The Database of European Forest Insect and Disease Disturbances: DEFID2

Insect and disease outbreaks in forests are biotic disturbances that can profoundly alter ecosystem dynamics. In many parts of the world, these disturbance regimes are intensifying as the climate changes and shifts the distribution of species and biomes. As a result, key forest ecosystem services, such as carbon sequestration, regulation of water flows, wood production, protection of soils, and the conservation of biodiversity, could be increasingly compromised. Despite the relevance of these detrimental effects, there are currently no spatially detailed databases that record insect and disease disturbances on forests at the pan-European scale. Here, we present the new Database of European Forest Insect and Disease Disturbances (DEFID2). It comprises over 650,000 harmonized georeferenced records, mapped as polygons or points, of insects and disease disturbances that occurred between 1963 and 2021 in European forests. The records currently span eight different countries and were acquired through diverse methods (e.g., ground surveys, remote sensing techniques). The records in DEFID2 are described by a set of qualitative attributes, including severity and patterns of damage symptoms, agents, host tree species, climate-driven trigger factors, silvicultural practices, and eventual sanitary interventions. They are further complemented with a satellite-based quantitative characterization of the affected forest areas based on Landsat Normalized Burn Ratio time series, and damage metrics derived from them using the LandTrendr spectral-temporal segmentation algorithm (including onset, duration, magnitude, and rate of the disturbance), and possible interactions with windthrow and wildfire events. The DEFID2 database is a novel resource for many large-scale applications dealing with biotic disturbances. It offers a unique contribution to design networks of experiments, improve our understanding of ecological processes underlying biotic forest disturbances, monitor their dynamics, and enhance their representation in land-climate models. Further data sharing is encouraged to extend and improve the DEFID2 database continuously. The database is freely available at https://jeodpp.jrc.ec.europa.eu/ftp/jrc-opendata/FOREST/DISTURBANCES/DEFID2/.

Divergent abiotic spectral pathways unravel pathogen stress signals across species

Plant pathogens pose increasing threats to global food security, causing yield losses that exceed 30% in food-deficit regions. Xylella fastidiosa (Xf) represents the major transboundary plant pest and one of the world's most damaging pathogens in terms of socioeconomic impact. Spectral screening methods are critical to detect non-visual symptoms of early infection and prevent spread. However, the subtle pathogen-induced physiological alterations that are spectrally detectable are entangled with the dynamics of abiotic stresses. Here, using airborne spectroscopy and thermal scanning of areas covering more than one million trees of different species, infections and water stress levels, we reveal the existence of divergent pathogen- and host-specific spectral pathways that can disentangle biotic-induced symptoms. We demonstrate that uncoupling this biotic-abiotic spectral dynamics diminishes the uncertainty in the Xf detection to below 6% across different hosts. Assessing these deviating pathways against another harmful vascular pathogen that produces analogous symptoms, Verticillium dahliae, the divergent routes remained pathogen- and host-specific, revealing detection accuracies exceeding 92% across pathosystems. These urgently needed hyperspectral methods advance early detection of devastating pathogens to reduce the billions in crop losses worldwide.

Chlorophyll content estimation in an open-canopy conifer forest with Sentinel-2A and hyperspectral imagery in the context of forest decline

With the advent of Sentinel-2, it is now possible to generate large-scale chlorophyll content maps with unprecedented spatial and temporal resolution, suitable for monitoring ecological processes such as vegetative stress and/or decline. However methodological gaps exist for adapting this technology to heterogeneous natural vegetation and for transferring it among vegetation species or plan functional types. In this study, we investigated the use of Sentinel-2A imagery for estimating needle chlorophyll (C_a+b) in a sparse pine forest undergoing significant needle loss and tree mortality. Sentinel-2A scenes were acquired under two extreme viewing geometries (June vs. December 2016) coincident with the acquisition of high-spatial resolution hyperspectral imagery, and field measurements of needle chlorophyll content and crown leaf area index. Using the high-resolution hyperspectral scenes acquired over 61 validation sites we found the CI chlorophyll index R₇₅₀/R₇₁₀ and Macc index (which uses spectral bands centered at 680 nm, 710 nm and 780 nm) had the strongest relationship with needle chlorophyll content from individual tree crowns (r² = 0.61 and r² = 0.59, respectively; p < 0.001), while TCARI and TCARI/OSAVI, originally designed for uniform agricultural canopies, did not perform as well (r² = 0.21 and r² = 0.01, respectively). Using lower-resolution Sentinel-2A data validated against hyperspectral estimates and ground truth needle chlorophyll content, the red-edge index CI and the Sentinel-specific chlorophyll indices CI-Gitelson, NDRE1 and NDRE2 had the highest accuracy (with r² values >0.7 for June and >0.4 for December; p < 0.001). The retrieval of needle chlorophyll content from the entire Sentinel-2A bandset using the radiative transfer model INFORM yielded r² = 0.71 (RMSE = 8.1 μg/cm²) for June, r² = 0.42 (RMSE = 12.2 μg/cm²) for December, and r² = 0.6 (RMSE = 10.5 μg/cm²) as overall performance using the June and December datasets together. This study demonstrates the retrieval of leaf C_a+b with Sentinel-2A imagery by red-edge indices and by an inversion method based on a hybrid canopy reflectance model that accounts for tree density, background and shadow components common in sparse forest canopies.

