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We present a synthetic hydraulic analysis of the propagation of oscillatory perturbations in a two-dimensional saturated zone bounded above by a capillary fringe. Unsaturated flows are simulated in a physical model using a hysteretic form of Richards' equation parameterized using the van Genuchten water retention curve and the Mualem hydraulic conductivity equation for a sand, loam, and intermediate soil. Soil type affects periodic responses as a function of their hydrodynamic and van Genuchten properties. We first analyze the effect of various hydraulic or signal properties on the oscillatory responses simulated at different locations and depths. We then test the imaging potential of oscillatory responses recorded in the saturated zone to spatially charaterize homogeneous or heterogeneous soils, also considering the effect of period of oscillation. We find that a separation of these responses into amplitude/phase couples permits to dissociate the characterization of different hydraulic properties. Periodic amplitudes decay with distance mainly as a function of hydraulic conductivity and phase lags decrease with frequency due to storage in the capillary fringe. Thus, responses amplitude appears to be especially sensitive to conductivity K , which allows to isolate this property from the others. Phases can then be used to better characterize the vertical flows effect, through the Van Genuchten parameters α and n . Higher periods will tend to accentuate the unsaturated flows effect on the responses and can therefore be adopted for a better characterization of α and n . However, using low-period responses can also be useful, as they provide better estimates of conductivity values in media with low heterogeneities. We consider this work as a useful preliminary analysis for future sandbox or field real cases applications and provide advices for such applications in the discussion.

Background: Candida auris (C. auris) is an emerging healthcare-associated pathogen resulting in significant morbidity and mortality. The aim of this study is to report data from the national C. auris surveillance system for 2019 and conduct a survival analysis of the reported cohort. Methods: a retrospective analysis was conducted for all C. auris cases reported nationally to the Oman Antimicrobial Surveillance System (OMASS) in 2019, and isolates were sent to the Central Public Health Laboratories (CPHL). Clinical and demographic data were obtained through the E-Surveillance reporting system and the Electronic System (NEHR Al-Shifa) at CPHL. Statistical analysis was done using Kaplan–Meier analysis and Cox proportional hazard models. Results: One hundred and twenty-nine isolates of C. auris were grown from 108 inpatients; 87% were isolated from clinical samples, of which blood was the most common (38.9%). Forty (37%) were ≥65 years of age, 72 (66.7%) were males, and 85 (78.7%) were Omani nationals. Of the total isolates, 43.5% were considered as colonization; 56.5% were considered infection, of which 61.8% of them were candidemia. At least one risk factor was present in 98.1% of patients. The mean time from admission to infection was 1.7 months (SD = 2.8), and the mean length of hospital stay was 3.5 months (SD = 4). Totals of 94.8% and 96.1% of the isolates were non-susceptible to fluconazole and amphotericin, respectively. The variables found to be significantly associated with longer survival post C. auris diagnosis (p < 0.05) were age < 65 years, absence of comorbidities, length of stay < 3 months, colonization, and absence of candidemia. The infection fatality rate was 52.5%. Conclusion: Including C. auris in an ongoing antimicrobial surveillance program provides important data for the comprehensive management of this growing public health threat. The current study shows health care outbreaks of C. auris are ongoing, with 52.5% infection fatality, although our isolates remained sensitive to Echinocandins in vitro.

International audience; Monitoring groundwater level (GWL) over long time periods is critical in understanding the variability of groundwater resources in the present context of global changes. However, in Normandy (France) for example, GWLs have only been systematically monitored for ~20 to 50 years. This study evaluates Long Short-Term Memory (LSTM) neural network modeling to reconstruct GWLs, fill gaps and extend existing time-series. The approach is illustrated by using available monitoring fluctuations in piezometers implanted in the chalk aquifer in the Normandy region, Northern France. Here GWL data recorded over 50 years at 31 piezometers in northwestern Normandy is employed to perform GWL prediction. To optimize the network performance, the most influential factors that impact the accuracy of prediction are first determined, such as the network architecture, data quantity and quality. The resulting network is adopted to reconstruct measurements in the piezometers step by step with an increment of missing observation time. The approach requires no calibration for the time-lag in data processing and the implementation relies only on the groundwater level fluctuations to retrieve missing data in the targeted piezometers.

