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Objectives: The empirical treatment of infective endocarditis is still debated. The aim of this study was to compare the impact of empirical treatment with antistaphylococcal penicillin (ASP) or cefazolin vs. other treatments in methicillin-susceptible Staphylococcus aureus (MSSA) endocarditis. Methods: A post hoc analysis of a prospective cohort study of patients hospitalized in a French reference centre with MSSA endocarditis was conducted between 2013 and 2022. The primary outcome was the duration of bacteraemia under treatment. Results: Of the 208 patients included, 101 patients (48.6%) were classified in the reference group (ASP or cefazolin) and 107 (52.4%) in the non-reference group. Empirical treatment with ASP/cefazolin was associated with a shorter duration of bacteraemia compared to other treatments (3.6 d vs. 4.6 d, P = 0.01). This difference was not corrected by the addition of an aminoglycoside (3.6 d vs. 4.7 d, P < 0.01). In multivariate analysis, empirical treatment with ASP/cefazolin was associated with a duration of bacteraemia ≤72 h (P = 0.02), whereas endocarditis on native valves (P = 0.01), and intracardiac abscess were associated with longer duration of bacteraemia (P = 0.01). Conclusions: Empirical treatment of endocarditis with ASP or Cefazolin is more effective than other treatments in MSSA endocarditis, even when the other treatments are combined with aminoglycosides.

The potential of chitosans to control grapevine trunk diseases (GTDs) has been studied in a public-private partnership. In vitro tests, vineyard efficacy trials and laboratory analyses were carried out to understand their mode of action. In vitro, low molecular weight (MW) chitosans, the most soluble, were often the most effective. In the vineyard, the most effective were those with a medium MW, in particular chitosan hydrochlorides which form a protective film. They could be used to dress wounds caused by pruning, re-trunking or curettage.

Dynamic positron emission tomography and kinetic modeling play a critical role in tracer development research using small animals. Kinetic modeling from dynamic PET imaging requires accurate knowledge of an input function, ideally determined through arterial blood sampling. Arterial cannulation in mice, however, requires complex, time-consuming and terminal surgery, meaning that longitudinal studies are impossible. The aim of the current work was to develop and evaluate a non-invasive, deep-learning-based prediction model (DLIF) that directly takes the PET data as input to predict a usable input function. We first trained and evaluated the DLIF model on 68 [18F]Fluorodeoxyglucose mouse scans with image-derived targets using cross validation. Subsequently, we evaluated the performance of a trained DLIF model on an external dataset consisting of 8 mouse scans where the input function was measured by continuous arterial blood sampling. The results showed that the predicted DLIF and image-derived targets were similar, and the net influx rate constants following from Patlak modeling using DLIF as input function were strongly correlated to the corresponding values obtained using the image-derived input function. There were somewhat larger discrepancies when evaluating the model on the external dataset, which could be attributed to systematic differences in the experimental setup between the two datasets. In conclusion, our non-invasive DLIF prediction method may be a viable alternative to arterial blood sampling in small animal [18F]FDG imaging. With further validation, DLIF could overcome the need for arterial cannulation and allow fully quantitative and longitudinal experiments in PET imaging studies of mice.

In Benin, adaptation to climate change in the livestock sector has led cattle farmers to develop different livestock practices. Most research has focused on evaluating the effects of these practices on livestock productivity. However, information on the effect of these practices on carbon (C) sequestration in farmland soils is lacking. Soil C sequestration has been identified as a potential strategy to offset greenhouse gas emissions. Thus, the present study aimed at filling this gap. The calculation was one hand based on inventory data obtained from literature sources (excrement production of each cattle category, moisture content of each crop, ratio of crop residue to main product, and C content of the main product and excrement) and on the other hand on activity data (cattle herd size, manure applied, land use area, crop yield, and crop residues management) obtained from surveys carried out among 360 cattle farmers belonging to 3 cattle farming types. The results revealed that whatever the cattle farming type, annual C input from manure was higher (p˂0.05) than C input from crop residues. Annual C sequestration in farmland soil of farms integrating livestock with cereal-legume and forage crops was significantly higher (Type 2: 158.07 ± 1.79 kg C ha−1 year−1) followed by farms integrating livestock with cereal-legume crops (Type 1: 99.51 ± 0.95 kg C ha−1 year−1), which in turn had a higher value than farms practicing pastoral mobility (Type 3: 78.46 ± 0.70 kg C ha−1 year−1). These results highlight the potential for climate change mitigation through these farming practices. This is justified because the quantity of C sequestered in farmland soil of all cattle farming types was significant. Thus, for future research, it is necessary to include soil C sequestration in the calculations of farms' carbon footprint.

