ED Sciences Chimiques
Role of emerging contaminants in promoting horizontal transfer of antimicrobial resistance genes: a multiscale approach in environmental context
by Ana REY SOGO (Environnements et Paléoenvironnements Océaniques et Continentaux)
The defense will take place at 9h30 - Salón de Grados de la Facultad de Ciencia y Tecnología University of the Basque Country (UPV/EHU) Faculty of Science and Technology, Sarriena Auzoa, 48940 Santsoena, Biscay
in front of the jury composed of
- Eric FOUQUET - Professeur des universités - Institut des Sciences Moléculaires (ISM), Université de Bordeaux - Examinateur
- Elisabeth GROHMANN - Professeure - Berlin University of Applied Sciences, Faculty of Life Sciences and Technology, Department of Microbiology, Berlin, Germany - Rapporteur
- Manel CAMPS - Full professor - UC Santa Cruz - Examinateur
- Nestor ETXEBARRIA LOIZATE - Full professor - Department of Analytical Chemistry Faculty of Science and Technology – Plentzia Marine Station (PIE) University of the Basque Country / Euskal Herriko Unibertsitatea - Examinateur
- Matxalen LLOSA BLAS - Professeure des universités - Facultad de Medicina, University of Cantabria (UC) - Rapporteur
The global dissemination of antimicrobial resistance (AMR) through horizontal gene transfer (HGT), and specifically through conjugative transfer, represents one of the most urgent challenges in environmental microbiology and public health. While antibiotics have long been recognized as drivers of AMR selection and spread, the role of contaminants of emerging concern (e.g., industrial chemicals, disinfectants, personal care products) as promoters of bacterial conjugation at environmentally relevant concentrations remains insufficiently understood. This thesis addresses that gap through a multiscale, integrative approach combining machine learning (ML)-based predictive modelling, in vitro experimentation across three conjugation systems, and in situ field assessment in a wastewater-influenced estuary. In the first chapter, a suite of ML models (Linear Regression, Random Forest, and XGBoost) was developed and evaluated using a curated dataset of published effects of chemical stressors on conjugation experiments. The best-performing model, XGBoost, achieved an internal validation R² of 0.719, demonstrating meaningful predictive capacity. Feature importance analysis revealed that chemical concentration, bacterial species and structural fingerprints were the dominant predictors. These findings establish a framework for HGT risk assessment and identify the boundaries of current predictive capacity, underscoring the need for larger, more homogeneous experimental datasets to extend model applicability. In the second chapter, the effects of twelve CECs from six functional groups on conjugative transfer were characterized using two intraspecies Escherichia coli mating systems sharing the same recipient HMS174 but differing in donor background and plasmid incompatibility (Inc) group (IncF/K12 and IncP/UB1637). Both systems responded to CEC exposure at 0.001–0.01 µg/mL, but the IncP system consistently showed stronger and more reproducible induction. This differential sensitivity was attributed to plasmid type and mechanistically explained by three factors: the higher basal transfer frequency of IncF, leaving less apparent fold-change induction; cell population heterogeneity; and the plasmid intrinsic regulatory system. Molecular mechanisms were further elucidated for individual CECs, demonstrating compound-specific pathways. In the third chapter, the investigation was extended to an in situ environmental context, characterizing the mobilizable plasmidome at four sampling points spanning wastewater treatment plant (WWTP) effluents and pristine receiving waters. Integration of captured plasmids, qPCR of AMR-related genes and site chemical context demonstrated that WWTP effluent discharge locations harbored high plasmid capture rates and diversity. Furthermore, exposure of the in vitro IncF/HMS174 conjugation system to WWTP effluent modulated conjugative transfer, providing a mechanistic link between complex chemical stressor mixtures and in situ HGT dynamics. Collectively, this thesis establishes that CECs at environmentally relevant concentrations constitute a modest but real risk factor for conjugation-driven AMR dissemination, whose magnitude is determined by the interplay of chemical identity, plasmid regulatory architecture, and population-level heterogeneity. The compound-specific mechanistic diversity uncovered highlights the importance of studying individual chemicals, while exposure to effluent mixtures and the in situ mobilizable plasmidome underscore that real-world risk is shaped by chemical complexity and ecological context in ways that single-compound laboratory-based experiments cannot fully capture. These findings argue for the integration of HGT-promoting potential into environmental risk frameworks, and for the development of standardized, multi-plasmid conjugation assays as regulatory tools for assessing chemical threats to the environmental resistome.
ED Sciences Physiques et de l'Ingénieur
Novel high-power, low-noise, infrared to ultraviolet single-frequency laser sources for quantum 2.0 applications
by Kentin PONCELET (Laboratoire Photonique, Numérique & Nanosciences)
The defense will take place at 9h30 - Amphitheatre André Ducasse 1 Rue François Mitterrand, Institut d'Optique Graduate School Nouvelle Aquitaine, 33400, Talence
in front of the jury composed of
- Giorgio SANTARELLI - Ingénieur de recherche - LP2N, Université de Bordeaux - Directeur de these
- Sébastien FéVRIER - Professeur des universités - XLIM, Université de Limoges - Rapporteur
- Stéphane TREBAOL - Maître de conférences - Institut Foton - Rapporteur
- Anne DHOLLANDE - Directrice de recherche - French-German Research Institute, ISL - Examinateur
- Inka MANEK-HöNNINGER - Professeure des universités - CELIA, Université de Bordeaux - Examinateur
- Olivier LLOPIS - Directeur de recherche - Université Paul Sabatier Toulouse III - Examinateur
This PhD thesis focuses on the design and optimization of high-power fiber laser sources operating in a single-frequency regime and exhibiting very low relative intensity noise, in order to meet the requirements of the second quantum revolution. Applications such as neutral-atom and trapped-ion quantum computers impose stringent constraints in terms of stability, spectral purity, and power scaling. Although the wavelengths of interest are often located in the visible or ultraviolet spectral regions, the approach de- veloped in this work relies on the use of thulium-doped fiber lasers to generate high optical powers in the infrared band between 1.7 and 1.9 μm. This radiation serves as an intermediate stage for the generation of the final wavelengths through nonlinear fre- quency conversion processes, such as sum-frequency generation or second-harmonic generation. Several amplification architectures have been designed and experimentally characterized around 1850 nm. A first wavelength-tunable system demonstrates ampli- fication up to 30 W between 1830 and 1880 nm, highlighting the feasibility of a power stage pumped in the cladding within this spectral range. A second architecture, based on a single-frequency seed laser with very low intensity noise, leads to the realization of an all-fiber amplifier delivering a record output power of 50 W at 1844 nm. This system maintains a relative intensity noise level close to the shot-noise limit, with no evidence of stimulated Brillouin scattering under the investigated operating conditions. This source is also used for the generation of visible wavelengths: sum-frequency generation with another MOPA operating at 1542 nm enables output powers up to 20 W at 840 nm, followed by second-harmonic generation in a resonant cavity leading to 15 W at 420 nm. Finally, additional developments are devoted to laser emission around 1700–1760 nm, a spectral region where reabsorption effects become more pronounced. A detailed study is carried out to investigate the impact of pump wavelength and injected signal power on the amplification performance, allowing favorable operating conditions to be identified. Based on these results, specific architectures relying on core pumping are implemented, together with the development of high-power, low-intensity-noise pump sources. These pump lasers are based on erbium–ytterbium-doped fiber MOPA architec- tures operating around 1570 nm and are dedicated to feeding the thulium power stages. Altogether, these developments enable output powers exceeding 30 W at 1730 nm and 1762 nm, with high-frequency RIN levels compatible with the specifications defined for the targeted quantum applications.