Objectives: To investigate the course of a community gastroenteritis outbreak by Salmonella and implement interventional activities and roles to prevent occurring such an outbreak in the future. Methods: From August 27 to 2 September 2015, 101 individuals were reported among a local community. All affected individuals had a history of food consumption at a local restaurant. A rapid response team conducted active surveillance and interview with the affected individuals and workers of the restaurant. Food items and stools from food handlers and affected individuals were cultured and sent for genotyping. An environmental audit of the restaurant had been conducted. Results: The total majority of the affected individuals were male and more than 70% belonged to the young age group from 15 to 45 years. Out of the total, 97% had diarrhea, 70% fever, 56% abdominal cramps and 49% vomiting. All those affected were managed symptomatically except for 14 cases admitted for intravenous rehydration. Breakdown of food safety and basic personal hygiene were detected in the environment of the restaurant and among the workers. There are 39 out of 49 stool cultures of cases, six out of 18 food handlers, and five food samples were positive for Salmonella spp. The identical DNA fingerprinting pattern among S. Weltevreden strains originating from human cases and food was detected. Conclusion: This is the first reported community foodborne of S. Weltevreden outbreak in Oman. The importance of food safety and rigors environmental safety is emphasized. Basic personal hygiene and training of food handlers in restaurants are recommended with public health measurements.

Highlights • Rt can be used to closely monitor the non-pharmaceutical interventions (NPI) of COVID-19 epidemic. • Generally, the activity of the epidemic in Oman. • Other factors, like the return of overseas students, have increased the epidemic activity. • Responses to NPI is different between migrants and natives., Background COVID-19’s emergence carries with it many uncertainties and challenges, one of which is epidemic management strategies. Oman has implemented non-pharmaceutical interventions (NPIs) to mitigate the impact of COVID-19. However, responses to NPIs may be different across different populations in a country with a large number of migrants like Oman. This study investigates the different responses to NPIs assessing the use of time-varying reproduction number (Rt) to monitor it. Methods Polymerase chain reaction (PCR) laboratory-confirmed COVID-19 data from Oman was used from February 24th to June 3rd, 2020 and included demographic and epidemiological information. Data were arranged into pairs of infector–infectee, and two main libraries of R software were used to estimate reproductive number (Rt). Rt was calculated for both Omanis and non-Omanis. Findings A total of 13,538 cases were included, 44·9% of which were Omanis. Among all, we identified 2769 infector–infectee pairs to calculate Rt. There was a sharp drop in Rt from 3·7, (95% confidence interval [CI] 2·8-4·6) mid-March to 1·4 (95% CI 1·2–1·7) in late March in response to NPIs. Then Rt decreased to 1·2 (95% CI 1·1–1·3) late April when it rose, corresponding to the easing up of NPIs. Comparing the two groups, the response to major public health controls was more evident in Omanis in reducing the Rt to 1·09 (95% CI 0·84–1·3) at the end of March. Interpretation Use of real-time estimation of Rt has allowed us to follow the effect of NPIs. The migrant population responds differently than the Omani population.

Objectives: The aim of the current study was to describe COVID-19’s epidemiological characteristics in Oman during the initial stages of the outbreak and compare findings with other countries’ reports. Methods: Data were drawn from a descriptive, records-based review of reported cases of COVID-19 collected through the national COVID-19 Surveillance System from February to April 2020. Results: A total of 2,443 confirmed cases were reported during the study period. The overall first-time testing rate for this period was 851.7 per 100,000, the positivity rate was 53.1 (confidence intervals [CI]: 51.0–55.2) and the death rate was 0.32 (CI: 0.20–0.54) per 100,000 population, respectively. The overall national positive ratio was 5.7% and ranged from 2.2–7.1% across various governorates. Muscat Governorate had the highest positive ratio (12.5%). People in the 51–60 year old age group (RR = 1.97), males (RR = 1.24), non-Omanis (RR = 2.33) and those living in Muscat (RR = 2.14) emerged as categories with significant demographic risk for COVID-19 cases when compared to the national average. The mean age was 35.6 ± 13.4. Asymptomatic cases accounted for nearly 16%. Conclusion: The overall rate of COVID-19 cases and deaths were low in Oman compared to the rest of the world during the study period. Keywords: Coronavirus; COVID-19; SARS-CoV2; Epidemiology; Pandemic; Oman.

Hydraulic characterization of a contaminated aquifer is an important step in depollution processes because its hydraulic parameters control the choice and efficiency of the depollution protocol to be adopted. The characterization presented in this article uses a 3D electrical resistivity imagery to identify the spatial heterogeneities of a contaminated aquifer under tidal influence. Indeed, we use a 3D resistivity model as a source of information to parameterize the reconstruction of the hydraulic conductivity in 3D by inverting a set of hydraulic data acquired on the 13 monitored wells in response to two pumping tests. This parameterization relies on the identification of the main electro-facies in the resistivity model in the saturated zone, which will then be exploited in the hydraulic characterization to find their corresponding hydraulic conductivity values. This strategy of parameterization permits to reduce the number of the hydraulic conductivity parameters to be identified to eight hydro-facies, with a stochastic algorithm called the Adaptive Metropolis Algorithm. The hydraulic responses associated with the pumping tests are obtained once the natural effect of the tide is removed. The hydraulic conductivity model has permitted to highlight the main heterogeneities in the aquifer in which the hydraulic conductivity is ranging between [10-4.6, 10-2.8 m/s]. This range of variability reveals the permeable and smooth character of the aquifer in which the presence of coarse sand and flint blocks enhances its transmissivity. These permeable zones are electrically identified by resistive anomalies in the 3D electrical resistivity imaging.

