Effect of the Bio-agents (Bacillus megaterium and Trichoderma album) on Citrus Nematode (Tylenchulus semipenetrans) Infecting Baladi orange and

The effect of two commercial compounds namely Bioarc TM (Bacillus megaterium) and Biozeid TM (Trichoderma album) at different rates against Tylenchulus semipenetrans was examined under laboratory and greenhouse conditions. In laboratory experiment, both compounds Bioarc and Biozeid as bio-control agents found to be highly nematostatic agents against J2 of T. semipenetrans. The rates of 20, 25 and 30g/l gave more than 60% J2 mortality after 72h exposure time. The highest effect was achieved at 30 g/l whereas, Bioarc (90.5 %) exhibited the highest effect followed by Biozeid (88.3%) at 30g/l after 72h exposure time. In greenhouse experiment, the bio-agents were evaluated at rates of 20, 25 and 30 g/l compared to nematicide Nemathorin 10% G at recommended dose (12.5 kg/ feddan) on the development of T. semipenetrans infecting Baladi orange and Lime seedlings. Results showed significant differences between the tested rates of both bio-agents. At the higher rate (30.0g/l), Bioarc (89.0, 89.5%; 76.6, 82.9%) was found to be more effective than Biozeid (88.3, 89.0%; 72.0, 77.9%) in reducing number of J2/100g soil and females/g root of Baladi orange and Lime infected with T. semipenetrans  respectively. Moreover, both Bioarc and Biozeid at 30.0g/l significantly increased plant growth of Baladi orange and Lime infected with T. semipenetrans

Surgical site infection after gastrointestinal surgery in high-income, middle-income, and low-income countries: a prospective, international, multicentre cohort study

Background: Surgical site infection (SSI) is one of the most common infections associated with health care, but its importance as a global health priority is not fully understood. We quantified the burden of SSI after gastrointestinal surgery in countries in all parts of the world. Methods: This international, prospective, multicentre cohort study included consecutive patients undergoing elective or emergency gastrointestinal resection within 2-week time periods at any health-care facility in any country. Countries with participating centres were stratified into high-income, middle-income, and low-income groups according to the UN's Human Development Index (HDI). Data variables from the GlobalSurg 1 study and other studies that have been found to affect the likelihood of SSI were entered into risk adjustment models. The primary outcome measure was the 30-day SSI incidence (defined by US Centers for Disease Control and Prevention criteria for superficial and deep incisional SSI). Relationships with explanatory variables were examined using Bayesian multilevel logistic regression models. This trial is registered with ClinicalTrials.gov, number NCT02662231. Findings: Between Jan 4, 2016, and July 31, 2016, 13 265 records were submitted for analysis. 12 539 patients from 343 hospitals in 66 countries were included. 7339 (58·5%) patient were from high-HDI countries (193 hospitals in 30 countries), 3918 (31·2%) patients were from middle-HDI countries (82 hospitals in 18 countries), and 1282 (10·2%) patients were from low-HDI countries (68 hospitals in 18 countries). In total, 1538 (12·3%) patients had SSI within 30 days of surgery. The incidence of SSI varied between countries with high (691 [9·4%] of 7339 patients), middle (549 [14·0%] of 3918 patients), and low (298 [23·2%] of 1282) HDI (p < 0·001). The highest SSI incidence in each HDI group was after dirty surgery (102 [17·8%] of 574 patients in high-HDI countries; 74 [31·4%] of 236 patients in middle-HDI countries; 72 [39·8%] of 181 patients in low-HDI countries). Following risk factor adjustment, patients in low-HDI countries were at greatest risk of SSI (adjusted odds ratio 1·60, 95% credible interval 1·05–2·37; p=0·030). 132 (21·6%) of 610 patients with an SSI and a microbiology culture result had an infection that was resistant to the prophylactic antibiotic used. Resistant infections were detected in 49 (16·6%) of 295 patients in high-HDI countries, in 37 (19·8%) of 187 patients in middle-HDI countries, and in 46 (35·9%) of 128 patients in low-HDI countries (p < 0·001). Interpretation: Countries with a low HDI carry a disproportionately greater burden of SSI than countries with a middle or high HDI and might have higher rates of antibiotic resistance. In view of WHO recommendations on SSI prevention that highlight the absence of high-quality interventional research, urgent, pragmatic, randomised trials based in LMICs are needed to assess measures aiming to reduce this preventable complication

Erratum to: 36th International Symposium on Intensive Care and Emergency Medicine

[This corrects the article DOI: 10.1186/s13054-016-1208-6.]

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Indirect Quantitative Analysis of Biochemical Parameters in Banana Using Spectral Reflectance Indices Combined with Machine Learning Modeling

The primary issues in collecting biochemical information in a large area using chemical laboratory procedures are low throughput, hard work, time-consuming, and requiring several samples. Thus, real-time and precise estimation of biochemical variables of various fruits using a proximal remote sensing based on spectral reflectance is critical for harvest time, artificial ripening, and food processing, which might be beneficial economically and ecologically. The main goal of this study was to assess the biochemical parameters of banana fruits such as chlorophyll a (Chl a), chlorophyll b (Chl b), respiration rate, total soluble solids (TSS), and firmness using published and newly developed spectral reflectance indices (SRIs), integrated with machine learning modeling (Artificial Neural Networks; ANN and support vector machine regression; SVMR) at different ripening degrees. The results demonstrated that there were evident and significant differences in values of SRIs at different ripening degrees, which may be attributed to the large variations in values of biochemical parameters. The newly developed two-band SRIs are more effective at measuring different biochemical parameters. The SRIs that were extracted from the visible (VIS), near-infrared (NIR), and their combination showed better R2 with biochemical parameters. SRIs combined with ANN and SVMR would be an effective method for estimating five biochemical parameters in the calibration (Cal.) and validation (Val.) datasets with acceptable accuracy. The ANN-TSS-SRI-13 model was built to determine TSS with greater performance expectations (R2 = 1.00 and 0.97 for Cal. and Val., respectively). Furthermore, the model ANN-Firmness-SRI-15 was developed for determining firmness, and it performed better (R2 = 1.00 and 0.98 for Cal. and Val., respectively). In conclusion, this study revealed that SRIs and a combination approach of ANN and SVMR models would be a useful and excellent tool for estimating the biochemical characteristics of banana fruits

