Search Results (17)

National-scale forest inventories such as the Forest Inventory and Analysis (FIA) program in the United States are designed to provide data and estimates that meet target precision at the national and state levels. However, such design-based direct estimates are often not accurate at a smaller geographic scale due to the small sample size. Small area estimation (SAE) techniques provide precise estimates at small domains by borrowing strength from remotely sensed auxiliary information. This study combined the FIA direct estimates with gridded mean canopy heights derived from recently published Global Ecosystem Dynamics Investigation (GEDI) Level 3 data and Landsat data to improve county-level estimates of total and merchantable volume, aboveground biomass, and basal area in the states of Alabama and Mississippi, USA. Compared with the FIA direct estimates, the area-level SAE models reduced root mean square error for all variables of interest. The multi-state SAE models had a mean relative standard error of 0.67. In contrast, single-state models had relative standard errors of 0.54 and 0.59 for Alabama and Mississippi, respectively. Despite GEDI’s limited footprints, this study reveals its potential to reduce direct estimate errors at the sub-state level when combined with Landsat bands through the small area estimation technique. Full article

Armed conflict remains a significant global issue, with several studies highlighting its detrimental impact on the affected communities, making it a critical area of research. This study aimed to examine the effects of prolonged armed conflict on food security among urban households in Tigray, Ethiopia, and to examine their coping mechanisms. Primary data were collected from 740 urban households between May and June 2024. The Food Insecurity Access Scale (FIAS), Food Insecurity Experience Scale (FIES), and Food Consumption Score (FCS) were employed to assess the levels of food security, while the Livelihood Coping Strategy Index (LCSI) was used to identify coping strategies. The findings revealed that female-headed households were more affected by food insecurity than male-headed households. FIAS (FIES) scores indicated that 17% (2%) of households were food-secure, with 20% (25%) mildly, 35% (32%) moderately, and 29% (30%) severely food-insecure. The FCS analysis showed that 52% of households had poor food consumption, 33% were borderline, and 16% were acceptable. The findings show that 39% of urban households experienced hunger in the post-conflict period. Stress-level strategies are the most widely adopted coping mechanisms. These findings underscore the urgent need for targeted policy interventions that address the specific vulnerabilities of female-headed households and ensure the development of sustainable coping strategies to mitigate the long-term effects of food insecurity in war-affected urban settings. This study offers novel insights into the urban dimensions of food insecurity and coping strategies in post-conflict settings. Full article

In response to increasing global temperatures and energy demands, optimizing buildings’ energy efficiency, particularly in hot climates, is an urgent challenge. While current research often relies on conventional energy estimation methods, there has been a decrease in the efforts dedicated to leveraging AI-based methodologies as technology advances. This implies a dearth of multiparameter examinations in AI-driven extreme case studies. For this reason, this study aimed to enhance the energy performance of residential buildings in the hot climates of Dubai and Riyadh by integrating Building Information Modeling (BIM) and Machine Learning (ML). Detailed BIM models of a typical residential villa in these regions were created using Revit, incorporating conventional, modern, and green building envelopes (BEs). These models served as the basis for energy simulations conducted with Green Building Studio (GBS) and Insight, focusing on crucial building features such as floor area, external and internal walls, windows, flooring, roofing, building orientation, infiltration, daylighting, and more. To predict Energy Use Intensity (EUI), four ML algorithms, namely, Gradient Boosting Machine (GBM), Random Forest (RF), Support Vector Machine (SVM), and Lasso Regression (LR), were employed. GBM consistently outperformed the others, demonstrating superior prediction accuracy with an R² of 0.989. This indicates that the model explains 99% of the variance in EUI, highlighting its effectiveness in capturing the relationships between building features and energy consumption. Feature importance analysis (FIA) revealed that roofs (29% in Dubai scenarios (DS) and 40% in Riyadh scenarios (RS)), external walls (19% in DS and 29% in RS), and windows (15% in DS and 9% in RS) have the most impact on energy consumption. Additionally, the study explored the potential for energy optimization, such as cavity green walls and green roofs in RS and double brick walls with VIP insulation and green roofs in DS. The findings of the paper should be interpreted in light of certain limitations but they underscore the effectiveness of combining BIM and ML for sustainable building design, offering actionable insights for enhancing energy efficiency in hot climates. Full article

