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Genome-wide association mapping studies (GWAS) based on Big Data are a potential approach to improve marker-assisted selection in plant breeding. The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing. Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects, but is hindered by data heterogeneity and lack of interoperability. In this study, we used genomic and phenotypic data sets, focusing on Central European winter wheat populations evaluated for heading date. We explored strategies for integrating these data and subsequently the resulting potential for GWAS. Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols, resulting in high quality integrated phenotypic data. In this context, genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series, which was low in our case. Contrary to expectations, fewer associations between markers and traits were found in the larger combined data than in the individual experimental series. However, the predictive power based on the marker-trait associations of the integrated data set was higher across data sets. Therefore, the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS. The results encourage further efforts to standardize and share data in the plant breeding community.

Abstract Background Despite dengue virus (DENV) outbreak in Gabon a decade ago, less is known on the potential circulation of DENV serotypes in the country. Previous studies conducted in some areas of the country, are limited to hospital-based surveys which reported the presence of some cases of serotype 2 and 3 seven years ago and more recently the serotype 1. As further investigation, we extend the survey to the community of Moyen Ogooué region with the aim to assess the presence of the dengue virus serotypes, additionally to characterize chikungunya (CHIKV) infection and describe the symptomatology associated with infections. Method A cross-sectional survey was conducted from April 2020 to March 2021. The study included participants of both sexes and any age one year and above, with fever or history of fever in the past seven days until blood collection. Eligible volunteers were clinically examined, and blood sample was collected for the detection of DENV and CHIKV using RT-qPCR. Positive samples were selected for the target sequencing. Results A total of 579 volunteers were included. Their mean age (SD) was 20 (20) years with 55% of them being female. Four cases of DENV infection were diagnosed giving a prevalence of 0.7% (95%CI: 0.2–1.8) in our cohort while no case of CHIKV was detected. The common symptoms and signs presented by the DENV cases included fatigue, arthralgia myalgia, cough, and loss of appetite. DENV-1was the only virus detected by RT-qPCR. Conclusion Our results confirm the presence of active dengue infection in the region, particularly DENV-1, and could suggest the decline of DENV-2 and DENV-3. Continuous surveillance remains paramount to comprehensively describe the extent of dengue serotypes distribution in the Moyen-Ogooué region of Gabon.

BackgroundLoiasis is a disease of relevance in endemic populations and there has been advocacy for its inclusion on the World Health Organization's neglected tropical diseases list. As loiasis-related healthcare-seeking behaviors and related costs are unknown, we aimed to evaluate these aspects in a population residing in an endemic region in Gabon.MethodsData were collected during a community-based, cross-sectional study assessing the disease burden due to loiasis. Diagnostics for microfilaremia were performed and a history of eyeworm was obtained. In addition, a standardized questionnaire about type of healthcare resources and frequency of use, as well as respective associated costs was administered to each participant. Loiasis related healthcare-seeking behaviors were evaluated, and the associated monetary burden was estimated as a secondary outcome of the study.FindingsIndividuals diagnosed with loiasis more frequently reported any healthcare-seeking (OR 1.52 (95%CI: 1.21-1.91)), self-medicating (OR 1.62 (1.26-2.08)), inability to work (OR 1.86 (1.47-2.35)), and consulting with traditional healers (logOdds 1.03 (0.52-1.53)), compared to loiasis negative individuals. The most frequently reported treatment for the eyeworm was traditional herbs. The estimated healthcare associated costs, per positive individual, was US-$ 58 (95% CI: 21-101) per year, which would correspond to 3.5% of the reported mean household income. Extrapolation to the rural population of Gabon (n = 204,000), resulted in an annual monetary burden estimate of US-$ 3,206,000 (1,150,000-5,577,000).InterpretationLoiasis patients have demonstrated healthcare needs, often consulted traditional healers, and used traditional treatments for disease specific symptoms. Further, loiasis seems to be associated with substantial direct and indirect costs for individuals and thus may cause a relevant economic burden for endemic populations and economies of affected countries.

