Microfluidic active loading of single cells enables analysis of complex clinical specimens

A fundamental trade-off between flow rate and measurement precision limits performance of many single-cell detection strategies, especially for applications that require biophysical measurements from living cells within complex and low-input samples. To address this, we introduce ‘active loading’, an automated, optically-triggered fluidic system that improves measurement throughput and robustness by controlling entry of individual cells into a measurement channel. We apply active loading to samples over a range of concentrations (1–1000 particles μL[superscript −1]), demonstrate that measurement time can be decreased by up to 20-fold, and show theoretically that performance of some types of existing single-cell microfluidic devices can be improved by implementing active loading. Finally, we demonstrate how active loading improves clinical feasibility for acute, single-cell drug sensitivity measurements by deploying it to a preclinical setting where we assess patient samples from normal brain, primary and metastatic brain cancers containing a complex, difficult-to-measure mixture of confounding biological debris.National Cancer Institute (U.S.) (R01 CA170592)National Cancer Institute (U.S.) (R33 CA191143)National Cancer Institute (U.S.) (Cancer Center Support (Core) Grant P30-CA14051)Bridge Projec

Microfluidic active loading of single cells enables analysis of complex clinical specimens

A fundamental trade-off between flow rate and measurement precision limits performance of many single-cell detection strategies, especially for applications that require biophysical measurements from living cells within complex and low-input samples. To address this, we introduce ‘active loading’, an automated, optically-triggered fluidic system that improves measurement throughput and robustness by controlling entry of individual cells into a measurement channel. We apply active loading to samples over a range of concentrations (1–1000 particles μL[superscript −1]), demonstrate that measurement time can be decreased by up to 20-fold, and show theoretically that performance of some types of existing single-cell microfluidic devices can be improved by implementing active loading. Finally, we demonstrate how active loading improves clinical feasibility for acute, single-cell drug sensitivity measurements by deploying it to a preclinical setting where we assess patient samples from normal brain, primary and metastatic brain cancers containing a complex, difficult-to-measure mixture of confounding biological debris.National Cancer Institute (U.S.) (R01 CA170592)National Cancer Institute (U.S.) (R33 CA191143)National Cancer Institute (U.S.) (Cancer Center Support (Core) Grant P30-CA14051)Bridge Projec

Cost of antimicrobial resistance in France : assessment from the medical-administrative databases