International audience; The paper deals with the identification of unknown storativity and transmissiv-ity distributions within a 2D confined aquifer using pumping tests. We introduce a change of variables that transforms the groundwater equation into a diffusion-reaction one, where the diffusion term is the fraction transmissivity/storativity whereas the reaction term yields the right hand side of a second order nonlinear partial differential equation satisfied by the unknown storativity function. Using records of the drawdown at some measuring wells within the monitored aquifer, we establish identifiability results on the introduced diffusion and reaction terms as well as on the storativity values at the employed wells. We develop an identification approach that starts by determining the auxiliary diffusion and reaction variables. Afterwards, this approach uses an assumption related to the incompressibility of water to develop a local determination procedure of the unknown storativity function. Besides, based on the interpolation of its values at the employed wells, a global determination procedure of this function is also developed. The unknown transmis-sivity is then determined by the product of the identified storativity and fraction transmissivity/storativity functions. Some numerical experiments are presented.

The prevalence of carbapenem-resistant Enterobacterales (CRE) in the Arabian Peninsula is predicted to be high, as suggested from published case reports. Of particular concern, is carbapenem-resistant E. coli (CR-EC), due to the importance of this species as a community pathogen. Herein, we conducted a comprehensive molecular characterization of putative CR-EC strains from Oman. We aim to establish a baseline for future molecular monitoring. We performed whole-genome sequencing (WGS) for 35 putative CR-EC. Isolates were obtained from patients at multiple centers in 2015. Genetic relatedness was investigated using several typing approaches such as MLST, SNP calling, phylogroup and CRISPR typing. Maxiuium likelihood SNP-tree was performed by RAxML after variant calling and removal of recombination regions with Snippy and Gubbins, respectively. Resistance genes, plasmid replicon types, virulence genes, and prophage were also characterised. The online databases CGE, CRISPRcasFinder, Phaster and EnteroBase were used for the in silico analyses. Screening for mutations in genes regulating the expression of porins and efflux pump as well as mutations lead to fluoroquinolones resistance were performed with CLC Genomics Workbench. The genetic diversity suggests a polyclonal population structure with 21 sequence types (ST), of which ST38 being the most prevalent (11%). SNPs analysis revealed possible transmission episodes. Whereas, CRISPR typing helped to spot outlier strains belonged to phylogroups other than B2 which was CRISPR-free. The virulent phylogroups B2 and D were detected in 4 and 9 isolates, respectively. In some strains bacteriophages acted as vectors for virulence genes. Regarding resistance to β-lactam, 22 were carbapenemase producers, 3 carbapenem non-susceptible but carbapenemase-negative, 9 resistant to expanded-spectrum cephalosporins, and one isolate with susceptibility to cephalosporins and carbapenems. Thirteen out of the 22 (59%) carbapenemase-producing isolates were NDM and 7 (23%) were OXA-48-like which mirrors the situation in Indian subcontinent. Two isolates co-produced NDM and OXA-48-like enzymes. In total, 80% (28/35) were CTX-M-15 producers and 23% (8/35) featured AmpC. The high-risk subclones ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC were detected, the latter associated with NDM. To our knowledge, this is the first report of ST1193-H64Rx subclone with NDM. In conclusion, strains showed polyclonal population structure with OXA-48 and NDM as the only carbapenemases in CR-EC from Oman. We detected the high-risk subclone ST131-H30Rx/C2, ST410-H24RxC and ST1193-H64RxC. The latter was reported with carbapenemase gene for the first time here.

Aim: The purpose of this viewpoint is to summarize the advantages and constraints of the tools and strategies available for reducing the annual incidence of tuberculosis (TB) by implementing the World Health Organization (WHO) End TB Strategy and the linked WHO TB Elimination Framework, with special reference to Oman. Methods: The case-study was built based on the presentations and discussions at an international workshop on TB elimination in low incidence countries organized by the Ministry of Health, Oman, which took place from September 5 to September 7, 2019, and supported by the WHO and European Society of Clinical Microbiology and Infectious Diseases (ESCMID). Results: Existing tools were reviewed, including the screening of migrants for latent TB infection (LTBI) with interferon-gamma release assays, clinical examination for active pulmonary TB (APTB) including chest X-rays, organization of laboratory services, and the existing centres for mandatory health examination of pre-arrival or arriving migrants, including examination for APTB. The need for public-private partnerships to handle the burden of screening arriving migrants for active TB was discussed at length and different models for financing were reviewed. Conclusions: In a country with a high proportion of migrants from high endemic countries, screening for LTBI is of high priority. Molecular typing and the development of public-private partnerships are needed. (C) 2020 Published by Elsevier Ltd on behalf of International Society for Infectious Diseases. Funding Agencies|WHOWorld Health Organization; ESCMID; Qiagen; Cepheid; Advanced Healthcare Solutions; PfizerPfizer; MSD; QIAGEN Sciences Inc.

