Biology subjects

Veziris, N.

Publications and source records attributed to Veziris, N..

8 recordsLinked to original sources

bioRxiv2026

Emergence of plasmid-borne erm(55)-associated macrolide resistance in Mycobacterium chelonae and other rapidly-growing non-tuberculous mycobacteria in Europe

Macrolides are key agents for treating infections caused by non-tuberculous mycobacteria (NTM). Nevertheless, chromosomal erm genes conferring inducible macrolide resistance are described in some NTM species, such as Mycobacterium abscessus and M. fortuitum, whereas M. chelonae had long been considered as lacking a functional erm. Recent descriptions from the USA and Japan of a new plasmid-borne erm(55) (erm(55)P) in M. chelonae and other rapidly growing mycobacteria (RGM) have challenged this assumption. We investigated erm(55)P occurrence in clinical RGM referred to the French National Reference Centre for Mycobacteria between 2012 and 2026 by genome screening and erm(55)P specific real-time PCR. Positive isolates underwent long-read whole genome sequencing (GridIon, Oxford Nanopore Technologies). Clarithromycin (CLR) minimum inhibitory concentration (MIC) was determined by broth microdilution (RAPMYCO and FRATMYC, Thermo Fisher) and read up to 14 days. Five clinical isolates showing inducible CLR resistance (MIC range <0.25-64 mg/L on day 3-4 and 128- >128 mg/L on day 14) were positive for erm(55)P: one M. chelonae, three M. neoaurum, and one M. parafortuitum. erm(55)P-positive M. chelonae genomes from this and previous descriptions did not cluster together in the phylogenetic analysis of 263 genomes. The assembled plasmids showed high similarity to previously reported erm(55)-carrying plasmids, especially within the erm(55)P region. The upstream sequence of erm(55)P showed a secondary structure compatible with a possible translation attenuation mechanism. These findings document the first report of a plasmid-borne erm(55) in Europe in M. chelonae and other RGM and raise concern about the emergence of plasmid macrolide resistance in NTM.

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↗

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↗

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↗

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↗