The global spread of antimicrobial resistance genes (ARGs) is a major public health concern. Mobile genetic elements (MGEs) are the main drivers of this spread by horizontal gene transfer (HGT). Escherichia coli is widespread in various environments and serves as an indicator for monitoring antimicrobial resistance (AMR). Therefore, the objective of this work was to evaluate the whole genome of multidrug-resistant E. coli strains isolated from human clinical, animal, and environmental sources. Four E. coli strains previously isolated from human urine (n = 2), retail meat (n = 1), and water from the Rio Grande River (n = 1) collected in northern Tamaulipas, Mexico, were analyzed. E. coli strains were evaluated for antimicrobial susceptibility, followed by whole genome sequencing and bioinformatic analysis. Several ARGs were detected, including bla_CTX-M-15, bla_OXA-1, bla_TEM-1B, bla_CMY-2, qnrB, catB3, sul2, and sul3. Additionally, plasmid replicons (IncFIA, IncFIB, IncFII, IncY, IncR, and Col) and intact prophages were also found. Insertion sequences (ISs) were structurally linked with resistance and virulence genes. Finally, these findings indicate that E. coli strains have a large repertoire of resistance determinants, highlighting a high pathogenic potential and the need to monitor them. Full article

Background and Objectives: The global spread of carbapenem resistance and the resulting increase in mortality forced the World Health Organization (WHO) to claim carbapenem-resistant enterobacteriaceae (CRE) as global priority pathogens. Our study aimed to determine the prevalence of carbapenemase-encoding genes and major plasmid incompatibility groups among Gram-negative hospital-based isolates in Egypt. Material and Methods: This cross-sectional study was carried out at Mansoura University Hospitals over 12 months, from January to December 2019. All the isolates were tested for carbapenem resistance. The selected isolates were screened by conventional polymerase chain reaction (PCR) for the presence of carbapenemase genes, namely bla_KPC, bla_IMP, bla_VIM, and bla_NDM-1. PCR-based plasmid replicon typing was performed using the commercial PBRT kit. Results: Out of 150 isolates, only 30 (20.0%) demonstrated carbapenem resistance. Klebsiella pneumoniae was the most resistant of all isolated bacteria, and bla_NDM was the predominant carbapenemases gene, while the most prevalent plasmid replicons were the F replicon combination (FIA, FIB, and FII) and A/C. Plasmids were detected only in Klebsiella pneumoniae, Escherichia coli, Enterobacter cloacae, and Pseudomonas aeruginosa. Remarkably, we found a statistically significant association between carbapenemase genes and plasmid replicons, including bla_NDM, IncA/C, and IncX. Conclusions: Our study demonstrated an alarming rise of plasmid-mediated carbapenem-resistant bacteria in our locality. The coexistence of resistance genes and plasmids highlights the importance of a targeted antibiotic surveillance program and the development of alternative therapeutic options at the local and international levels. Based on our results, we suggest a large-scale study with more Enterobacteriaceae isolates, testing other carbapenemase-encoding genes, and comparing the replicon typing method with other plasmid detection methods. We also recommend a national action plan to control the irrational use of antibiotics in Egypt. Full article

To characterize environmental antimicrobial resistance (AMR) in urban areas, extended-spectrum β-lactamase- (ESBL)/carbapenemase-producing bacteria (EPB/CPB, respectively) from urban wastewater treatment plant effluents in Tokyo were isolated on CHROMagar ESBL plate. Complete genome sequence analysis, including plasmids, indicated that 126 CTX-M-positive isolates (31%) were identified among the 404 obtained isolates. The CTX-M-9 group was predominant (n = 65, 52%), followed by the CTX-M-1 group (n = 44, 35%). Comparative genome analysis revealed that CTX-M-27-positive E. coli O16:H5-ST131-fimH41 exhibited a stable genome structure and clonal-global dissemination. Plasmidome network analysis revealed that 304 complete plasmid sequences among 85 isolates were grouped into 14 incompatibility (Inc) network communities (Co1 to Co14). Co10 consisted of primarily IncFIA/IncFIB plasmids harboring bla_CTX-M in E. coli, whereas Co12 consisted primarily of IncFIA(HI1)/Inc FIB(K) plasmids harboring bla_CTX-M, bla_KPC, and bla_GES in Klebsiella spp. Co11 was markedly located around Co10 and Co12. Co11 exhibited bla_CTX-M, bla_KPC, and bla_NDM, and was mainly detected in E. coli and Klebsiella spp. from human and animal sources, suggesting a mutual role of Co11 in horizontal gene transfer between E. coli and Klebsiella spp. This comprehensive resistome analysis uncovers the mode of relational transfer among bacterial species, highlighting the potential source of AMR burden on public health in urban communities. Full article