In this manuscript, we discuss the capabilities of a deep learning algorithm implemented with the Conventional Neural Network concept to characterize the hydraulic properties of aquifers. The algorithm called CNN-HT is designed to predict the inverse operator of hydraulic tomography using a synthetic training dataset in which the hydraulic head data associated with pumping tests are linked to hydraulic transmissivity field. This approach relies on an adaptation of the SegNet network that was initially developed to process image segmentation. The SegNet is composed of encoders and decoders networks. In the encoder, sequential operations with multiple filters, as convolution, batch normalization, max-pooling are performed to identify feature maps of the input data. In the decoder, the up-sampling, convolution, batch normalization and regression operations are used to prepare the output by recovering the loss of spatial resolution that occurred in the encoder process. In this adaptation, we used the least-square iterative formulation at the initial iteration with Jacobian matrix to resize the hydraulic head data to match the size of the output (transmissivity field). This protocol was applied to the hydraulic head data computed numerically by solving the groundwater flow equation for a given transmissivity field, generated geostatistically with Gaussian and spherical variograms. A part of this data was used for training the network and the other part to test its performance. The test step confirmed the effectiveness of this tool in reconstructing the main heterogeneities of the hydraulic properties, and its effectiveness is related to the nature and quantity of the training data. Moreover, the CNN-HT method provided inversion results of the same quality than those obtained with the Gauss-Newton algorithm using the finite difference or adjoint state method in the computation of the Jacobian matrix. However, the computational time is longer in CNN-HT but this time can be less or of the same order as that of Gauss-Newton using finite difference method.

(IF 3.67; Q1); International audience; In this work, we present a novel method to interpret, at a field scale, the preferential flows generated by harmonic pumping tests, in which the pumped flowrate varies according to a sinusoidal function with a given period. The experimental protocol relies on the application of harmonic pumping tests in a karstic field located near to Montpellier (Southern France) at 4 different boreholes, each time with a shorter and a longer period, and the analysis of the hydraulic responses recorded at the 13 observation wells. A qualitative analysis of the oscillatory component in the hydraulic responses, in term of amplitude decay and phase lag, permitted to propose a preliminary model of degree of connectivity between the boreholes, through the network of conduits. Then, a quantitative interpretation of the harmonic responses was applied to image the spatial heterogeneity of the hydraulic properties (hydraulic conductivity and storage coefficient) by using a deterministic inverse algorithm called CADI. This algorithm is based on an equivalent porous medium concept and parameterized by a Cellular Automata approach in order to provide a realistic reconstruction of the karstic network. This algorithm is linked to the groundwater flow equation, reformulated in frequency domain, to simulate the amplitudes and phase shifts responses to the harmonic pumping tests. The inverse process was successfully applied on the dataset collected with both periods, in a separate and joint way. The results obtained allowed for a discussion on the efficiency of the harmonic pumping tomography for the characterization of the karstic structures.

To fulfil the World Health Organization (WHO) End TB strategy, screening for tuberculosis (TB) in immigrants is an important component of the strategy to reduce the TB burden in low-incidence countries. Oman has an annual TB incidence rate of 5.7 per 100000 and transmission from migrants with activated latent TB infection (LTBI) to nationals is a concern. The aim of this study was to determine the proportion of migrants to the Sultanate of Oman with LTBI. The study used an interferon-gamma release assay (IGRA) to assess previous exposure to TB, defining LTBI and a positive IGRA with a normal chest X-ray. 1049 subjects were surveyed. Six participants were excluded from the analysis as they had been recently vaccinated and 1 had an indeterminate result, thus 1042 subjects were included. The overall IGRA-positive rate was 22.4% (234/1042), 30.9% and 21.2% of African and Asian migrants, respectively, were IGRA-positive. Fifty-eight of the participants had a strong IGRA reactivity defined as more than 4 IU/ml. The study shows the proportion of migrants from Asia and Africa with LTBI and 24.7% (58/234) of IGRA-positive migrants had an IGRA of >4 IU/ml, defining a subpopulation with a high risk of developing active TB in the first two years of arrival to the country.

