Improving sparse recovery on structured images with bagged clustering

International audience—The identification of image regions associated with external variables through discriminative approaches yields ill-posed estimation problems. This estimation challenge can be tackled by imposing sparse solutions. However, the sensitivity of sparse estimators to correlated variables leads to non-reproducible results, and only a subset of the important variables are selected. In this paper, we explore an approach based on bagging clustering-based data compression in order to alleviate the instability of sparse models. Specifically, we design a new framework in which the estimator is built by averaging multiple models estimated after feature clustering, to improve the conditioning of the model. We show that this combination of model averaging with spatially consistent compression can have the virtuous effect of increasing the stability of the weight maps, allowing a better interpretation of the results. Finally, we demonstrate the benefit of our approach on several predictive modeling problems

Assessing and tuning brain decoders: cross-validation, caveats, and guidelines

International audienceDecoding, ie prediction from brain images or signals, calls for empirical evaluation of its predictive power. Such evaluation is achieved via cross-validation, a method also used to tune decoders' hyper-parameters. This paper is a review on cross-validation procedures for decoding in neuroimaging. It includes a didactic overview of the relevant theoretical considerations. Practical aspects are highlighted with an extensive empirical study of the common decoders in within-and across-subject predictions, on multiple datasets –anatomical and functional MRI and MEG– and simulations. Theory and experiments outline that the popular " leave-one-out " strategy leads to unstable and biased estimates, and a repeated random splits method should be preferred. Experiments outline the large error bars of cross-validation in neuroimaging settings: typical confidence intervals of 10%. Nested cross-validation can tune decoders' parameters while avoiding circularity bias. However we find that it can be more favorable to use sane defaults, in particular for non-sparse decoders

Mejora en el manejo de las cistitis en atención primaria después de la implementación de una intervención multimodal simple

Primary health care; Urinary tract infections; Urine cultureAtención primaria; Infecciones del tracto urinario; UrocultivoAtenció primària; Infeccions del tracte urinari; UrocultiuObjective We assessed the impact of the implementation of a simple multifaceted intervention aimed at improving management of cystitis in primary care. Design Quality control before and after study. Site Primary care centres in Barcelona city provided by the Catalonian Institute of Health. Participants The multifaceted intervention consisted of (1) creation of a group with a leader in each of the primary care centres, out of hours services, sexual and reproductive centres, and home visit service, (2) session on management of cystitis in each centre, (3) result feedback for professionals, and (4) provision of infographics for professionals and patients with urinary tract infections. Interventions started in November 2020 and ended in the summer of 2021. Main measurements Variation in the prescription of first-line antibiotics, usage of antibiotics, and request for urine cultures before and after this intervention. Results Training sessions took place in 93% of the centres. The use of first-line therapies cystitis increased by 6.4% after the intervention (95% confidence interval [CI], 5.7–7.1%). The use of nitrofurantoin in recurrent cystitis increased, mainly in out of hours service (8.7%; 95% CI, 5.2–12.2%). Urine cultures were more frequently requested after the intervention for recurrent cystitis in both primary care centres and out of hours services, with a 7.2% increase [95% CI, 5.9–8.5%), but also for uncomplicated urinary tract infections (3.1%; 95% CI, 1.8–4.4%). Conclusions A low-intensity multifaceted intervention on management of cystitis, with strong institutional support, resulted in a better choice of antibiotic in antibiotic prescribing, but the intervention had less impact on the adequacy of urine cultures.Objetivo Evaluamos el impacto de una intervención multimodal en la mejora del manejo de las cistitis en atención primaria. Diseño Estudio de calidad antes-después. Emplazamiento Centros de atención primaria de la ciudad de Barcelona proporcionados por el Institut Català de la Salut. Participantes La intervención multimodal consistió en: (1) creación de un grupo de trabajo con líderes en cada uno de los equipos de atención primaria, servicios de urgencias, centros de atención sexual y reproductiva y servicio de atención domiciliaria, (2) sesión formativa sobre el manejo de las infecciones del tracto urinario en cada centro, (3) retorno de resultados a profesionales, y (4) difusión de infografías a profesionales y pacientes. Las intervenciones comenzaron en noviembre de 2020 y finalizaron en verano de 2021. Mediciones principales Variación en la prescripción de antibióticos de primera línea, uso de antibióticos y solicitud de urocultivos antes y después de esta intervención. Resultados Las sesiones de formación se realizaron en el 93% de los centros. La selección de fármacos de primera línea en cistitis aumentó en un 6,4% después de la intervención (intervalo de confianza [IC] 95%: 5,7-7,1%). El uso de nitrofurantoína en cistitis recurrente aumentó, principalmente en servicios de urgencias (8,7%; IC 95%: 5,2-12,2%). Las solicitudes de urocultivos aumentaron después de la intervención en equipos de atención primaria y servicios de urgencias en cistitis recurrentes (7,2%; IC 95%: 5,9-8,5%), pero también en cistitis simples (3,1%; IC 95%: 1,8-4,4%). Conclusiones Una intervención multimodal de baja intensidad sobre el manejo de las cistitis junto con el apoyo institucional explícito mejoró claramente la selección de antibióticos, pero tuvo menos impacto en la adecuación de los urocultivos