Abstract To facilitate a prospective estimation of the effective dose of an CT scan prior to the actual scanning in order to use sophisticated patient risk minimizing methods, a prospective spatial dose estimation and the known anatomical structures are required. To this end, a CT reconstruction method is required to reconstruct CT volumes from as few projections as possible, i.e. by using the topograms, with anatomical structures as correct as possible. In this work, an optimized CT reconstruction model based on a generative adversarial network (GAN) is proposed. The GAN is trained to reconstruct 3D volumes from an anterior-posterior and a lateral CT projection. To enhance anatomical structures, a pre-trained organ segmentation network and the 3D perceptual loss are applied during the training phase, so that the model can then generate both organ-enhanced CT volume and organ segmentation masks. The proposed method can reconstruct CT volumes with PSNR of 26.49, RMSE of 196.17, and SSIM of 0.64, compared to 26.21, 201.55 and 0.63 using the baseline method. In terms of the anatomical structure, the proposed method effectively enhances the organ shapes and boundaries and allows for a straight-forward identification of the relevant anatomical structures. We note that conventional reconstruction metrics fail to indicate the enhancement of anatomical structures. In addition to such metrics, the evaluation is expanded with assessing the organ segmentation performance. The average organ dice of the proposed method is 0.71 compared with 0.63 for the baseline model, indicating the enhancement of anatomical structures.

Abstract Background Gabon still bears significant malaria burden despite numerous efforts. To reduce this burden, policy-makers need strategies to design effective interventions. Besides, malaria distribution is well known to be related to the meteorological conditions. In Gabon, there is limited knowledge of the spatio-temporal effect or the environmental factors on this distribution. This study aimed to investigate on the spatio-temporal effects and environmental factors on the distribution of malaria prevalence among children 2–10 years of age in Gabon. Methods The study used cross-sectional data from the Demographic Health Survey (DHS) carried out in 2000, 2005, 2010, and 2015. The malaria prevalence was obtained by considering the weighting scheme and using the space–time smoothing model. Spatial autocorrelation was inferred using the Moran’s I index, and hotspots were identified with the local statistic Getis-Ord General Gi. For the effect of covariates on the prevalence, several spatial methods implemented in the Integrated Nested Laplace Approximation (INLA) approach using Stochastic Partial Differential Equations (SPDE) were compared. Results The study considered 336 clusters, with 153 (46%) in rural and 183 (54%) in urban areas. The prevalence was highest in the Estuaire province in 2000, reaching 46%. It decreased until 2010, exhibiting strong spatial correlation (P

BackgroundMore than 20 million people are infected with L. loa, and around 40 million live in high or intermediate-risk areas in West- and Central Africa. Although loiasis is associated with significant morbidity and excess mortality, little is known about the perception of loiasis by affected communities. This study assessed the knowledge, attitudes, and practices in the rural population of Sindara, Gabon, a region characterized by high loiasis prevalence.MethodsA community-based cross-sectional survey was conducted in Gabon between January and June 2022. During systematic door-to-door visits, randomly selected inhabitants were invited to participate in this questionnaire based survey. Venous blood was collected at midday from all participants for microscopic detection of filarial infection and clinical signs of loiasis were assessed.ResultsA total of 150 participants were recruited, of which 66% were infected by L. loa. While almost everyone had some knowledge about L. loa, 72% of the participants understood that L. loa is a parasitic worm. The transmission of L. loa via the deer fly was known to only 21% of participants. The most frequently mentioned clinical symptoms attributed to loiasis were itching (84%), eye worm migration (59%), and conjunctivitis-like symptoms (53%). Participants who experienced migratory loiasis had better knowledge of loiasis and considered it as more serious. Traditional and herbal medicine was reported most often as an available treatment option (72%). While the formal healthcare sector was mentioned as the preferred treatment provider, 60% of the reported infections were treated by traditional medical practitioners.ConclusionLoiasis is in general well known by this community residing in a region of high L. loa transmission. Important gaps in knowledge were discovered foremost regarding the mode of transmission. The available healthcare system does not seem to provide adequate management for loiasis.