Abstract Genomic structural variants (SVs) are now recognized as an integral component of intraspecific polymorphism and are known to contribute to evolutionary processes in various organisms. However, they are inherently difficult to detect and genotype from readily available short‐read sequencing data, and therefore remain poorly documented in wild populations. Salmonid species displaying strong interpopulation variability in both life history traits and habitat characteristics, such as Atlantic salmon (Salmo salar), offer a prime context for studying adaptive polymorphism, but the contribution of SVs to fine‐scale local adaptation has yet to be explored. Here, we performed a comparative analysis of SVs, single nucleotide polymorphisms (SNPs) and small indels (

IntroductionSpinal cord stimulation is a common treatment option for neuropathic pain conditions. Despite its extensive use and multiple technological evolutions, long term efficacy of spinal cord stimulation is debated. Most studies on spinal cord stimulation include a rather limited number of patients and/or follow-ups over a limited period. Therefore, there is an urgent need for real-world, long-term data.MethodsIn 2018, the Belgian government initiated a nationwide secure platform for the follow-up of all new and existing spinal cord stimulation therapies. This is a unique approach used worldwide. Four years after the start of centralized recording, the first global extraction of data was performed.ResultsHerein, we present the findings, detailing the different steps in the centralized procedure, as well as the observed patient and treatment characteristics. Furthermore, we identified dropouts during the screening process, the reasons behind discontinuation, and the evolution of key indicators during the trial period. In addition, we obtained the first insights into the evolution of the clinical impact of permanent implants on the overall functioning and quality of life of patients in the long-term.DiscussionAlthough these findings are the results of the first data extraction, some interesting conclusions can be drawn. The long-term outcomes of neuromodulation are complex and subject to many variables. Future data extraction will allow us to identify these confounding factors and the early predictors of success. In addition, we will propose further optimization of the current process.

Summary: Background: Although immunomodulators have established benefit against the new coronavirus disease (COVID-19) in general, it is uncertain whether such agents improve outcomes without increasing the risk of secondary infections in the specific subgroup of previously immunocompromised patients. We assessed the effect of immunomodulators on outcomes of immunocompromised patients hospitalized for COVID-19. Methods: The protocol was prospectively registered with PROSPERO (CRD42022335397). MEDLINE, Cochrane Central Register of Controlled Trials and references of relevant articles were searched up to 01-06-2022. Authors of potentially eligible randomized controlled trials were contacted to provide data on immunocompromised patients randomized to immunomodulators vs control (i.e., placebo or standard-of-care). Findings: Eleven randomized controlled trials involving 397 immunocompromised patients hospitalized for COVID-19 were included. Ten trials had low risk of bias. There was no difference between immunocompromised patients randomized to immunomodulators vs control regarding mortality [30/182 (16.5%) vs 41/215 (19.1%); RR 0.93, 95% CI 0.61–1.41; p = 0.74], secondary infections (RR 1.00, 95% CI 0.64–1.58; p = 0.99) and change in World Health Organization ordinal scale from baseline to day 15 (weighed mean difference 0.27, 95% CI -0.09–0.63; p = 0.15). In subgroup analyses including only patients with hematologic malignancy, only trials with low risk of bias, only trials administering IL-6 inhibitors, or only trials administering immunosuppressants, there was no difference between comparators regarding mortality. Interpretation: Immunomodulators, compared to control, were not associated with harmful or beneficial outcomes, including mortality, secondary infections, and change in ordinal scale, when administered to immunocompromised patients hospitalized for COVID-19. Funding: Hellenic Foundation for Research and Innovation.