Diagnosis of leishmaniasis

This work was supported by EK Elmahallawy, who has a PhD scholarship (number 736) from Erasmus Mundus Scholarship Programme (ELEMENT Action 1 First call).Leishmaniasis is a clinically heterogeneous syndrome caused by intracellular protozoan parasites of the genus Leishmania. The clinical spectrum of leishmaniasis encompasses subclinical ( not apparent), localized (skin lesion), and disseminated (cutaneous, mucocutaneous, and visceral) infection. This spectrum of manifestations depends on the immune status of the host, on the parasite, and on immunoinflammatory responses. Visceral leishmaniasis causes high morbidity and mortality in the developing world. Reliable laboratory methods become mandatory for accurate diagnosis, especially in immunocompromised patients such as those infected with HIV. In this article, we review the current state of the diagnostic tools for leishmaniasis, especially the serological test.Erasmus Mundus Scholarship Programme (ELEMENT Action 1 First call) 73

Oral fosfomycin for treatment of acute bacterial prostatitis caused by multidrug-resistant Enterobacterales

Acute prostatitis; Fosfomycin-tromethamine; Multidrug resistanceProstatitis aguda; Fosfomicina-trometamina; Resistència a múltiples medicamentsProstatitis aguda; Fosfomicina-trometamina; Resistencia a múltiples medicamentosTo assess the feasibility of oral fosfomycin-tromethamine (FT) for the management of acute bacterial prostatitis (ABP) caused by multidrug-resistant (MDR) Enterobacterales. An observational study of adult patients diagnosed with ABP from Vall d’Hebron University Hospital (Barcelona, Spain), treated with oral FT. The primary outcome was clinical cure defined as symptom relief at the control visit, 2–4 weeks post-end of treatment. Secondary outcomes included microbiological cure, relapse, and adverse events related to the treatment. Eighteen patients with ABP caused by Enterobacterales (15 Escherichia coli and three Klebsiella pneumoniae) were included. Microorganisms were MDR bacteria [14 extended-spectrum beta-lactamase (ESBL) producers and two carbapenemase producing K. pneumoniae]. Patients received treatment with FT 3 g/48 hours during a median of 14 days (Q25–Q75, 12–17.75). Fifteen patients received a lead-in phase of intravenous suitable antimicrobial during a median of 7 days (Q25–Q75, 3.75–8). No patient had to stop treatment due to adverse events, and the only side effect reported in two patients was diarrhea. Clinical cure was achieved in all (18/18) patients and microbiological cure in 11/12 patients. After a median of follow-up of 5 months (Q25–Q75, 2–11), 2/18 patients relapsed with an orchitis and a new episode of ABP. FT is an attractive step-down therapy for ABP in patients with resistance or side effects to first-line drugs. The availability of oral treatment could reduce the use of the carbapenems, with a benefit in the quality of life of the patient, health costs, and an ecological impact

Increasing trend of antimicrobial resistance in Shigella associated with MSM transmission in Barcelona, 2020–21: outbreak of XRD Shigella sonnei and dissemination of ESBL-producing Shigella flexneri

Antimicrobial resistance; Shigella sonnei; Sexually transmitted infectionResistencia antimicrobiana; Shigella sonnei; Infección de transmisión sexualResistència antimicrobiana; Shigella sonnei; Infecció de transmissió sexualBackground Several countries have recently reported the detection of ESBL-producing Shigella sonnei associated with transmission among MSM. In a previous study by our group, 2.8% of Shigella spp. obtained from MSM in Barcelona between 2015 and 2019 were ESBL producers. Objectives To describe and characterize the emerging ESBL-producing Shigella spp. associated with sexual transmission among MSM detected from 2020 to 2021 in Barcelona, elucidating their connectivity with contemporaneous ESBL-producing Shigella spp. from other countries. Results From 2020 to 2021, we identified that among MSM, 68% of S. sonnei were XDR harbouring blaCTX-M-27 and 14% of Shigella flexneri were MDR harbouring blaCTX-M-27. WGS analysis showed that the ESBL-producing S. sonnei were part of a monophyletic cluster, which included isolates responsible for the prolonged outbreak occurring in the UK. Our data also reveal the first emergence and clonal dissemination of ESBL-producing and fluoroquinolone-resistant S. flexneri 2a among MSM. Conclusions We report an increasing trend of antimicrobial resistance in Shigella spp. among MSM in Barcelona since 2021, mainly as a consequence of the dissemination of XDR ESBL-producing S. sonnei, previously reported in the UK. These results highlight the importance of international collaborative surveillance of MDR/XDR S. sonnei and S. flexneri for rapid identification of their emergence and the prevention of the transmission of these pathogens.This work was partially supported by the ‘Ministerio de Economía y Competitividad’, ‘Instituto de Salud Carlos III’, and co-financed by the European Regional Development Fund (ERDF) ‘A Way to Achieve Europe’ (Spanish Network for Research in Infectious Diseases, grant number RD16/0016/0003) and by the Centro de Investigación Biomédica en Red (CIBER de Enfermedades Infecciosas, grant no. CB21/13/00054). A.M.M. is supported by a grant from the ‘Fondo de Investigación Sanitaria’ (Contratos Predoctorales de Formación en Investigación, grant number FI19/00315)

