Molecular Analysis of the Mangrove Oysters (Mollusca: Bivalvia) in Lagos Lagoon, Nigeria Based on Mitochondrial Genome

The commercial and economic importance of the mangrove oysters in the Lagos Lagoon provokes a great deal of biotic investigation, which provides a convincing justification for sequencing an oyster genome. Differentiating oysters based on their morphological characteristics for species identification and taxonomy is highly challenging because of the high intensity of phenotypic changes they exhibit. The genomic resources available for the mangrove oysters are incomparable to resources for any other bivalve invertebrates.  In this study, unidentified mangrove oysters were collected from three different mangrove swamps off the Lagos Lagoon, Nigeria. Molecular procedures were used to identify the oysters genetically while pairwise and multiple alignments of mitochondrial DNA gene sequences of representative oyster strains within the clusters were used to relate them phenotypically to other oysters from various locations. Genetic diversity present in the selected mangrove oyster samples based on cytochrome oxidase I (COI) gene sequences reveals that the unidentified species at the three locations are Crassostrea gasar (Adanson, 1757) and were shown to be more like Brazilian oysters (Crassostrea brasiliana) with 99.55% similarity but clustered in a different clade of mangrove oysters in the GenBank. Similarities in the genetic makeup can principally be accredited to high levels of constant gene flow that are aftermaths of dispersal facilitated by a relatively long pelagic larval stage while the morphological differences can be primarily attributed to ontogeny with environmental conditions. A phylogenetic tree was constructed. The significance of these existing resources for a broad range of evolutionary and environmental sciences will be critically leveraged by having a recent or current genome sequence. The information obtained from this report is crucial to the understanding of diversity, systematics, and population genetics of mangrove oyster species of the Lagos Lagoon

Using satellite image fusion to evaluate the impact of land use changes on ecosystem services and their economic values

Shuangao, W., Padmanaban, R., Mbanze, A. A., Silva, J. M. N., Shamsudeen, M., Cabral, P., & Campos, F. S. (2021). Using satellite image fusion to evaluate the impact of land use changes on ecosystem services and their economic values. Remote Sensing, 13(5), 1-21. [851]. https://doi.org/10.3390/rs13050851Accelerated land use change is a current challenge for environmental management world-wide. Given the urgent need to incorporate economic and ecological goals in landscape planning, cost-effective conservation strategies are required. In this study, we validated the benefit of fusing imagery from multiple sensors to assess the impact of landscape changes on ecosystem services (ES) and their economic values in the Long County, Shaanxi Province, China. We applied several landscape metrics to assess the local spatial configuration over 15 years (2004–2019) from fused image-ries. Using Landsat-7 Enhanced Thematic Mapper Plus (ETM+), Landsat-8 Operational Land Im-ager (OLI) and Indian Remote Sensing Satellite System Linear Imaging Self Scanning Sensor 3 (IRS LISS 3) imageries fused for 2004, 2009, 2014 and 2019, we reclassified land use/land cover (LULC) changes, through the rotation forest (RF) machine-learning algorithm. We proposed an equivalent monetary metric for estimating the ES values, which also could be used in the whole China. Results showed that agriculture farmland and unused land decreased their spatial distribution over time, with an observed increase on woodland, grassland, water bodies and built-up area. Our findings suggested that the patterns of landscape uniformity and connectivity improved, while the distribution of landscape types stabilized, while the landscape diversity had a slight improvement. The overall ES values increased (4.34%) under a benefit transfer approach, mainly concerning woodland and grassland. A sensitivity analysis showed the selected economic value (EV) was relevant and suitable for the study area associated with our ES for LULC changes. We suggested that changes in landscape patterns affected the ESV trends, while the increases on some LULC classes slightly improved the landscape diversity. Using an interdisciplinary approach, we recommend that local au-thorities and environmental practitioners should balance the economic benefits and ecological gains in different landscapes to achieve a sustainable development from local to regional scales.publishersversionpublishe

Antimicrobial resistance among migrants in Europe: a systematic review and meta-analysis