Background Influenza is a serious vaccine-preventable disease with high incidence, hospitalization, and mortality in high-risk groups. The epidemiology, seasonality, and risk factors for influenza are well defined in most of the temperate countries, but estimating influenza burden in the World Health Organization (WHO) Region for the Eastern Mediterranean is scarce. In Oman, despite the advancements in influenza surveillance, the clinical burden and seasonality of influenza remain not fully understood. Objectives To estimate the incidence of influenza-associated hospitalizations and in-hospital death in Oman. Patients and methods Influenza-associated hospitalizations and in-hospital deaths were estimated using hospital discharge records based on ICD-10 codes (J09-J18), results of virological analysis and population census for the period between 2012 and 2015. Results During 2012 and 2015, we identified a total of 19 405 influenza-associated hospitalization and 847 deaths. Influenza positivity percentage ranged from 6.4% in 2013 to 20.6% in 2015. Influenza-associated hospitalization incidence rate was 7.3 (95% CI: 6.4-8.1) per 100 000 in 2013 and 27.5 (95% CI: 25.9-29.1) per 100 000 in 2015 with an overall rate of 20.6 (95% CI: 19.9-21.3) per 100 000. The highest incidence of influenza-associated death was among those aged ≥65 years and ranged between 39.5 (95% CI: 27.3-51.8) per 100 000 in 2014 and 11.3 (95% CI: 7.5-15.1) in 2015. Conclusions Influenza causes a substantial number of hospitalizations and deaths in Oman. Hospitalization rates were highest among children, and adults ≥65 years showed the highest death rate. The potential value of using seasonal influenza vaccine in these groups should be considered.

Background: Immunological cross-reactivity between common cold coronaviruses (CCC) and SARS-CoV-2 might account for the reduced incidence of COVID-19 in children. Evidence to support speculation includes in vitro evidence for humoral and cellular cross-reactivity with SARS-CoV-2 in specimens obtained before the pandemic started. Method: We used retrospective health insurance enrollment records, claims, and laboratory results to assemble a cohort of 869,236 insured individuals who had a PCR test for SARS-CoV-2. We estimated the effects of having clinical encounters for various diagnostic categories in the year preceding the study period on the risk of a positive test result. Findings: After adjusting for age, gender and care seeking behavior, we identified that individuals with diagnoses for common cold symptoms, including acute sinusitis, bronchitis, or pharyngitis in the preceding year had a lower risk of testing positive for SARS-CoV-2 (OR=0.76, 95%CI=0.75, 0.77). No reduction in the odds of a positive test for SARS-CoV-2 was seen in individuals under 18 years. The reduction in odds in adults remained stable for four years but was strongest in those with recent common cold symptoms. Interpretation: While this study cannot attribute this association to cross-immunity resulting from a prior CCC infection, it is one potential explanation. Regardless of the cause, the reduction in the odds of being infected by SARS-CoV-2 among those with a recent diagnosis of common cold symptoms may have a role in shifting future COVD-19 infection patterns from endemic to episodic.

Objectives: Considering the increasing, significant burden that coronavirus disease 2019 (COVID-19) imposes on the healthcare system, the need for simple, rapid, and affordable diagnostic tests to support the existing costly and demanding polymerase chain reaction (PCR) assay becomes required. This prospective diagnostic test accuracy study aims to evaluate the performance of four different COVID-19 rapid antigen tests compared to real-time reverse transcription PCR (rRT-PCR) between June and July 2020 to determine the feasibility of integrating these tests into the diagnostic algorithm in clinical settings. Methods: Swabs were collected from 306 patients and analyzed using rRT-PCR and antigen tests from four different providers. Results: The antigen tests’ sensitivities were 65.8%, 69.8%, 64.0%, and 64.3% for the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid fluorescent immunoassay (FIA) test, BIOCREDIT COVID-19 Ag test, and Sofia SARS-CoV-2 antigen FIA test, respectively. Specificity was 94.1% for PCL COVID-19 Ag Rapid test and 100% for the other three assays. All assays showed a significant negative correlation between the reference rRT-PCR Ct values and Ag test results. Besides, sensitivities of the STANDARD™ Q COVID-19 Ag test, PCL COVID-19 Ag Rapid FIA test, and BIOCREDIT COVID-19 Ag test improved to ≥ 85% after exclusion of samples with PCR Ct values > 30. Conclusions: The high specificity of the rapid antigen tests and other parameters like simplicity, rapidity, and affordability suggest that antigen tests are likely to be helpful if integrated and interpreted appropriately in stepwise diagnostic algorithms. Given the low sensitivity of 64.0–69.8% of the antigen tests, we recommend that clinically relevant negative results undergo further testing Ag to confirm or exclude a COVID-19 diagnosis.