This study aimed to investigate the influence of cocoa cortex ash (CCA) compare to syenite (SY) on the technological properties of stoneware ceramics. Mixtures of clay powders (EB) and each flux were prepared in ratios of 90/10, 80/20, and 70/30, and then sintered at 1100 °C. Obtained samples were characterized by water absorption (WA), bulk density (BD), and flexural strength (FS). For mixtures of EB and SY, the sample containing 30 % SY and 70 % EB demonstrated favorable properties, including WA of 3.87 %, BD of 2.37 g/cm3, and FS of 29.6 MPa. For the mixtures of EB and CCA, the sample with 10 % CCA showed interesting properties, with a WA of 2 %, BD of 2.41 g/cm3, and FS of 32 MPa. Based on the ISO 13006 standard, sample with 10 % CCA exhibited the characteristics of vitrified stoneware, while samples containing SY displayed characteristics of semi-vitrified stoneware.

Abstract Background Little is known about susceptibility of Staphylococcus lugdunensis to antiseptics. The objective of this study was to evaluate, at the molecular and phenotypic level, the susceptibility of 49 clinical S. lugdunensis strains (belonging to the seven clonal complexes [CCs] defined by multilocus sequence typing) to two antiseptics frequently used in healthcare settings (chlorhexidine digluconate [CHX] and chloride benzalkonium [BAC]). Results The minimum inhibitory concentrations (MICs), by broth microdilution method, varied for BAC from 0.25 mg/L to 8 mg/L (MIC50 = 1 mg/L, MIC90 = 2 mg/L) and for CHX from 0.5 mg/L to 2 mg/L (MIC50 = 1 mg/L, MIC90 = 2 mg/L). The BAC and CHX minimum bactericidal concentrations (MBCs) varied from 2 mg/L to 8 mg/L (MBC50 = 4 mg/L, MBC90 = 8 mg/L) and from 2 mg/L to 4 mg/L (MBC50 and MBC90 = 4 mg/L), respectively. A reduced susceptibility to CHX (MIC = 2 mg/L) was observed for 12.2% of the strains and that to BAC (MIC ≥ 4 mg/L) for 4.1%. The norA resistance gene was detected in all the 49 isolates, whereas the qacA gene was rarely encountered (two strains; 4.1%). The qacC, qacG, qacH, and qacJ genes were not detected. The two strains harboring the qacA gene had reduced susceptibility to both antiseptics and belonged to CC3. Conclusion The norA gene was detected in all the strains, suggesting that it could belong to the core genome of S. lugdunensis. S. lugdunensis is highly susceptible to both antiseptics tested. Reduced susceptibility to BAC and CHX was a rare phenomenon. Of note, a tendency to higher MICs of BAC was detected for CC3 isolates. These results should be confirmed on a larger collection of strains.