Coronavirus disease 2019 (COVID-19) initiated global health care challenges such as the necessity for new diagnostic tests. Diagnosis by real-time PCR remains the gold-standard method, yet economical and technical issues prohibit its use in points of care (POC) or for repetitive tests in populations. A lot of effort has been exerted in developing, using, and validating antigen-based tests (ATs). Since individual studies focus on few methodological aspects of ATs, a comparison of different tests is needed. Herein, we perform a systematic review and meta-analysis of data from articles in PubMed, medRxiv and bioRxiv. The bivariate method for meta-analysis of diagnostic tests pooling sensitivities and specificities was used. Most of the AT types for SARS-CoV-2 were lateral flow immunoassays (LFIA), fluorescence immunoassays (FIA), and chemiluminescence enzyme immunoassays (CLEIA). We identified 235 articles containing data from 220,049 individuals. All ATs using nasopharyngeal samples show better performance than those with throat saliva (72% compared to 40%). Moreover, the rapid methods LFIA and FIA show about 10% lower sensitivity compared to the laboratory-based CLEIA method (72% compared to 82%). In addition, rapid ATs show higher sensitivity in symptomatic patients compared to asymptomatic patients, suggesting that viral load is a crucial parameter for ATs performed in POCs. Finally, all methods perform with very high specificity, reaching around 99%. LFIA tests, though with moderate sensitivity, appear as the most attractive method for use in POCs and for performing seroprevalence studies. Full article

Little information is available on the local epidemiology of mobile genetic elements such as plasmids harboring acquired beta-lactamase genes in Western African Ghana. In the present study, we screened for plasmids in three Escherichia coli and four Klebsiella pneumoniae isolates expressing extended spectrum beta-lactamases (ESBL) mediated by the bla_CTX-M-15 gene from chronically infected wounds of Ghanaian patients. Bacterial isolates were subjected to combined short-read and long-read sequencing to obtain the sequences of their respective plasmids. In the bla_CTX-M-15-gene-carrying plasmids of the four ESBL-positive K. pneumoniae isolates, IncFIB/IncFII (n = 3) and FIA (n = 1) sequences were detected, while in the bla_CTX-M-15-gene-carrying plasmids of the three ESBL-positive E. coli isolates, IncFIA/IncFIB (n = 2) and IncFIB (n = 1) sequences were found. The three IncFIB/IncFII sequence-containing plasmids were almost identical to a K. pneumoniae plasmid reported from France. They belonged to the clonal lineages ST17, ST36 and ST39 of K. pneumoniae, suggesting transversal spread of this obviously evolutionary successful plasmid in Ghana. Other resistance gene-encoding plasmids observed in the assessed Enterobacterales harbored IncFIA/IncR and IncFII sequences. International spread was confirmed by the high genetic similarity to resistance-mediating plasmids published from Asia, Australia, Europe and Northern America, including a bla_CTX-M-15-gene-carrying plasmid isolated from a wild bird in Germany. In conclusion, the study contributed to the scarcely available information on the epidemiology of third-generation cephalosporine resistance-mediating plasmids in Ghana. Furthermore, the global spread of resistance-mediating plasmids provided hints on the evolutionary success of individual resistance-harboring plasmids by transversal spread among K. pneumoniae lineages in Ghana. Full article

A flow-based method for the spectrophotometric determination of chromium (VI) in recreational waters with different salinities was developed. Chromium can occur in the environment in different oxidation states with different related physiological properties. With regard to chromium, the speciation is particularly important, as the hexavalent chromium is considered to be carcinogenic. To achieve that purpose, the use of the diphenylcarbazide (DPC) selective colored reaction with the hexavalent chromium was the chosen strategy. The main objective was to develop a direct and simple spectrophotometric method that could cope with the analysis of different types of environmental waters, within different salinity ranges (fresh to marine waters). The potential interference of metal ions, that can usually be present in environmental waters, was assessed and no significant interferences were observed (<10%). For a complete Cr(VI) determination (three replicas) cycle, the corresponding reagents consumption was 75 µg of DPC, 9 mg of ethanol and 54 mg of sulfuric acid. Each cycle takes about 5 min, including the system clean-up. The limit of detection was 6.9 and 12.2 µg L⁻¹ for waters with low and high salt content, respectively. The method was applied for the quantification of chromium (VI) in both fresh and marine water, and the results were in agreement with the reference procedure. Full article