Objectives: Previously, web-based tools for cross-sectional antimicrobial point prevalence surveys (PPSs) have been used in adults to develop indicators of quality improvement. We aimed to determine the feasibility of developing similar quality indicators of improved antimicrobial prescribing focusing specifically on hospitalized neonates and children worldwide. Methods: A standardized antimicrobial PPS method was employed. Included were all inpatient children and neonates receiving an antimicrobial at 8:00 am on the day of the PPS. Denominators included the total number of inpatients. A web-based application was used for data entry, validation and reporting. We analysed 2012 data from 226 hospitals (H) in 41 countries (C) from Europe (174H; 24C), Africa (6H; 4C), Asia (25H; 8C), Australia (6H), Latin America (11H; 3C) and North America (4H). Results: Of 17693 admissions, 6499 (36.7%) inpatients received at least one antimicrobial, but this varied considerably between wards and regions. Potential indicators included very high broad-spectrum antibiotic prescribing in children of mainly ceftriaxone (ranked first in Eastern Europe, 31.3%; Asia, 13.0%; Southern Europe, 9.8%), cefepime (ranked third in North America, 7.8%) and meropenem (ranked first in Latin America, 13.1%). The survey identified worryingly high use of critically important antibiotics for hospital-acquired infections in neonates (34.9%; range from 14.2% in Africa to 68.0% in Latin America) compared with children (28.3%; range from 14.5% in Africa to 48.9% in Latin America). Parenteral administration was very common among children in Asia (88%), Latin America (81%) and Europe (67%). Documentation of the reasons for antibiotic prescribing was lowest in Latin America (52%). Prolonged surgical prophylaxis rates ranged from 78% (Europe) to 84% (Latin America). Conclusions: Simple web-based PPS tools provide a feasible method to identify areas for improvement of antibiotic use, to set benchmarks and to monitor future interventions in hospitalized neonates and children. To our knowledge, this study has derived the first global quality indicators for antibiotic use in hospitalized neonates and children., peer-reviewed

International audience; The flow of the ground water in an aquifer or during pumping test generates an electrical current (called the streaming current), which is of advective nature. The resulting electrical field (streaming potential field, one of the components of the self-potential field) can be remotely measured at the ground surface or in boreholes. We first discuss the underlying physics of this electrokinetic effect and the role of the electrical double layer coating the surface of the grains. We show how the drag of the excess of electrical charge of the pore water by the flow is equivalent to a source current density. Then, we discuss the metrological aspects, the type of voltmeter and electrodes required to carry out good measurements in field conditions. Two applications are discussed in steady-state conditions. The first is dedicated to the flow of water in shallow aquifers. In this case, the streaming current and the conduction current are nearly balanced and, inside the aquifer, the electrical equipotentials mimic the hydraulic equipotentials. They have, however, the advantage to extend the shape of these hydraulic equipotentials up to the ground surface. The second case is related to the flow of water in the vadose zone, here again investigated in steady-state conditions. In this situation, the vadose zone is polarized and the ground surface electrical potential map reflects essentially the depth of the vadose zone. A case study is shown for a small watershed in the South of France. The resistivity tomography shows no contrast in resistivity between the vadose zone and the aquifer and the observed self-potential data are observed to be linearly correlated to the depth of the water table.

(IF 3.73; Q1); International audience; We apply a stochastic Newton (SN) approach to solve a high-dimensional hydraulic inverse problem in highly heterogeneous geological media. By recognizing the connection between the cost function of deterministic optimizations and the posterior probability density of stochastic inversions, the Markov chain Monte Carlo (MCMC) sampler of SN is constructed by two parts: a deterministic part, which corresponds to a Newton step of deterministic optimization, and a stochastic part, which is a Gaussian distribution with the inverse of the local Hessian as the covariance matrix. The hybrid inverse method exploits the efficient tools for fast solution of deterministic inversions to improve the efficiency of the MCMC sampler. To address the ill-posedness of the inverse problem, a priori models, generated by a transition-probability geostatistical method, and conditioned to inter-well connection data, are used as regularization constraints.The effectiveness of the stochastic Newton method is first demonstrated by a synthetic test. The transmissivity field of the synthetic model is highly heterogeneous, and includes sharp variations. The inverse approach was then applied to a field hydraulic tomography investigation in a fractured and karstified aquifer to reconstruct its transmissivity field from a collection of real hydraulic head measurements. From the inversions, a series of transmissivity fields that produce good correlations between the inverted and the measured hydraulic heads were obtained. The inverse approach produced slightly different a posteriori transmissivity patterns for different a priori structure models of transmissivity; however, the trend and location of the high-transmissivity channels are consistent among various realizations. In addition, the uncertainty associated with each realization of the inverted transmissivity fields was quantified.