BackgroundThe parasitic disease loiasis is associated with significant morbidity and mortality. Individuals with hyper-microfilaremia (greater than 20,000 microfilariae per mL of blood) may suffer from serious treatment-related or spontaneous adverse events. Diagnosing loiasis remains complex and primarily relies on direct parasite detection. In this study, we analyzed the performance of various diagnostic tests and the influence of parasitological and clinical factors on test outcomes in samples from individuals living in an endemic region.MethodsData and samples were collected from rural Gabon. Loiasis was defined as either detectable microfilaremia, or a positive history of eyeworm as assessed by the RAPLOA questionnaire. Diagnostic testing included a quantitative PCR (qPCR) for detection of Loa loa DNA in blood samples, an in-house crude L. loa antigen IgG ELISA, and a rapid test for antibodies against the Ll-SXP-1 antigen (RDT). Sensitivity and specificity were determined for each test and factors potentially influencing outcomes were evaluated in an exploratory analysis.ResultsELISA, RDT and qPCR results were available for 99.8%, 78.5%, and 100% of the 1,232 participants, respectively. The ELISA and RDT had only modest diagnostic accuracy. qPCR was specific for L. loa microfilaremia and Cycle threshold values correlated with microfilarial density. Anti-L. loa IgG levels were highest in occult loiasis, and antibody levels correlated inversely with L. loa microfilarial density as did RDT line intensities. Only 84.6% and 16.7% of hyper-microfilaremic individuals tested positive by ELISA (11/13) and RDT (2/12), respectively.ConclusionNone of the tests demonstrated high sensitivity and specificity for loiasis. Indirect diagnostic assays were characterized by low specificity. Additionally, hyper-microfilaremic individuals often tested negative by RDT and ELISA, indicating that these tests are not suitable for individual case management in endemic populations.

Abstract Background Aedes albopictus and Aedes aegypti are known for their potential as vectors of dengue (DENV) and chikungunya (CHIKV) viruses. However, entomological surveys are mostly carried out during epidemics. In Gabon where outbreaks of both viruses have occurred, there is no vector control program targeting these arboviruses. Therefore, we assessed the presence of Aedes species along a rural–urban gradient in Lambaréné (Gabon) and its surroundings and determined ecological factors associated to their presence. Methods An entomological survey was conducted in Lambaréné and its surrounding rural areas. Mosquitoes were collected with aspirators around human dwellings, and ecological and environmental data were collected from each study area. Morphological identification keys were used to identify Aedes species. RNA was extracted from pools of female mosquitoes and amplified by RT-qPCR to detect the presence of DENV and CHIKV. Results Overall, the most common vector collected was Aedes albopictus (97%, 4236/4367 specimens), followed by Aedes aegypti (3%, 131/4367). Albopictus vectors was more abundant in the rural area (Wilcoxon signed-rank test, Z = 627, P = 0.043) than in the urban area. In the urban area, a higher number of mosquitoes (45%) were recorded in the economic zone (zone 3) than in the historical and administrative zones (zone 1 and 2). In the rural area, the proportions of species numbers were significantly higher along the south rural transect (92%) compared to the north rural transect (Wilcoxon signed-rank test, Z = 43, P ˂ 0.016). We also noted a high abundance of vectors in environments characterized by monocultures of Hevea brasiliensis (Hevea) and Manihot esculenta (cassava) (Kruskal–Wallis H-test, H = 25.7, df = 2, P