Morphological, morphometrical and molecular identification of root-knot nematode (Meloidogyne javanica) infecting banana in Assiut governorate, Egypt

Plant-parasitic nematodes are extremely dangerous pests in a variety of economically important crops. Root-knot nematodes (RKN) Meloidogyne spp. are between the major important pests causing serious crops havoc worldwide because of their wide geographical distribution and variety of hosts. Therefore, both of identification that is true and trustworthy of these pests is required for evaluating various suitable management strategies. This study, aimed to characterize morphological, morphometric and molecularly isolate of Meloidogyne related to banana plants. Second-stage juveniles (body length, tail length, stylet length, hyaline terminus length, and DEGO) were used in morphometric and morphological studies and female in perineal patterns. The results revealed that the identified nematode species, Meloidogyne javanica, is the most common root knot nematode species in all three localities. To prove the identification, a polymerase chain reaction (PCR)-based experiment using a species-specific sequence described amplified regions (SCAR) primer series was used. The Fjav/Rjav primer effectively enhanced SCAR markers of 670 bp previously identified in M. javanica. This study confirms the use of an effective and reliable diagnosis of RKN using the three approaches

Using RGB Imaging, Optimized Three-Band Spectral Indices, and a Decision Tree Model to Assess Orange Fruit Quality

Point samples and laboratory testing have historically been used to evaluate fruit quality criteria. Although this method is precise, it is slow, expensive, and destructive, making it unsuitable for large-scale monitoring of these parameters. The main objective of this research was to develop a non-invasive protocol by combining color RGB indices (CIs) and previously published and newly developed three-band spectral reflectance indices (SRIs) with a decision tree (DT) model to evaluate the fruit quality parameters of navel orange. These parameters were brightness (L*), red–green (a*), blue–yellow (b*), chlorophyll meter (Chlm), total soluble solids (TSS), and TSS/acid ratio. The characteristics of fruit quality of navel orange samples were measured at various stages of ripening. The outcomes demonstrated that at various levels of ripening, the fruit quality parameters, RGB imaging indices, and published and newly developed three-band SRIs differed. The newly developed three-band SRIs based on the wavelengths of blue, green, red, red-edge, and NIR are most effective for estimating the six measured parameters in this study. For example, NDI574,592,724, NDI572,584,724, and NDI574,722,590 had the largest R2 value (0.90) with L*, whereas NDI526,664,700 and NDI524,700,664 exhibited the highest R2 value (0.97) with a*. Moreover, integrating CIs and SRIs with the DT model has provided a potentially useful tool for the accurate measurement of the six studied parameters. For instance, the DT-SRIs-CIs-30 model performed better in terms of measuring a* using 30 various indices. The R2 value was 0.98 and RMSE = 1.121 in the cross-validation, while R2 value was 0.964 and RMSE = 2.604 in the test set. Otherwise, based on the fusion of five various indices, the DT-SRIs-CIs-5 model was the most precise for recognizing b* (R2 = 0.957 and 0.929, with RMSE = 1.713 and 3.309 for cross-validation and test set, respectively). Overall, this work proves that integrating the different characteristics of proximal reflectance sensing systems such as color RGB indices and SRIs via the DT model may be considered a reliable instrument for evaluating the quality of different fruits

Surgical site infection after gastrointestinal surgery in children : an international, multicentre, prospective cohort study

Introduction Surgical site infection (SSI) is one of the most common healthcare-associated infections (HAIs). However, there is a lack of data available about SSI in children worldwide, especially from low-income and middle-income countries. This study aimed to estimate the incidence of SSI in children and associations between SSI and morbidity across human development settings. Methods A multicentre, international, prospective, validated cohort study of children aged under 16 years undergoing clean-contaminated, contaminated or dirty gastrointestinal surgery. Any hospital in the world providing paediatric surgery was eligible to contribute data between January and July 2016. The primary outcome was the incidence of SSI by 30 days. Relationships between explanatory variables and SSI were examined using multilevel logistic regression. Countries were stratified into high development, middle development and low development groups using the United Nations Human Development Index (HDI). Results Of 1159 children across 181 hospitals in 51 countries, 523 (45 center dot 1%) children were from high HDI, 397 (34 center dot 2%) from middle HDI and 239 (20 center dot 6%) from low HDI countries. The 30-day SSI rate was 6.3% (33/523) in high HDI, 12 center dot 8% (51/397) in middle HDI and 24 center dot 7% (59/239) in low HDI countries. SSI was associated with higher incidence of 30-day mortality, intervention, organ-space infection and other HAIs, with the highest rates seen in low HDI countries. Median length of stay in patients who had an SSI was longer (7.0 days), compared with 3.0 days in patients who did not have an SSI. Use of laparoscopy was associated with significantly lower SSI rates, even after accounting for HDI. Conclusion The odds of SSI in children is nearly four times greater in low HDI compared with high HDI countries. Policies to reduce SSI should be prioritised as part of the wider global agenda.Peer reviewe