(IF 1.06; Q3); International audience; Hydrocarbon contamination, which can alter the physiochemical and biological properties of the subsurface, can be monitored by using geochemical analyses and integrated geophysical techniques. Electrical resistivity tomography, induced polarization, ground-penetrating radar, and self-potential methods were used in this work to characterise the hydrocarbon contamination and investigate the geoelectrical properties of a site impacted by an aged hydrocarbon plume. Throughout the investigation, geoelectrical measurements supported the conductive plume model and consistently recorded low-resistivity anomalies and high-chargeability values in the contaminated aquifer. Furthermore, the low-resistivity anomalies were found to be coincident with regions of ground-penetrating radar attenuated reflections and significant negative self-potential anomalies associated with oxidation– reduction processes. These findings were supported by the geochemical measurements, which revealed depleted concentrations of terminal electron acceptors (TEAs) and elevated amounts of ions and total dissolved solids, which could be attributed to bacterial biodegradation of hydrocarbons. The study showed that biological alterations of hydrocarbon-induced subtle changes in the pore water biogeochemistry, which consequently modified the geophysical properties of the contaminated sediments. Based on these observations, the extent of groundwater contamination was delineated according to the geophysical contrast between the contaminated and clean zones. The combination of different geophysical methods constrained by geochemical point measurements provided insight on the different processes that might have modified the soil and groundwater biogeochemical properties.

Melioidosis is an infectious disease caused by the bacterium Burkholderia pseudomallei. It is most commonly described in Southeast Asia and Northern Australia and some imported cases in non-endemic areas. We describe the case of a 55-year-old Omani man with fulminant sepsis who worked in Laos, Cambodia. B. pseudomallei was isolated from the patient’s blood and was identified by means of microbiological and biochemical tests. We highlight the importance of careful attention to non-fermentative gram-negative rods in a septic patients who have worked or travelled to Southeast Asia.

(IF 3.67 [2018]; Q1); International audience; Clogging due to transport and accumulation of the colloids in the pore space has been recognized as one of the most significant challenges in water management research and environmental engineering. This paper proposes an inversion algorithm in time-lapse mode to track that complex process through the assessment of alteration in the transmissivity field produced by the injection of colloids. The concept is based on a joint inversion of hydraulic head and colloidal particles concentration data acquired during the injection of colloids in the porous aquifer to reconstruct the spatial variability of the transmissivity field at different times. The inversion code is deterministic and was implemented in the time-lapse scheme by adding in the objective function a temporal geostatistical constraint to control changes of the hydraulic transmissivity. This algorithm is linked to a forward problem that consists of the groundwater flow and transport equations, which were solved numerically and jointly by considering the effect of particles deposition on the decrease of hydraulic properties. As the inverse problem is deterministic and underdetermined, we have opted to use the efficient adjoint state technique to derive the sensitivity matrices. The approach has been successfully applied to a theoretical case in which the hydraulic head responses have been used alone and jointly to assess the evolution of the clogging impact on hydraulic transmissivity.

Background: In December 2018, routine surveillance identified an autochthonous outbreak of dengue fever in Muscat Governorate, Oman, a region previously free of dengue fever. Methods: Routine surveillance confirmed locally acquired cases in the second week of December, leading to a rapid public health response including case management guidance and epidemiological investigations. The main activity was the vector survey using systematic sampling to assess extent of previously unreported Aedes aegypti presence followed by a campaign aimed to eliminate breeding sites of A. aegypti”. Results: During a 5-month period, 343 suspected cases were reported from Muscat Governorate with 122 from the outbreak affected area. Out of 207 probable cases eligible for laboratory testing as per guidelines issued, 59 cases were confirmed. The vector elimination campaign started on January 8, 2019 after a media advocacy using television and social media and concluded on January 23. By the end of campaign, the case load had decreased significantly in the affected area with no reports of locally acquired cases from adjoining areas of Muscat Governorate, indicating no further spread. Conclusions: Rapid notification and early community-wide, extensive vector control activities effectively contained the autochthonous dengue fever virus outbreak. Keywords: Dengue fever, Autochthonous outbreak, Oman, Aedes aegypti, Vector-borne illness, Disease surveillance

(IF 3.19 [2018]; Q1); International audience; The study on the hydraulic properties of coastal aquifers has significant implications both in hydrological sciences and environmental engineering. Although many analytical solutions are available, most of them are based on the same basic assumption that assumes aquifers extend landward semi‐infinitely, which does not necessarily reflect the reality. In this study, the general solutions for a leaky confined coastal aquifer have been developed that consider both finitely landward constant‐head and no‐flow boundaries. The newly developed solutions were then used to examine theoretically the joint effects of leakage and aquifer length on hydraulic head fluctuations within the leaky confined aquifer, and the validity of using the simplified solution, which assumes the aquifer is semi‐infinite. The results illustrated that the use of the simplified solution may cause significant errors, depending on joint effects of leakage and aquifer length. A dimensionless characteristic parameter was then proposed as an index for judging the applicability of the simplified solution. In addition, practical application of the general solution for the constant‐head inland boundary was used to characterize the hydraulic properties of a leaky confined aquifer using the data collected from a field site at the Seine River estuary, France, and the versatility of the general solution was further justified.

