidal activity than the oral BDQ. ConclusionWe demonstrated that the MED of oral BDQ against M. leprae was 3.3 mg/kg in mice and the addition of CFZ to oral BDQ may improve the efficacy of BDQ. BDQ-LA IM was similar or less active than oral BDQ at equivalent dosing and frequency but should be tested at higher dosing in order to reach equivalent exposure in further experiments.

microbiology↗

bioRxiv2022

MSclassifR: an R package for supervised classification of mass spectra with machine learning methods

MSclassifR is an R package that has been specifically designed to improve the classification of mass spectra obtained from MALDI-TOF mass spectrometry. It offers a comprehensive range of functions that are focused on processing mass spectra, identifying discriminant m/z values, and making accurate predictions. The package introduces innovative algorithms for selecting discriminating m/z values and making predictions. To assess the effectiveness of these methods, extensive tests were conducted using challenging real datasets, including bacterial subspecies of the Mycobacterium abscessus complex, virulent and avirulent phenotypes of Escherichia coli, different species of Streptococci and nasal swabs from individuals infected and uninfected with SARS-CoV-2. Additionally, multiple datasets of varying sizes were created from these real datasets to evaluate the robustness of the algorithms. The results demonstrated that the Machine Learning-based pipelines in MSclassifR achieved high levels of accuracy and Kappa values. On an in-house dataset, some pipelines even achieved more than 95% mean accuracy, whereas commercial system only achieved 62% mean accuracy. Certain methods showed greater resilience to changes in dataset sizes when constructing Machine Learning-based pipelines. These simulations also helped determine the minimum sizes of training sets required to obtain reliable results. The package is freely available online, and its open-source nature encourages collaborative development, customization, and fosters innovation within the community focused on improving diagnosis based on MALDI-TOF spectra. Key pointsO_LIMSclassifR is a comprehensive R package enabling the construction of data analysis pipelines for the precise classification of mass spectra. C_LIO_LIOur R package contains an innovative method for variable selection from random forests, which delivered excellent results on real data. C_LIO_LIIn-depth analysis of various machine learning-based pipelines using our package allowed us to make conclusions about the optimal m/z selection and prediction methods depending on the size of the training dataset. C_LIO_LIUsing a publicly available dataset of mass spectra obtained from various MALDI-TOF instruments across different countries, MSclassifR is able to build robust pipelines capable of adapting to different instruments in an automatic way. C_LIO_LIWhen tested on an in-house dataset, MSclassifR pipelines consistently outperformed a commercial software in terms of prediction accuracy. C_LI

bioinformatics↗

bioRxiv2022

Dynamic Sex Differences in Reactive and Appetitive Aggression

Aggression is an evolutionarily conserved, adaptive component of social behavior. Studies in male mice illustrate that aggression is influenced by numerous factors including the degree to which an individual finds aggression rewarding and will work for access to attack and subordinate mice. While such studies have expanded our understanding of the molecular and circuit mechanisms of male aggression very little is known about female aggression, owed in part to limited availability of valid mouse models in females. Here we use an ethologically relevant model of male vs. female aggression by pair housing adult male and female outbred CFW mice with opposite sex cage mates. We assess reactive (defensive) aggression in the resident intruder (RI) test and appetitive (rewarding) aggression in the aggression conditioned place preference (CPP) and operant self-administration (SA) tests. Our results show dramatic sex differences in both qualitative and quantitative aspects of reactive vs. appetitive aggression. Males exhibit more wrestling and less investigative behavior during RI, find aggression rewarding and will work for access to a subordinate to attack. Females exhibit more bites, alternate between aggressive behaviors and investigative behaviors more readily during RI, however, they do not find aggression to be rewarding or reinforcing. These results establish sex differences in aggression in mice, providing an important resource for the field to better understand the circuit and molecular mechanisms of aggression in both sexes.

neuroscience↗

bioRxiv2019

Q203 containing fully intermittent oral regimens exhibited high sterilizing activity against Mycobacterium ulcerans in mice

Buruli ulcer (BU), caused by Mycobacterium ulcerans is currently treated by a daily combination of rifampin and either injectable streptomycin or oral clarithromycin. An intermittent oral regimen would facilitate the treatment supervision. We first evaluated the bactericidal activity of newer antimicrobials against M. ulcerans using a BU animal model. The imidazopyridine amine Q203 exhibited high bactericidal activity whereas tedizolid (oxazolidinone close to linezolid), selamectine and ivermectine (avermectine compound) and the benzothiazinone PBTZ169 were not active. Consequently, Q203 was evaluated for its bactericidal and sterilizing activities in combined intermittent regimens. Q203 given twice a week in combination with one of the other long half-life compounds, rifapentine or bedaquiline, sterilized the mice footpads in 8 weeks, i.e. after a total of only 16 doses, and prevented relapse during a period of 20 weeks after stopping the treatment. These results are very promising for future intermittent oral regimens which would greatly simplify BU treatments in the field.\n\nAuthor summaryThe current treatment of Buruli ulcer (BU), infection caused by Mycobacterium ulcerans is based on a daily antibiotic combination of rifampin associated with streptomycin or clarithromycin. A shorter or intermittent treatment without an injectable drug would clearly simplify the management on the field. We evaluated the bactericidal activity of several new antimicrobials drugs in a mice model of BU and found that the Q203 exhibited the highest bactericidal effect. We subsequently identified new antibiotic combinations containing Q203 with high sterilizing activity when administrated twice a week for 8 weeks.

microbiology↗