La résistance aux antibiotiques est considérée comme une menace majeure pour la santé publique mondiale. Le traitement des infections à germe résistant est plus difficile et conduit à des modifications de l’organisation des soins avec une augmentation des durées de séjour, de la morbidité et de la mortalité. L’évaluation du poids économique de la résistance aux antibiotiques pourrait éclairer les décideurs sur les priorités d’action à mener en termes de prévention, de recherche et de prise en charge. L’objectif général de cette thèse est d’évaluer l’impact économique de la résistance aux antibiotiques à partir des données du Système National des Données de Santé (SNDS). L’utilisation du SNDS permet d’identifier de façon exhaustive les patients hospitalisés atteints d’une infection bactérienne, suivis ou non par les professionnels libéraux ou en structure adaptée. Le suivi des séjours hospitaliers avec les consultations en médecine de ville rend possible la reconstitution des parcours de soins et les coûts qui y sont associés. La population étudiée concerne l’ensemble des patients hospitalisés présentant une infection bactérienne aiguë (regroupé en 13 sites infectieux). Dans un premier travail, nous nous sommes intéressés au coût hospitalier, du point de vue du payeur. Une étude cas-témoins appariés a permis d’estimer un surcoût hospitalier attribuable à la résistance de 110 millions € en 2015 et une extrapolation conduit à un surcoût de 290 millions €. Dans un second temps, nous nous sommes concentrés sur les conséquences à 12 mois d’une hospitalisation à germe résistant aux travers de quatre études : (1) Pour les patients ayant eu une infection à germe résistant, une analyse de séquence a permis d’identifier cinq parcours hospitaliers types. Les parcours hospitaliers les plus longs étaient observés suite à une infection ostéo-articulaire et une mortalité élevée concernait principalement les infections du cœur et du médiastin ou des voies respiratoires basses ; (2) La dépense ambulatoire étudiée par une approche de double différence, a montré que la surconsommation attribuable à la résistance aux antibiotiques était faible et limitée au premier mois qui suit une hospitalisation ; (3) La consommation de ressources hospitalières mesurée par la durée d’hospitalisations (en jours) attribuable à l’antibiorésistance est augmentée pour deux secteurs : en séjours hospitaliers en soins de courte durée pour infection et en hospitalisation à domicile ; (4) le surcoût hospitalier attribuable à la résistance aux antibiotiques l’année qui suit l’hospitalisation initiale a été estimé à 618 € [IC95% 419 ; 817] par patient. À travers 5 indicateurs économiques, cette thèse a mise en évidence que l’antibiorésistance provoque un coût substantiel pour l’assurance maladie.Antimicrobial resistance (AMR) is a major threat to global public health, makes infections more difficult to treat, and potentially jeopardizes medical progress and innovation. AMR is also associated with higher morbidity and mortality. Assessing the economic burden of AMR could highlight priorities in prevention, research and management for decision-makers. The main objective of this Ph.D. dissertation is to assess the economic impact of AMR in France based on data from the National Health Data System (SNDS) database. SNDS contains patient-level medical data and inpatient and outpatient care costs reimbursed by national health insurance. We thus used SNDS to analyse care pathways and associated costs among a population that included all hospitalized patients with acute bacterial infection (classified into 13 infectious sites). First, we investigated the hospital cost from the payer's perspective. Through a matched case-control design, we estimated an additional hospital cost of €110 million caused by AMR in 2015, with an extrapolation showing that the overall cost could reach €290 million. Second, we focused on the effects at 12 months of hospitalization with AMR. In this context, four studies were developed. (1) For patients with resistant infections, a sequence analysis identified five distinct hospital pathways. Longest hospital stays were observed for bone and joint infections, whereas patients with heart and mediastinum infections or lower respiratory tract infections had higher mortality rates. (2) Ambulatory expenditure was studied using a difference-in-difference approach and we showed a low overconsumption due to AMR, limited to the first month following hospitalization. (3) Hospital resource consumption measured by duration of hospitalization due to AMR was increased in acute care hospital stays for infection and in hospitalization at home. (4) Additional hospital cost due to antibiotic resistance during the year following initial hospitalization was estimated at €618 [IC95% 419; 817] per patient. In conclusion, using five economic criteria this Ph.D dissertation has shown that AMR bears a substantial cost burden on the French public health insurance system

Coût de l’antibiorésistance en France : évaluation à partir des bases de données médico-administratives