Abstract p-Hydroxycinnamic acids, such as sinapic, ferulic, p-coumaric and caffeic acids, are among the most abundant phenolic compounds found in plant biomass and agro-industrial by-products (e.g. cereal brans, sugar-beet and coffee pulps, oilseed meals). These p-hydroxycinnamic acids, and their resulting decarboxylation products named vinylphenols (canolol, 4-vinylguaiacol, 4-vinylphenol, 4-vinylcatechol), are bioactive molecules with many properties including antioxidant, anti-inflammatory and antimicrobial activities, and potential applications in food, cosmetic or pharmaceutical industries. They were also shown to be suitable precursors of new sustainable polymers and biobased substitutes for fine chemicals such as bisphenol A diglycidyl ethers. Non-oxidative microbial decarboxylation of p-hydroxycinnamic acids into vinylphenols involves cofactor-free and metal-independent phenolic acid decarboxylases (EC 4.1.1 carboxyl lyase family). Historically purified from bacteria (Bacillus, Lactobacillus, Pseudomonas, Enterobacter genera) and some yeasts (e.g. Brettanomyces or Candida), these enzymes were described for the decarboxylation of ferulic and p-coumaric acids into 4-vinylguaiacol and 4-vinylphenol, respectively. The catalytic mechanism comprised a first step involving p-hydroxycinnamic acid conversion into a semi-quinone that then decarboxylated spontaneously into the corresponding vinyl compound, in a second step. Bioconversion processes for synthesizing 4-vinylguaiacol and 4-vinylphenol by microbial decarboxylation of ferulic and p-coumaric acids historically attracted the most research using bacterial recombinant phenolic acid decarboxylases (especially Bacillus enzymes) and the processes developed to date included mono- or biphasic systems, and the use of free- or immobilized cells. More recently, filamentous fungi of the Neolentinus lepideus species were shown to natively produce a more versatile phenolic acid decarboxylase with high activity on sinapic acid in addition to the others p-hydroxycinnamic acids, opening the way to the production of canolol by biotechnological processes applied to rapeseed meal. Few studies have described the further microbial/enzymatic bioconversion of these vinylphenols into valuable compounds: (i) synthesis of flavours such as vanillin, 4-ethylguaiacol and 4-ethylphenol from 4-vinylguaiacol and 4-vinylphenol, (ii) laccase-mediated polymer synthesis from canolol, 4-vinylguaiacol and 4-vinylphenol.

Abstract Automatic monitoring of wildlife is becoming a critical tool in the field of ecology. In particular, Radio‐Frequency IDentification (RFID) is now a widespread technology to assess the phenology, breeding and survival of many species. While RFID produces massive datasets, no established fast and accurate methods are yet available for this type of data processing. Deep learning approaches have been used to overcome similar problems in other scientific fields and hence might hold the potential to overcome these analytical challenges and unlock the full potential of RFID studies. We present a deep learning workflow, coined “RFIDeep”, to derive ecological features, such as breeding status and outcome, from RFID mark‐recapture data. To demonstrate the performance of RFIDeep with complex datasets, we used a long‐term automatic monitoring of a long‐lived seabird that breeds in densely packed colonies, hence with many daily entries and exits. To determine individual breeding status and phenology and for each breeding season, we first developed a one‐dimensional convolution neural network (1D‐CNN) architecture. Second, to account for variance in breeding phenology and technical limitations of field data acquisition, we built a new data augmentation step mimicking a shift in breeding dates and missing RFID detections, a common issue with RFIDs. Third, to identify the segments of the breeding activity used during classification, we also included a visualisation tool, which allows users to understand what is usually considered a “black box” step of deep learning. With these three steps, we achieved a high accuracy for all breeding parameters: breeding status accuracy = 96.3%; phenological accuracy = 86.9%; and breeding success accuracy = 97.3%. RFIDeep has unfolded the potential of artificial intelligence for tracking changes in animal populations, multiplying the benefit of automated mark‐recapture monitoring of undisturbed wildlife populations. RFIDeep is an open source code to facilitate the use, adaptation, or enhancement of RFID data in a wide variety of species. In addition to a tremendous time saving for analysing these large datasets, our study shows the capacities of CNN models to autonomously detect ecologically meaningful patterns in data through visualisation techniques, which are seldom used in ecology.

The experimental work focuses on the detailed monitoring of the interaction of commercial hydroxyapatite (HA) granules with various morphologies and surfaces with simulated body fluid (SBF) under varied in vitro test conditions. The ISO 23317:2014 standard, which specifies methods for the detection of apatite formation on the surface of materials in a simulated body fluid, mainly focuses on one-piece samples (tablets, rectangular shaped samples) under static conditions. The SBF solution modelling the inorganic part of blood plasma is buffered with a Tris buffer which can, under certain conditions, affect the in vitro test results by its own interaction with the tested material. Changes on the surfaces of the tested bioceramic granules with varied porosity and leachates from the buffered and unbuffered SBF solutions were characterised at selected time intervals using the available methods (SEM, BET, AAS, UV-VIS). The kinetics of the formation and morphology of the precipitated hydroxyapatite (HAp) was found to vary under different in vitro test conditions. The leachates from the solutions confirmed different rates of calcium and phosphate ions depletion, especially at the beginning of the assay. The pH analyses of the buffered and unbuffered SBF solutions also showed a Tris buffer effect.