International audience

(IF 3.91 [2018]; Q1); International audience; The self-potential method can be used to detect and monitor anomalous seepages in dams and embankments. In such a case, an electrical field of electrokinetic nature (i.e., associated with pore water flow) can be measured using a set of non-polarizable electrodes typically located at the ground surface or in some wells. This field can be in turn related to the pattern of groundwater flow. We built an experimental dam to investigate to which extent the self-potential method can help characterizing seepages in dams. We first use the finite element method to simulate the ground water flow in a heterogeneous porous and permeable material by solving the groundwater flow equation. The resulting groundwater flow solution is then used to compute the electrical potential distribution by solving the corresponding elliptic partial differential equation. In a preliminary experiment, we could not measure any self-potential anomaly associated with the infiltration of water in the dam. Our numerical simulations showed that the magnitudes of the self-potential anomalies were controlled by (1) the nature of the flow regime (viscous laminar versus inertial laminar flow regimes) and (2) the presence of insulating Polyvinyl Chloride (PVC) tubes located at the end of the preferential flow channels in the structure of the dam. Thanks to these numerical simulations, we added sand at the entrance of the infiltration area in order to reduce the effects of the PVC tubes and to restrain the flow regime to the viscous laminar flow regime. New experiments allowed for detecting a self-potential anomaly with an amplitude of around −9 mV consistent with that obtained through numerical modelling with a finite element simulator. This comparison was used to test the accuracy of the modelling approach and define the strengths and weaknesses of the self-potential method to determine preferential seepages in earth dam structures.

Background Crimean-Congo hemorrhagic fever (CCHF) is a serious disease with a high fatality rate reported in many countries. The first case of CCHF in Oman was detected in 1995 and serosurveys have suggested widespread infection of humans and livestock throughout the country. Methodology Cases of CCHF reported to the Ministry of Health (MoH) of Oman between 1995 and 2017 were retrospectively reviewed. Diagnosis was confirmed by serology and/or molecular tests in Oman. Stored RNA from recent cases was studied by sequencing the complete open reading frame (ORF) of the viral S segment at Public Health England, enabling phylogenetic comparisons to be made with other S segments of strains obtained from the region. Findings Of 88 cases of CCHF, 4 were sporadic in 1995 and 1996, then none were detected until 2011. From 2011–2017, incidence has steadily increased and 19 (23.8%) of 80 cases clustered around Eid Al Adha. The median (range) age was 33 (15–68) years and 79 (90%) were male. The major risk for infection was contact with animals and/or butchering in 73/88 (83%) and only one case was related to tick bites alone. Severe cases were over-represented: 64 (72.7%) had a platelet count < 50 x 109/L and 32 (36.4%) died. There was no intrafamilial spread or healthcare-associated infection. The viral S segments from 11 patients presenting in 2013 and 2014 were all grouped in Asia 1 (IV) lineage. Conclusions CCHF is well-established throughout Oman, with a single strain of virus present for at least 20 years. Most patients are men involved in animal husbandry and butchery. The high mortality suggests that there is substantial under-diagnosis of milder cases. Preventive measures have been introduced to reduce risks of transmission to animal handlers and butchers and to maintain safety in healthcare settings., Author summary Crimean-Congo hemorrhagic fever, an often fatal tick-borne viral disease, has made an impact in the Sultanate of Oman—affecting nationals and expatriates alike—for the past 20 years. In this retrospective review of the epidemiology and outcomes of cases in Oman from 1995 to 2017, we identified 4 sporadic cases in 1995 and 1996, then none until 2011, followed by a steady increase until 2017. The mortality rate of 32 of 88 cases (36.4%) is high in comparison to studies from other countries and this could be explained by under-diagnoses of milder cases in the Sultanate. Transmission is commonly associated with animal husbandry and butchering and 88% cases were infected by contact with animals, whereas transmission by tick bite is more commonly recorded in some countries. A proportion of cases (23.8%) were clustered around the Eid-Al-Ahda festival which has, from 2011–2017, occurred in the summer months, which have a higher risk of transmission. This additional risk has been noted and preventive measures have been introduced to reduce the risk of transmission to animal handlers and butchers.