Antimicrobial resistance (AMR) is a major threat to global public health, makes infections more difficult to treat, and potentially jeopardizes medical progress and innovation. AMR is also associated with higher morbidity and mortality. Assessing the economic burden of AMR could highlight priorities in prevention, research and management for decision-makers. The main objective of this Ph.D. dissertation is to assess the economic impact of AMR in France based on data from the National Health Data System (SNDS) database. SNDS contains patient-level medical data and inpatient and outpatient care costs reimbursed by national health insurance. We thus used SNDS to analyse care pathways and associated costs among a population that included all hospitalized patients with acute bacterial infection (classified into 13 infectious sites). First, we investigated the hospital cost from the payer's perspective. Through a matched case-control design, we estimated an additional hospital cost of €110 million caused by AMR in 2015, with an extrapolation showing that the overall cost could reach €290 million. Second, we focused on the effects at 12 months of hospitalization with AMR. In this context, four studies were developed. (1) For patients with resistant infections, a sequence analysis identified five distinct hospital pathways. Longest hospital stays were observed for bone and joint infections, whereas patients with heart and mediastinum infections or lower respiratory tract infections had higher mortality rates. (2) Ambulatory expenditure was studied using a difference-in-difference approach and we showed a low overconsumption due to AMR, limited to the first month following hospitalization. (3) Hospital resource consumption measured by duration of hospitalization due to AMR was increased in acute care hospital stays for infection and in hospitalization at home. (4) Additional hospital cost due to antibiotic resistance during the year following initial hospitalization was estimated at €618 [IC95% 419; 817] per patient. In conclusion, using five economic criteria this Ph.D dissertation has shown that AMR bears a substantial cost burden on the French public health insurance system.La résistance aux antibiotiques est considérée comme une menace majeure pour la santé publique mondiale. Le traitement des infections à germe résistant est plus difficile et conduit à des modifications de l’organisation des soins avec une augmentation des durées de séjour, de la morbidité et de la mortalité. L’évaluation du poids économique de la résistance aux antibiotiques pourrait éclairer les décideurs sur les priorités d’action à mener en termes de prévention, de recherche et de prise en charge. L’objectif général de cette thèse est d’évaluer l’impact économique de la résistance aux antibiotiques à partir des données du Système National des Données de Santé (SNDS). L’utilisation du SNDS permet d’identifier de façon exhaustive les patients hospitalisés atteints d’une infection bactérienne, suivis ou non par les professionnels libéraux ou en structure adaptée. Le suivi des séjours hospitaliers avec les consultations en médecine de ville rend possible la reconstitution des parcours de soins et les coûts qui y sont associés. La population étudiée concerne l’ensemble des patients hospitalisés présentant une infection bactérienne aiguë (regroupé en 13 sites infectieux). Dans un premier travail, nous nous sommes intéressés au coût hospitalier, du point de vue du payeur. Une étude cas-témoins appariés a permis d’estimer un surcoût hospitalier attribuable à la résistance de 110 millions € en 2015 et une extrapolation conduit à un surcoût de 290 millions €. Dans un second temps, nous nous sommes concentrés sur les conséquences à 12 mois d’une hospitalisation à germe résistant aux travers de quatre études : (1) Pour les patients ayant eu une infection à germe résistant, une analyse de séquence a permis d’identifier cinq parcours hospitaliers types. Les parcours hospitaliers les plus longs étaient observés suite à une infection ostéo-articulaire et une mortalité élevée concernait principalement les infections du cœur et du médiastin ou des voies respiratoires basses ; (2) La dépense ambulatoire étudiée par une approche de double différence, a montré que la surconsommation attribuable à la résistance aux antibiotiques était faible et limitée au premier mois qui suit une hospitalisation ; (3) La consommation de ressources hospitalières mesurée par la durée d’hospitalisations (en jours) attribuable à l’antibiorésistance est augmentée pour deux secteurs : en séjours hospitaliers en soins de courte durée pour infection et en hospitalisation à domicile ; (4) le surcoût hospitalier attribuable à la résistance aux antibiotiques l’année qui suit l’hospitalisation initiale a été estimé à 618 € [IC95% 419 ; 817] par patient. À travers 5 indicateurs économiques, cette thèse a mise en évidence que l’antibiorésistance provoque un coût substantiel pour l’assurance maladie

Mutational burden and immune recognition of gliomas

International audiencePurpose of review Recent evidence suggests high tumor mutational burden (TMB-H) as a predictor of response to immune checkpoint blockade (ICB) in cancer. However, results in TMB-H gliomas have been inconsistent. In this article, we discuss the main pathways leading to TMB-H in glioma and how these might affect immunotherapy response. Recent findings Recent characterization of TMB-H gliomas showed that "post-treatment hypermutation" related to mismatch repair (MMR) deficiency is the most common mechanism leading to TMB-H in gliomas. Unexpectedly, preliminary evidence suggested no benefit with ICB as compared to chemotherapy in this population. In contrast, ICB response was reported in a subset of TMB-H gliomas associated with constitutional MMR or polymerase epsilon (POLE) defects (e.g., constitutional biallelic MMRd deficiency). In other cancers, several trials suggest increased ICB efficacy is critically associated with increased lymphocyte infiltration at baseline which is missing in most gliomas. Further characterization of the immune microenvironment of gliomas is needed to identify biomarkers to select the patients who will benefit from ICB