Aplicación de la tecnología MALDI-TOF MS para la detección de carbapenemasas

Tesis Univ. Granada. Programa Oficial de Doctorado en: Medicina Clínica y Salud PÚblic

FReM – scalable and stable decoding with fast regularized ensemble of models

International audienceBrain decoding relates behavior to brain activity through predictive models. These are also used to identify brain regions involved in the cognitive operations related to the observed behavior. Training such multivariate models is a high-dimensional statistical problem that calls for suitable priors. State of the art priors –eg small total-variation– enforce spatial structure on the maps to stabilize them and improve prediction. However, they come with a hefty computational cost. We build upon very fast dimension reduction with spatial structure and model ensembling to achieve decoders that are fast on large datasets and increase the stability of the predictions and the maps. Our approach, fast regularized ensemble of models (FReM), includes an implicit spatial regularization by using a voxel grouping with a fast clustering algorithm. In addition, it aggregates different estimators obtained across splits of a cross-validation loop, each time keeping the best possible model. Experiments on a large number of brain imaging datasets show that our combination of voxel clustering and model ensembling improves decoding maps stability and reduces the variance of prediction accuracy. Importantly, our method requires less samples than state-of-the-art methods to achieve a given level of prediction accuracy. Finally, FreM is highly parallelizable, and has lower computation cost than other spatially-regularized methods

OXA-244-Producing Escherichia coli Isolates, a Challenge for Clinical Microbiology Laboratories

International audienceOXA-244 is a single-point-mutant derivative of OXA-48 displaying reduced carbapenemase activity. Here, we report the microbiological features of seven OXA-244-producing Escherichia coli isolates. Only one isolate grew on ChromID Carba Smart medium (bioMérieux), but six of the seven isolates grew on ChromID extended-spectrum-β-lactamase (ESBL) medium (bioMérieux), as they coproduced an ESBL and/or a plasmid-encoded cephalosporinase. The production of a carbapenemase was detected in 57.1%, 71.4%, 71.4%, and 100% of the E. coli isolates using the Carba NP test, the Rapidec Carba NP test (bioMérieux), a matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) hydrolysis assay (Bruker), and the OXA-48 K-SeT assay (Coris BioConcept), respectively. Our results indicate that OXA-244-producing E. coli isolates are difficult to detect, which may lead to their silent spread

New paradigms on antibiotic recommendations for community-acquired infections in Spain

Over the last years, the susceptibility activity of the most common microorganisms causing community-acquired infections has significantly changed in Spain. Based on the susceptibility rates of Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli, and Klebsiella pneumoniae collected from outpatients aged 15 or older with symptoms of respiratory or urinary tract infections in several Microbiology Departments in Catalonia in 2021, penicillin V should be first choice for most respiratory tract infections, amoxicillin and clavulanate for chronic obstructive pulmonary disease exacerbations and a single dose of fosfomycin or a short-course nitrofurantoin should remain first-line treatments for uncomplicated urinary tract infections. Updated information on antimicrobial resistance for general practitioners is crucial for achieving appropriate empirical management of the most common infections by promoting more rational antibiotic use. Resumen: En los últimos años han cambiado significativamente los porcentajes de sensibilidad de los microorganismos más comunes que causan infecciones adquiridas en la comunidad en España. A partir de los porcentajes de sensibilidad de Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli y Klebsiella pneumoniae, recogidas de aislados de pacientes ambulatorios de 15 años o más, con síntomas de infecciones respiratorias o urinarias en servicios de microbiología de Cataluña en 2021, fenoximetilpenicilina debería ser la primera opción en la mayoría de los infecciones respiratorias, amoxicilina y ácido clavulánico en las exacerbaciones de la enfermedad pulmonar obstructiva crónica y la monodosis de fosfomicina o la pauta corta de nitrofurantoína como tratamiento de primera línea en las infecciones urinarias no complicadas. Es importante que los médicos de familia dispongan de información actualizada sobre la resistencia a los antimicrobianos para lograr un manejo empírico adecuado de las infecciones más frecuentes al promover un uso más racional de los antibióticos