New Delhi metallo-β-lactamase (NDM) carbapenemase has been considered a global threat due to its worldwide widespread in recent years. In Portugal, a very low number of infections with NDM-producing Enterobacterales has been reported. A total of 52 strains from 40 patients and 1 environmental sample isolated during COVID-19 pandemic were included in this study. Wholegenome sequencing (WGS) was performed on 20 carbapenemase-producing strains, including 17 NDM-1-producing Klebsiella pneumoniae ST11-KL105 lineage strains, one NDM-1-producing Escherichia coli ST58 strain and one KPC-3-producing K. pneumoniae ST147 strain, recovered from a total of 19 patients. Of interest, also one NDM-1-producing K. pneumoniae ST11-KL105 was collected from the hospital environment. Genome-wide phylogenetic analysis revealed an ongoing dissemination of NDM-1-producing K. pneumoniae ST11 strains (n = 18) with the same genetic features seen across multiple wards. Furthermore, the ST58 E. coli strain, collected from a patient rectal swab that was also colonised with a K. pneumoniae strain, also showed the IncFIA plasmid replicon and the bla_NDM-1 gene (preceded by IS30 and followed by genes ble_MBL, trpF, dsbC, cutA, groES and groEL). The bla_NDM-1 is part of Tn125-like identical to those reported in Poland, Italy and India. The bla_KPC-3 K. pneumoniae ST147-KL64 strain has the genetic environment Tn4401d isoform. In conclusion, herein we report the molecular epidemiology, resistome, virulome and mobilome of the first NDM-1 carbapenemase outbreak caused by K. pneumoniae ST11-KL105 lineage during the COVID-19 pandemic in Portugal. Moreover, the outbreak strains characterised included seventeen different patients (infected and colonised) and one environmental sample which also emphasises the role of commensal and hospital environment strains in the dissemination of the outbreak. Full article

Background: Globally, bla_CTX-M-15 beta-lactamases are the most popular extended spectrum beta-lactamase alleles that are widely distributed due its mobilisation by mobile genetic elements in several compartments. We aimed to determine the conjugation frequencies and replicon types associated with plasmids carrying bla_CTX-M-15 gene from Extended Spectrum Beta-lactamase producing isolates in order to understand the dissemination of resistance genes in different compartments. Material and methods: A total of 51 archived isolates carrying bla_CTX-M-15 beta-lactamases were used as donors in this study. Antibiotic susceptibility tests were performed as previously described for both donors and transconjugants. Conjugation experiment was performed by a modified protocol of the plate mating experiment, and plasmid replicon types were screened among donor and transconjugant isolates by multiplex Polymerase Chain Reaction in a set of three primer panels. Results: The conjugation efficiency of plasmids carrying bla_CTX-M-15 was 88.2% (45/51) with conjugation frequencies in the order of 10⁻¹ to 10⁻⁹ and a 100% transfer efficiency observed among E. coli of animal origin. Majority of donors (n = 21) and transconjugants (n = 14) plasmids were typed as either Inc FIA or Inc FIB. Resistance to non-beta-lactam antibiotics was transferrable in 34/45 (75.6%) of events. Ciprofloxacin, tetracycline and sulphamethoxazole-trimethoprim resistance was co-transferred in 29/34 (85.3%) such events. Gentamicin resistance was transferred in 17/34 (50%) of events. Conclusions: Majority of plasmids carrying bla_CTX-M-15 were conjugatively transferred by IncF plasmids along with non-beta lactam resistance. There is a need for more research on plasmids to understand how plasmids especially multi replicon plasmids interact and the effect of such interaction on conjugation. One Health approach is to be intensified to address antimicrobial resistance which is a public health threat. Full article

The most widely distributed bla_CTX-M gene on a global scale is bla_CTX-M-15. The dissemination has been associated with clonal spread and different types of mobile genetic elements. The objective of this review was to describe the genetic environments of the bla_CTX-M-15 gene detected from Enterobacteriaceae in published literature from Africa. A literature search for relevant articles was performed through PubMed, AJOL, and Google Scholar electronic databases; 43 articles from 17 African countries were included in the review based on the eligibility criteria. Insertion sequences were reported as part of the genetic environment of bla_CTX-M-15 gene in 32 studies, integrons in 13 studies, and plasmids in 23 studies. In this review, five insertion sequences including ISEcp1, IS26, orf447, IS903, and IS3 have been detected which are associated with the genetic environment of bla_CTX-M-15 in Africa. Seven different genetic patterns were seen in the bla_CTX-M-15 genetic environment. Insertion sequence ISEcp1 was commonly located upstream of the end of the bla_CTX-M-15 gene, while the insertion sequence orf477 was located downstream. In some studies, ISEcp1 was truncated upstream of bla_CTX-M-15 by insertion sequences IS26 and IS3. The class 1 integron (Intl1) was most commonly reported to be associated with bla_CTX-M-15 (13 studies), with Intl1/dfrA17–aadA5 being the most common gene cassette array. IncFIA-FIB-FII multi-replicons and IncHI2 replicon types were the most common plasmid replicon types that horizontally transferred the bla_CTX-M-15 gene. Aminoglycoside-modifying enzymes, and plasmid-mediated quinolone resistance genes were commonly collocated with the bla_CTX-M-15 gene on plasmids. This review revealed the predominant role of ISEcp1, Intl1 and IncF plasmids in the mobilization and continental dissemination of the bla_CTX-M-15 gene in Africa. Full article