Abstract Proteogenomic methodologies have enabled the identification of protein sequences in wild species without annotated genomes, shedding light on molecular mechanisms affected by pollution. However, proteomic resources for sentinel species are limited, and organ-level investigations are necessary to expand our understanding of their molecular biology. This study presents proteomic resources obtained from proteogenomic analyses of key organs (hepatopancreas, gills, hemolymph) from three established aquatic sentinel invertebrate species of interest in ecotoxicological/ecological research and environmental monitoring: Gammarus fossarum, Dreissena polymorpha, and Palaemon serratus. Proteogenomic analyses identified thousands of proteins for each species, with over 90% of them being annotated to putative function. Functional analysis validated the relevance of the proteomic atlases by revealing similarities in functional annotation of catalogues of proteins across analogous organs in the three species, while deep contrasts between functional profiles are delimited across different organs in the same organism. These organ-level proteomic atlases are crucial for future research on these sentinel animals, aiding in the evaluation of aquatic environmental risks and providing a valuable resource for ecotoxicological studies.

The prejudices often associated with the perception of people with disability can limit their access to the opportunities and resources available in society, leading them to live in a climate of great socio-economic uncertainty exacerbated since the COVID-19 pandemic. This research focuses on the perceptions of young people in France, defined as those aged between 18 and 30, towards people with disability. The study draws on the principles of social psychology to understand these perceptions, the factors that influence them and the most effective ways of promoting greater inclusion. A survey of 660 young people confirms that, despite recent progress, people with disabilities are still perceived as socially excluded. The results show that familiarity with disability, open-mindedness, the visibility of disability and the quality of interactions with people with disabilities have a strong influence on perceptions. To improve these perceptions, disability training and awareness raising are considered more effective than communication or positive discrimination measures. This research is the first to explore perceptions of disability among young people in France, with the potential to influence future behavior. It suggests ways to promote effective inclusive practices and support policies that encourage positive interactions with people with disabilities.

People have been exposed to the 900 MHz mobile phone electromagnetic field for approximately 30 years. There is still no conclusion from immature rodent experiments regarding the potential effects of nonthermal radiofrequency (RF) 900 MHz continuous wave exposure during biological development. Here, we test the hypothesis that mother rats exposed at a whole-body specific absorption rate (wbSAR) occupational (Oc) limit of the International Commission on Non-Ionizing Radiation Protection for humans (0.4 W/kg) will show impairments in development, with less effect at the public (Pu) limit (0.08 W/kg). The wbSAR was estimated at 0.4 W/kg to mimic working mothers (OcM exposure) and 0.08 W/kg for non-working mothers, i.e., public (PuM exposure). This pre- and postnatal study is the first to compare public and occupational exposure limits on rat pup physical development. Litter endpoints and the descendants’ body weights and lengths were recorded regularly from birth concomitantly with the age of developmental landmarks. Male neonates showed earlier pinna ear detachment and earlier eye opening in both the OcM and PuM groups, but earlier incisor eruption only in the PuM group. The OcM-exposed males showed lower body weight as juveniles until adolescence. The OcM- and PuM-exposed descendant females showed earlier pinna ear detachment and eye opening with similar body weight. These data suggest variations in the development time of descendant rats when the mother rats received daily 900 MHz continuous waves at human limits for workers and non-workers (public).