BACKGROUND: Rates of antimicrobial resistance (AMR) are rising globally and there is concern that increased migration is contributing to the burden of antibiotic resistance in Europe. However, the effect of migration on the burden of AMR in Europe has not yet been comprehensively examined. Therefore, we did a systematic review and meta-analysis to identify and synthesise data for AMR carriage or infection in migrants to Europe to examine differences in patterns of AMR across migrant groups and in different settings. METHODS: For this systematic review and meta-analysis, we searched MEDLINE, Embase, PubMed, and Scopus with no language restrictions from Jan 1, 2000, to Jan 18, 2017, for primary data from observational studies reporting antibacterial resistance in common bacterial pathogens among migrants to 21 European Union-15 and European Economic Area countries. To be eligible for inclusion, studies had to report data on carriage or infection with laboratory-confirmed antibiotic-resistant organisms in migrant populations. We extracted data from eligible studies and assessed quality using piloted, standardised forms. We did not examine drug resistance in tuberculosis and excluded articles solely reporting on this parameter. We also excluded articles in which migrant status was determined by ethnicity, country of birth of participants' parents, or was not defined, and articles in which data were not disaggregated by migrant status. Outcomes were carriage of or infection with antibiotic-resistant organisms. We used random-effects models to calculate the pooled prevalence of each outcome. The study protocol is registered with PROSPERO, number CRD42016043681. FINDINGS: We identified 2274 articles, of which 23 observational studies reporting on antibiotic resistance in 2319 migrants were included. The pooled prevalence of any AMR carriage or AMR infection in migrants was 25·4% (95% CI 19·1-31·8; I2 =98%), including meticillin-resistant Staphylococcus aureus (7·8%, 4·8-10·7; I2 =92%) and antibiotic-resistant Gram-negative bacteria (27·2%, 17·6-36·8; I2 =94%). The pooled prevalence of any AMR carriage or infection was higher in refugees and asylum seekers (33·0%, 18·3-47·6; I2 =98%) than in other migrant groups (6·6%, 1·8-11·3; I2 =92%). The pooled prevalence of antibiotic-resistant organisms was slightly higher in high-migrant community settings (33·1%, 11·1-55·1; I2 =96%) than in migrants in hospitals (24·3%, 16·1-32·6; I2 =98%). We did not find evidence of high rates of transmission of AMR from migrant to host populations. INTERPRETATION: Migrants are exposed to conditions favouring the emergence of drug resistance during transit and in host countries in Europe. Increased antibiotic resistance among refugees and asylum seekers and in high-migrant community settings (such as refugee camps and detention facilities) highlights the need for improved living conditions, access to health care, and initiatives to facilitate detection of and appropriate high-quality treatment for antibiotic-resistant infections during transit and in host countries. Protocols for the prevention and control of infection and for antibiotic surveillance need to be integrated in all aspects of health care, which should be accessible for all migrant groups, and should target determinants of AMR before, during, and after migration. FUNDING: UK National Institute for Health Research Imperial Biomedical Research Centre, Imperial College Healthcare Charity, the Wellcome Trust, and UK National Institute for Health Research Health Protection Research Unit in Healthcare-associated Infections and Antimictobial Resistance at Imperial College London

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

Spatio-Temporal Analysis of the Impact of Landscape Changes on Vegetation and Land Surface Temperature over Tamil Nadu

Shamsudeen, M., Padmanaban, R., Cabral, P., & Morgado, P. (2022). Spatio-Temporal Analysis of the Impact of Landscape Changes on Vegetation and Land Surface Temperature over Tamil Nadu. Earth, 3(2), 614-638. https://doi.org/10.3390/earth3020036 ----------------------- This study was partially supported by national funds through FCT (Fundação para a Ciência e a Tecnologia) under the project UIDB/04152/2020 (Centro de Investigação em Gestão de Informação (MagIC)).Land-use changes adversely may impact ecological entities and humans by affecting the water cycle, environmental changes, and energy balance at global and regional scales. Like many megaregions in fast emerging countries, Tamil Nadu, one of the largest states and most urbanized (49%) and industrial hubs in India, has experienced extensive landuse and landcover change (LULC). However, the extent and level of landscape changes associated with vegetation health, surface permeability, and Land Surface Temperature (LST) has not yet been quantified. In this study, we employed Random Forest (RF) classification on Landsat imageries from 2000 and 2020. We also computed vegetation health, soil moisture, and LST metrics for two decades from Landsat imageries to delineate the impact of landscape changes in Tamil Nadu using Google Earth Engine (GEE). The level of vegetation health and drought for 2020 was more accurately assessed by combining the Temperature Condition Index (TCI) and Vegetation Condition Index (VCI). A Soil moisture index was subsequently used to identify surface permeability. A 75% expansion in urban areas of Tamil Nadu was detected mainly towards the suburban periphery of major cities between 2000 and 2020. We observed an overall increase in the coverage of urban areas (built-up), while a decrease for vegetated (cropland and forest) areas was observed in Tamil Nadu between 2000 and 2020. The Soil-Adjusted Vegetation Index (SAVI) values showed an extensive decline in surface permeability and the LST values showed an overall increase (from a maximum of 41 °C to 43 °C) of surface temperature in Tamil Nadu’s major cities with the highest upsurge for urban built-up areas between 2000 and 2020. Major cities built-up and non-vegetation areas in Tamil Nadu were depicted as potential drought hotspots. Our results deliver significant metrics for surface permeability, vegetation condition, surface temperature, and drought monitoring and urges the regional planning authorities to address the current status and social-ecological impact of landscape changes and to preserve ecosystem services.publishersversionpublishe