Abstract Background Non-tuberculous mycobacteria (NTM) are a group of bacteria that cause rare lung infections and are increasingly recognized as causative agents of opportunistic and device-associated infections in humans. In Gabon, there is a lack of data on NTM species identification and drug susceptibility. The aim of this study was to identify the frequency of NTM species and their genotypic susceptibility pattern to commonly used antibiotics for NTM infections in Gabon. Methods A cross-sectional study was conducted at the CERMEL TB laboratory from January 2020 to December 2022, NTM subspecies identification and drug susceptibility testing to macrolides and aminoglycosides were performed using the genotype NTM-DR kit. Results The study found that out of 524 culture-positive specimens, 146 (28%) were NTM, with the predominant group being Mycobacterium avium complex (MAC) and Mycobacterium abscessus complex (MABC). All MAC isolates were fully susceptible to macrolides and aminoglycosides, while five MABC isolates carried mutations indicative of reduced susceptibility to macrolide and aminoglycoside drugs. Conclusions These findings suggest that clinicians may use macrolides and aminoglycosides to manage NTM infections caused by MAC, but further investigation is required to determine MABC drug susceptibility.

Objectives: Malaria is still one of the main reasons for hospitalization in children living in sub-Saharan Africa. Rapid risk stratification at admission is essential for optimal medical care and improved prognosis. Whereas coma, deep breathing, and, to a lesser degree, severe anemia are established predictors of malaria-related death, the value of assessing prostration for risk stratification is less certain. Methods: Here we used a retrospective multi-center analysis comprising over 33,000 hospitalized children from four large studies, including two observational studies from the Severe Malaria in African Children network, a randomized controlled treatment study, and the phase-3-clinical RTS,S-malaria vaccine trial, to evaluate known risk factors of mortality and with a specific emphasis on the role of prostration. Results: Despite comparable age profiles of the participants, we found significant inter- and intra-study variation in the incidence of fatal malaria as well as in the derived risk ratios associated with the four risk factors: coma, deep breathing, anemia, and prostration. Despite pronounced variations, prostration was significantly associated with an increased risk of mortality (P

Acute respiratory infections are a major global burden in resource-limited countries, including countries in Africa. Although COVID-19 has been well studied since the pandemic emerged in Gabon, Central Africa, less attention has been paid to other respiratory viral diseases, and very little data are available. Herein, we provide the first data on the genetic diversity and detection of 18 major respiratory viruses in Gabon during the COVID-19 pandemic. Of 582 nasopharyngeal swab specimens collected from March 2020 to July 2021, which were SARS-CoV-2 negative, 156 were positive (26%) for the following viruses: enterovirus (20.3%), human rhinovirus (HRV) (4.6%), human coronavirus OC43 (1.2%), human adenovirus (0.9%), human metapneumovirus (hMPV) (0.5%), influenza A virus (IAV) (0.3%), and human parainfluenza viruses (0.5%). To determine the genetic diversity and transmission route of the viruses, phylogenetic analyses were performed using genome sequences of the detected viruses. The IAV strain detected in this study was genetically similar to strains isolated in the USA, whereas the hMPV strain belonging to the A2b subtype formed a cluster with Kenyan strains. This study provides the first complete genomic sequences of HRV, IAV, and hMPV detected in Gabon, and provides insight into the circulation of respiratory viruses in the country.

Snakebite envenoming (SBE) is a neglected tropical disease (NTD). Community-based studies from sub-Saharan Africa are urgently required as data on the incidence are scarce. This study aimed to determine the lifetime prevalence of snakebites in rural Gabon by preparing the conduct of a larger regional survey. A cross-sectional community-based epidemiological survey in Sindara, Ngounie province, was conducted. Households were interviewed about the history of snakebites of household members to calculate lifetime prevalence. In addition, the average annual incidence rate per 100,000 over the last 5 years was calculated. A total of 771 inhabitants were enrolled, of which 5 (0.65%; 95% confidence interval (95% CI: 0.2–1.5%)) were victims of snakebites. Over the past 5 years, annual incidence was 77 bites per 100,000 (95% CI: 0–620). This study provides a first rough estimate of the incidence of SBE from rural central Gabon, demonstrating the importance of this NTD. Key Contribution: The estimated annual incidence of snakebites found was 77 per 100,000. Snakebites occurred mainly during agricultural activities.