COVID-19 pandemic is a dramatic health, social and economic global challenge. There is urgent need to maximize testing capacity. Rapid Antigen Tests (RAT) represent good candidates for point-of-care and mass surveillance testing to rapidly identify SARS-CoV-2-infected people, counterbalancing lower sensitivity vs. gold standard molecular tests with fast results and possible recurrent testing. We describe the results obtained with the testing algorithm implemented at points of entry (airports and ports) in the Lazio Region (Italy), using the STANDARD F COVID-19 Antigen Fluorescence ImmunoAssay (FIA), followed by molecular confirmation of FIA-positive samples. From mid-August to mid-October 2020, 73,643 RAT were reported to the Regional Surveillance Information System for travelers at points of entry in Lazio Region. Of these, 1176 (1.6%) were FIA-positive, and the proportion of RT-PCR-confirmed samples was 40.5%. Our data show that the probability of confirmation was directly dependent from the semi-quantitative FIA results. In addition, the molecularly confirmed samples were those with high levels of virus and that were actually harboring infectious virus. These results support public health strategies based on early mass screening campaigns by RAT in settings where molecular testing is not feasible or easily accessible, such as points of entry. This approach would contribute to promptly controlling viral spread through travel, which is now of particular concern due to the spread of SARS-CoV-2 variants. Full article

Globally, forests are a crucial natural resource, and their sound management is critical for human and ecosystem health and well-being. Efforts to manage forests depend upon reliable data on the status of and trends in forest resources. When these data come from well-designed natural resource monitoring (NRM) systems, decision makers can make science-informed decisions. National forest inventories (NFIs) are a cornerstone of NRM systems, but require capacity and skills to implement. Efficiencies can be gained by incorporating auxiliary information derived from remote sensing (RS) into ground-based forest inventories. However, it can be difficult for countries embarking on NFI development to choose among the various RS integration options, and to develop a harmonized vision of how NFI and RS data can work together to meet monitoring needs. The NFI of the United States, which has been conducted by the USDA Forest Service’s (USFS) Forest Inventory and Analysis (FIA) program for nearly a century, uses RS technology extensively. Here we review the history of the use of RS in FIA, beginning with general background on NFI, FIA, and sampling statistics, followed by a description of the evolution of RS technology usage, beginning with paper aerial photography and ending with present day applications and future directions. The goal of this review is to offer FIA’s experience with NFI-RS integration as a case study for other countries wishing to improve the efficiency of their NFI programs. Full article

Pine forests in the southern United States are a major contributor to the global economy. Through the last three decades, however, there have been concerns about the decline of pine forests attributed mostly to pests and pathogens. A combination of biotic agents and environmental factors and their interaction often influences outbreaks and the resultant damage in the forests. Southern pines experience periodic mortality from bark beetles and root rot fungi and losses from fusiform rust and pitch canker have long been important for management. In recent years, there is also growing evidence of increasing damage from foliar disease in southern pines. Early detection of diseases following changes in foliar characteristics and assessment of potential risks will help us better utilize our resources and manage these forests sustainably. In this study, we used Forest Inventory and Analysis (FIA) data to explore the intensity of foliar disease in three common pines: loblolly (Pinus taeda L.), longleaf (Pinus palustris Mill.), and slash (Pinus elliottii Engelm.) in spatial and temporal terms using tree-level and climatic variables. Results from a tree-level model suggests that crown ratio may be an important factor in pine foliar disease (p < 0.1). We applied the MaxEnt model, a presence-only species distribution model (SDM), to explore any association of foliar disease incidences with the climatic variables at a landscape level. Results indicate that mean dew point temperature, maximum vapor pressure deficit, and precipitation during cold months had more influence over disease incidences than other climatic variables. While the sample size is limited as this is an emerging disease in the region, our study provides a basis for further exploration of disease detection methods, disease etiology studies, and hazard mapping. Full article