Landscape Impacts on Ecosystem Service Values Using the Image Fusion Approach

Wang, S., Padmanaban, R., Shamsudeen, M., Campos, F. S., & Cabral, P. (2022). Landscape Impacts on Ecosystem Service Values Using the Image Fusion Approach. Land, 11(8), 1-18. [1186]. https://doi.org/10.3390/land11081186 --- FUNDING: This study was supported by the Research on Capitalization of Natural Resources and Corresponding Market Construction in China (grant number 15ZDB162); and partially through the FCT (Fundação para a Ciência e a Tecnologia) under the projects PTDC/CTA-AMB/28438/2017—ASEBIO and UIDB/04152/2020—Centro de Investigação em Gestão de Informação (MagIC). This research was also funded by the Forest Research Centre, a research unit funded by Fundação para a Ciência e a Tecnologia I.P. (FCT), Portugal (UIDB/00239/2020).The landscape is a complex mosaic of physical and biological patches with infrastructures, cultivable lands, protected ecosystems, water bodies, and many other landforms. Varying land-use changes are vulnerable to the world and need the mitigation and management of landforms to achieve sustainable development, which without proper oversight, may lead to habitat destruction, degradation, and fragmentation. In this study, we quantify the land-use and land-cover (LULC) changes using downscaled satellite imagery and assess their effects on ecosystem services (ES) and economic values in Ningxia Province, China. Various landscape metrics are derived to study the pattern and spatial configuration over 15 years (2005–2020), in which the landscapes are evolving. The impact of LULC change in various ES is analyzed using ecosystem service values (ESV) and validated with a sensitivity index. Finally, the level of urban sprawl (US) due to overpopulation is established using Renyi’s entropy. Using Landsat 8′s Operational Land Imager (OLI) datasets, we downscaled the MODIS data of 2005, 2010, 2015, and 2020 to prepare the LULC map through a rotation forest algorithm. Results demonstrate that water bodies, woodlands, and built-up landscapes increased in their spatial distribution over time and that there was a decrease in farmlands. Results further suggest that the connectivity and uniformity of the landscape pattern improved in the later period due to several plans formulated by the government with a slight improvement in landscape diversity. Overall ESV get improved, while LULC classes such as farmland and water bodies have decreased and increased ESV, respectively, and a sensitivity analysis is used to test the reliability of ESV on LULC classes. The level of US is 0.91 in terms of Renyi’s entropy, which reveals the presence of a dispersion of settlements in urban fringes. The simulated US for 2025 shows urbanization is more severe over a prolonged time and finally the impacts of the US in ESV are analyzed. Using an interdisciplinary approach, several recommendations are formulated to maintain the ESV despite rapid LULC changes and to achieve sustainable development globally.publishersversionpublishe