BackgroundThere is a lack of systematic evidence for strategies to control loiasis transmission in highly endemic regions. Here we assessed albendazole and ivermectin based treatment regimens to reduce Loa loa microfilaraemia in Gabon.MethodsEligible adult patients with L. loa microfilaraemia between 5,000 and 50,000 microfilariae/ml were randomized to either a control or one of three intervention groups (1:2:2:2 allocation ratio) consisting of three-week twice daily 400mg oral albendazole followed by 1) no treatment, 2) two further weeks of twice daily 400mg albendazole, or 3) a single dose of ivermectin in this open label randomized assessor blinded controlled clinical trial. The primary outcome was the proportion of participants with L. loa microfilaraemia ≤ 100 mf/ml at Day 168.ResultsIn the efficacy-population of 42 patients 0 (0%; control group), 1 (9%; 3-week albendazole), 5 (39%; 5-weeks albendazole) and 2 (22%; 3-week albendazole plus single dose ivermectin) participants met the primary outcome of microfilaraemia below 100/ml at day 168. A 80-90% reduction of microfilaraemia was observed in the active treatment groups.ConclusionThe 5-week regimen of albendazole or a 3-week regimen of albendazole followed by ivermectin were most efficacious to reduce microfilaraemia. All therapeutic regimens were well tolerated and safe.Trial registrationTrial registered at the Pan-African Clinical Trials Registry: PACTR201807197019027.

ABSTRACT Wildlife can be a reservoir and source of zoonotic pathogens for humans. For instance, pangolins were considered one of the potential animal reservoirs of SARS-CoV-2. The aim of this study was to assess the prevalence of antimicrobial-resistant species (e.g., extended-spectrum β-lactamase [ESBL]-producing Enterobacterales) and Staphylococcus aureus-related complex and to describe the bacterial community in wild Gabonese pangolins. The pharyngeal colonization of pangolins sold in Gabon (n = 89, 2021 to 2022) was analyzed using culture media selective for ESBL-producing Enterobacterales, S. aureus-related complex, Gram-positive bacteria and nonfermenters. Phylogenetic analyses of ESBL-producing Enterobacterales was done using core-genome multilocus sequence typing (cgMLST) and compared with publicly available genomes. Patterns of cooccurring species were detected by network analysis. Of the 439 bacterial isolates, the majority of species belonged to the genus Pseudomonas (n = 170), followed by Stenotrophomonas (n = 113) and Achromobacter (n = 37). Three Klebsiella pneumoniae isolates and one Escherichia coli isolate were ESBL-producers, which clustered with human isolates from Nigeria (MLST sequence type 1788 [ST1788]) and Gabon (ST38), respectively. Network analysis revealed a frequent cooccurrence of Stenotrophomonas maltophilia with Pseudomonas putida and Pseudomonas aeruginosa. In conclusion, pangolins can be colonized with human-related ESBL-producing K. pneumoniae and E. coli. Unlike in other African wildlife, S. aureus-related complex was not detected in pangolins. IMPORTANCE There is an ongoing debate if pangolins are a relevant reservoir for viruses such as SARS-CoV-2. Here, we wanted to know if African pangolins are colonized with bacteria that are relevant for human health. A wildlife reservoir of antimicrobial resistance would be of medical relevance in regions were consumption of so-called bushmeat is common. In 89 pangolins, we found three ESBL-producing Klebsiella pneumoniae strains and one ESBL-producing Escherichia coli strains, which were closely related to isolates from humans in Africa. This points toward either a transmission between pangolins and humans or a common source from which both humans and pangolins became colonized.