Abstract Background Current knowledge on prognostic biomarkers (especially BRAFV600E/RAS mutations) in metastatic colorectal cancer (mCRC) is mainly based on mCRC patients with proficient mismatch repair (pMMR) tumors. It is uncertain whether these biomarkers have the same prognostic value in mCRC patients with deficient mismatch repair (dMMR) tumors. Methods This observational cohort study combined a population‐based Dutch cohort (2014–2019) and a large French multicenter cohort (2007–2017). All mCRC patients with a histologically proven dMMR tumor were included. Results In our real‐world data cohort of 707 dMMR mCRC patients, 438 patients were treated with first‐line palliative systemic chemotherapy. Mean age of first‐line treated patients was 61.9 years, 49% were male, and 40% had Lynch syndrome. BRAFV600E mutation was present in 47% of tumors and 30% harbored a RAS mutation. Multivariable regression analysis on OS showed significant hazard rates (HR) for known prognostic factors as age and performance status, however showed no significance for Lynch syndrome (HR: 1.07, 95% CI: 0.66–1.72), BRAFV600E mutational status (HR: 1.02, 95% CI: 0.67–1.54), and RAS mutational status (HR: 1.01, 95% CI: 0.64–1.59), with similar results for PFS. Conclusion BRAFV600E and RAS mutational status are not associated with prognosis in dMMR mCRC patients, in contrast to pMMR mCRC patients. Lynch syndrome is also not an independent prognostic factor for survival. These findings underline that prognostic factors of patients with dMMR mCRC are different of those with pMMR, which could be taken into consideration when prognosis is used for clinical decision‐making in dMMR mCRC patients and underline the complex heterogeneity of mCRC.

Background: Grade of non–muscle-invasive bladder cancer (NMIBC) is an important prognostic factor for progression. Currently, two World Health Organization (WHO) classification systems (WHO1973, categories: grade 1–3, and WHO2004 categories: papillary urothelial neoplasm of low malignant potential [PUNLMP], low-grade [LG], high-grade [HG] carcinoma) are used. Objective: To ask the European Association of Urology (EAU) and International Society of Urological Pathology (ISUP) members regarding their current practice and preferences of grading systems. Design, setting, and participants: A web-based, anonymous questionnaire with ten questions on grading of NMIBC was created. The members of EAU and ISUP were invited to complete an online survey by the end of 2021. Thirteen experts had previously answered the same questions. Outcome measurements and statistical analysis: The submitted answers from 214 ISUP members, 191 EAU members, and 13 experts were analyzed. Results and limitations: Currently, 53% use only the WHO2004 system and 40% use both systems. According to most respondents, PUNLMP is a rare diagnosis with management similar to Ta-LG carcinoma. The majority (72%) would consider reverting back to WHO1973 if grading criteria were more detailed. Separate reporting of WHO1973-G3 within WHO2004-HG would influence clinical decisions for Ta and/or T1 tumors according the majority (55%). Most respondents preferred a two-tier (41%) or a three-tier (41%) grading system. The current WHO2004 grading system is supported by a minority (20%), whereas nearly half (48%) supported a hybrid three- or four-tier grading system composed of both WHO1973 and WHO2004. The survey results of the experts were comparable with ISUP and EAU respondents. Conclusions: Both the WHO1973 and the WHO2004 grading system are still widely used. Even though opinions on the future of bladder cancer grading were strongly divided, there was limited support for WHO1973 and WHO2004 in their current formats, while the hybrid (three-tier) grading system with LG, HG-G2, and HG-G3 as categories could be considered the most promising alternative. Patient summary: Grading of non–muscle-invasive bladder cancer (NMIBC) is a matter of ongoing debate and lacks international consensus. We surveyed urologists and pathologists of European Association of Urology and International Society of Urological Pathology on their preferences regarding NMIBC grading to generate a multidisciplinary dialogue. Both the “old” World Health Organization (WHO) 1973 and the “new” WHO2004 grading schemes are still used widely. However, continuation of both the WHO1973 and the WHO2004 system showed limited support, while a hybrid grading system composed of both the WHO1973 and the WHO2004 classification system may be considered a promising alternative.