Emerging circulating biomarkers in glioblastoma: promises and challenges

International audienceGlioblastoma (GBM) is the most common and devastating primary malignant brain tumor in adults. The past few years have seen major progress in our understanding of the molecular basis of GBM. These advances, which have contributed to the development of novel targeted therapies, will change the paradigms in GBM therapy from disease-based to individually tailored molecular target-based treatment. No validated circulating biomarkers have yet been integrated into clinical practice for GBM. There is thus a critical need to implement minimally invasive clinical tests enabling molecular stratification and prognosis assessment, as well as the prediction and monitoring of treatment response. After examination of data from recent studies exploring several categories of tumor-associated biomarkers (circulating tumor cells, extracellular vesicles, nucleic acids and oncometabolites) identified in the blood, cerebrospinal fluid and urine, this article discusses the challenges and prospects for the development of circulating biomarkers in GBM

BRAF mutation in overlapping forms of Erdheim-Chester and Rosai-Dorfman diseases: A unique case restricted to the central nervous system

International audienceA 48-year-old man with a history of pleural tuberculosis presented in 2019 with paraesthesia of the left hemiface. The clinical examination was consistent with a fifth cranial nerve involvement. A brain MRI revealed three hyper-FLAIR and contrast enhanced lesions in the left cerebellar peduncle (Fig. 1), the left temporal lobe and the left occipital lobe. Perfusion images showed no hyperperfusion, and spectroscopy revealed a tumour profile, with a pick of choline and low NAA. A whole-body CT scan, PET CT scan, spinal MRI, CSF analysis and blood tests were normal, leading to the conclusion of an isolated brain disease. Therefore, a biopsy of the left temporal lesion was performed to differentiate the three main diagnostic hypotheses: infectious (tuberculosis); inflammatory (neurosarcoïdosis, neuro-Behcet); tumoral (primary CNS lymphoma) disease

Antibiotic prescriptions and risk factors for antimicrobial resistance in patients hospitalized with urinary tract infection: a matched case-control study using the French health insurance database (SNDS)

International audienceBackground: Antibiotic resistance is increasing among urinary pathogens, resulting in worse clinical and economic outcomes. We analysed factors associated with antibiotic-resistant bacteria (ARB) in patients hospitalized for urinary tract infection, using the comprehensive French national claims database. Methods: Hospitalized urinary tract infections were identified from 2015 to 2017. Cases (due to ARB) were matched to controls (without ARB) according to year, age, sex, infection, and bacterium. Healthcare-associated (HCAI) and community-acquired (CAI) infections were analysed separately; logistic regressions were stratified by sex. Results: From 9460 cases identified, 6468 CAIs and 2855 HCAIs were matched with controls. Over a 12-months window, the risk increased when exposure occurred within the last 3 months. The following risk factors were identified: antibiotic exposure, with an OR reaching 3.6 [2.8-4.5] for men with CAI, mostly associated with broadspectrum antibiotics; surgical procedure on urinary tract (OR 2.0 [1.5-2.6] for women with HCAI and 1.3 [1.1-1.6] for men with CAI); stay in intensive care unit > 7 days (OR 1.7 [1.2-2.6] for men with HCAI). Studied co-morbidities had no impact on ARB. Conclusions: This study points out the critical window of 3 months for antibiotic exposure, confirms the impact of broad-spectrum antibiotic consumption on ARB, and supports the importance of prevention during urological procedures, and long intensive care unit stays