Polymorphism of prion protein gene (PRNP) in Nigerian sheep

ABSTRACTPolymorphism of the prion protein gene (PRNP) gene determines an animal’s susceptibility to scrapie. Three polymorphisms at codons 136, 154, and 171 have been linked to classical scrapie susceptibility, although many variants of PRNP have been reported. However, no study has investigated scrapie susceptibility in Nigerian sheep from the drier agro-climate zones. In this study, we aimed to identify PRNP polymorphism in nucleotide sequences of 126 Nigerian sheep by comparing them with public available studies on scrapie-affected sheep. Further, we deployed Polyphen-2, PROVEAN, and AMYCO analyses to determine the structure changes produced by the non-synonymous SNPs. Nineteen (19) SNPs were found in Nigerian sheep with 14 being non-synonymous. Interestingly, one novel SNP (T718C) was identified. There was a significant difference (P < 0.05) in the allele frequencies of PRNP codon 154 between sheep in Italy and Nigeria. Based on the prediction by Polyphen-2, R154H was probably damaging while H171Q was benign. Contrarily, all SNPs were neutral via PROVEAN analysis while two haplotypes (HYKK and HDKK) had similar amyloid propensity of PRNP with resistance haplotype in Nigerian sheep. Our study provides valuable information that could be possibly adopted in programs targeted at breeding for scrapie resistance in sheep from tropical regions

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

Use of Telemedicine for Post-discharge Assessment of the Surgical Wound: International Cohort Study, and Systematic Review with Meta-analysis

Objective: This study aimed to determine whether remote wound reviews using telemedicine can be safely upscaled, and if standardised assessment tools are needed. Summary background data: Surgical site infection is the most common complication of surgery worldwide, and frequently occurs after hospital discharge. Evidence to support implementation of telemedicine during postoperative recovery will be an essential component of pandemic recovery. Methods: The primary outcome of this study was surgical site infection reported up to 30-days after surgery (SSI), comparing rates reported using telemedicine (telephone and/or video assessment) to those with in-person review. The first part of this study analysed primary data from an international cohort study of adult patients undergoing abdominal surgery who were discharged from hospital before 30-days after surgery. The second part combined this data with the results of a systematic review to perform a meta-analysis of all available data conducted in accordance with PRIMSA guidelines (PROSPERO:192596). Results: The cohort study included 15,358 patients from 66 countries (8069 high, 4448 middle, 1744 low income). Of these, 6907 (45.0%) were followed up using telemedicine. The SSI rate reported using telemedicine was slightly lower than with in-person follow-up (13.4% vs. 11.1%, P&lt;0.001), which persisted after risk adjustment in a mixed-effects model (adjusted odds ratio: 0.73, 95% confidence interval 0.63-0.84, P&lt;0.001). This association was consistent across sensitivity and subgroup analyses, including a propensity-score matched model. In nine eligible non-randomised studies identified, a pooled mean of 64% of patients underwent telemedicine follow-up. Upon meta-analysis, the SSI rate reported was lower with telemedicine (odds ratio: 0.67, 0.47-0.94) than in-person (reference) follow-up (I2=0.45, P=0.12), although there a high risk of bias in included studies. Conclusions: Use of telemedicine to assess the surgical wound post-discharge is feasible, but risks underreporting of SSI. Standardised tools for remote assessment of SSI must be evaluated and adopted as telemedicine is upscaled globally

Exploring the cost-effectiveness of high versus low perioperative fraction of inspired oxygen in the prevention of surgical site infections among abdominal surgery patients in three low- and middle-income countries

Background: This study assessed the potential cost-effectiveness of high (80–100%) vs low (21–35%) fraction of inspired oxygen (FiO2) at preventing surgical site infections (SSIs) after abdominal surgery in Nigeria, India, and South Africa. Methods: Decision-analytic models were constructed using best available evidence sourced from unbundled data of an ongoing pilot trial assessing the effectiveness of high FiO2, published literature, and a cost survey in Nigeria, India, and South Africa. Effectiveness was measured as percentage of SSIs at 30 days after surgery, a healthcare perspective was adopted, and costs were reported in US dollars ($). Results: High FiO2 may be cost-effective (cheaper and effective). In Nigeria, the average cost for high FiO2 was$216 compared with $222 for low FiO2 leading to a −$6 (95% confidence interval [CI]: −$13 to −$1) difference in costs. In India, the average cost for high FiO2 was $184 compared with$195 for low FiO2 leading to a −$11 (95$15 to −$6) difference in costs. In South Africa, the average cost for high FiO2 was$1164 compared with $1257 for low FiO2 leading to a −$93 (95% CI: −$132 to −$65) difference in costs. The high FiO2 arm had few SSIs, 7.33% compared with 8.38% for low FiO2, leading to a −1.05 (95% CI: −1.14 to −0.90) percentage point reduction in SSIs. Conclusion: High FiO2 could be cost-effective at preventing SSIs in the three countries but further data from large clinical trials are required to confirm this