Optical identification is often done with spatial or temporal visual pattern recognition and localization. Temporal pattern recognition, depending on the technology, involves a trade-off between communication frequency, range, and accurate tracking. We propose a solution with light-emitting beacons that improves this trade-off by exploiting fast event-based cameras and, for tracking, sparse neuromorphic optical flow computed with spiking neurons. The system is embedded in a simulated drone and evaluated in an asset monitoring use case. It is robust to relative movements and enables simultaneous communication with, and tracking of, multiple moving beacons. Finally, in a hardware lab prototype, we demonstrate for the first time beacon tracking performed simultaneously with state-of-the-art frequency communication in the kHz range.

Introduction: The Bacillus Calmette-Guérin (BCG) used as anti-tuberculous vaccine is also a well-known therapy for superficial urothelial cancer. Local or general side effects can occur, although it is generally well tolerated. Case: We present the case of a 65 year-old caucasian man consulting for gross hematuria and lower urinary tract symptoms. Magnetic resonance imaging (MRI) demonstrated a non-invasive urothelial carcinoma (NMIBC) and Prostate Imaging–Reporting and Data System (PIRADS) IV lesions. Transurethral resection of the bladder tumor revealed a non-invasive transitional cell carcinoma. Intravesical Bacillus Calmette Guerin (BCG) therapy was provided. After 6 intravesical instillations, the patient presented with prostato-epididymitis. Forthcoming BCG instillations were canceled, and cancer treatment was switched to epirubicine. Treatment with ethambutol, rifampicin and isoniazid was started with rapid resolution of the symptoms. Urinary and semen cultures grew Mycobacterium tuberculosis complex strain BCG. As prostate specific antigen (PSA) rose, prostate’s biopsies were performed showing extensive necrosis boarded by granulomas without signs of malignancy. Discussion: BCGitis is a rare complication in patients treated for non-invasive urothelial cancer. Several risk factors, local and systemic, should be considered prior to this immunotherapy. BCGitis (local or disseminated) or hypersensitivity reactions to BCG must be included in the differential diagnosis even if therapy was administered several years before the symptoms. Adequate treatment must be started as fast as possible to avoid serious complications.

Abstract Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome‐scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta‐)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third‐generation sequencing, and we discuss the opportunities of long‐read sequencing, strain‐level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.

The seasonal dynamics of esca leaf symptom development were monitored and modelled over 10 years (from 2004 to 2006, 2012 to 2014, and 2018 to 2021) in eleven vineyards near Bordeaux (France) and on five cultivars, including three susceptible and two tolerant Field observations performed once or twice a week from the end of May to mid-September confirmed i) the evolution over time of esca leaf symptoms, ii) the presence under the bark of a discolored xylem longitudinal stripe with nonfunctional vessels, and iii) a gradual increase in the number of symptomatic plants within each vineyard. Of the three models tested, nonlinear logistic regression was the best fitting curve, showing a clear and systematic progressive sigmoidal pattern of cumulative esca leaf symptom observations regardless of ‘vineyard*year’ situation. Relationships with climatic data confirmed that all periods of symptom expression corresponded to the warmest and driest period of each vegetative season. Examinations of key dates corresponding to four threshold levels of cumulative incidence of leaf symptomatic vines [S1 (first observed symptoms), S10 %, S50 % and S90 %] showed that tolerant cultivars (Merlot noir and Malbec) generally developed leaf symptoms later than susceptible cultivars (Cabernet-Sauvignon, Cabernet franc, and Sauvignon blanc). A variance analysis and a principal component analysis (PCA) confirmed that compared to susceptible cultivars, tolerant cultivars were associated with increased temperature sums above 10 °C from 1st January, reaching the same symptom thresholds S1 and S10 % and with more cumulative rainfall at the S1 stage. Overall, this study reveals the key role of temperature as a triggering factor for esca symptom expression in relation to fungal activity. The results indicate that the S10 % stage can be used as a discriminant variable to separate cultivars according to their susceptibility. Finally, logistic modelling can be used as a descriptive and analytical tool to study the seasonal dynamics of esca.