High-resolution imagery acquired from an unmanned platform to estimate biophysical and geometrical parameters of olive trees under different irrigation regimes

The experiments were conducted in a fully-productive olive orchard (cv. Frantoio) at the experimental farm of University of Pisa at Venturina (Italy) in 2015 to assess the ability of an unmanned aerial vehicle (UAV) equipped with RGB-NIR cameras to estimate leaf area index (LAI), tree height, canopy diameter and canopy volume of olive trees that were either irrigated or rainfed. Irrigated trees received water 4-5 days a week (1348 m3 ha-1), whereas the rainfed ones received a single irrigation of 19 m3 ha-1 to relieve the extreme stress. The flight altitude was 70 m above ground level (AGL), except for one flight (50 m AGL). The Normalized Difference Vegetation Index (NDVI) was calculated by means of the map algebra technique. Canopy volume, canopy height and diameter were obtained from the digital surface model (DSM) obtained through automatic aerial triangulation, bundle block adjustment and camera calibration methods. The NDVI estimated on the day of the year (DOY) 130 was linearly correlated with both LAI and leaf chlorophyll measured on the same date (R2 = 0.78 and 0.80, respectively). The correlation between the on ground measured canopy volumes and the ones by the UAV-RGB camera techniques yielded an R2 of 0.71-0.86. The monthly canopy volume increment estimated from UAV surveys between (DOY) 130 and 244 was highly correlated with the daily water stress integral of rainfed trees (R2 = 0.99). The effect of water stress on the seasonal pattern of canopy growth was detected by these techniques in correspondence of the maximum level of stress experienced by the rainfed trees. The highest level of accuracy (RMSE = 0.16 m) in canopy height estimation was obtained when the flight altitude was 50 m AGL, yielding an R2 value of 0.87 and an almost 1:1 ratio of measured versus estimated canopy height.

Previsual symptoms of Xylella fastidiosa infection revealed in spectral plant-trait alterations

Plant pathogens cause significant losses to agricultural yields and increasingly threaten food security¹, ecosystem integrity and societies in general^2-5. Xylella fastidiosa is one of the most dangerous plant bacteria worldwide, causing several diseases with profound impacts on agriculture and the environment⁶. Primarily occurring in the Americas, its recent discovery in Asia and Europe demonstrates that X. fastidiosa's geographic range has broadened considerably, positioning it as a reemerging global threat that has caused socioeconomic and cultural damage^7,8. X. fastidiosa can infect more than 350 plant species worldwide⁹, and early detection is critical for its eradication⁸. In this article, we show that changes in plant functional traits retrieved from airborne imaging spectroscopy and thermography can reveal X. fastidiosa infection in olive trees before symptoms are visible. We obtained accuracies of disease detection, confirmed by quantitative polymerase chain reaction, exceeding 80% when high-resolution fluorescence quantified by three-dimensional simulations and thermal stress indicators were coupled with photosynthetic traits sensitive to rapid pigment dynamics and degradation. Moreover, we found that the visually asymptomatic trees originally scored as affected by spectral plant-trait alterations, developed X. fastidiosa symptoms at almost double the rate of the asymptomatic trees classified as not affected by remote sensing. We demonstrate that spectral plant-trait alterations caused by X. fastidiosa infection are detectable previsually at the landscape scale, a critical requirement to help eradicate some of the most devastating plant diseases worldwide.

Interventions to decrease short-term peripheral venous catheter-related bloodstream infections: impact on incidence and mortality

BACKGROUND

Short-term peripheral venous catheters are a significant source of healthcare-acquired bloodstream infections and a preventable cause of death.

AIM

To assess the effectiveness of interventions applied to reduce the incidence and mortality associated with short-term peripheral venous catheter-related bloodstream infections (PVCR-BSIs).

METHODS

The intervention included continuous PVCR-BSI surveillance, implementation of preventive measures related to catheter insertion and maintenance in accordance with evidence-based recommendations and the hospital's own data, front-line staff educational campaigns, and assessment of adherence to hospital guidelines by ward rounds. A Poisson regression model was used to estimate the trend of rate per year.

FINDINGS

From January 2003 to December 2016, 227 episodes of PVCR-BSI were identified among hospitalized patients at a university hospital. The mean age of patients was 67 years (standard deviation 14 years), 69% were male and the median Charlson score was 3 (interquartile range 2-5). Staphylococcus aureus caused 115 (50.7%) episodes. Thirty-day mortality was 13.2%. After implementation of the intervention, the incidence of PVCR-BSIs decreased significantly from 30 episodes in 2003 (1.17 episodes/10,000 patient-days) to eight episodes in 2016 (0.36/10,000 patient-days). The number of episodes caused by S. aureus decreased from 18 episodes in 2003 (0.70/10,000 patient-days) to three episodes in 2016 (0.14/10,000 patient-day), and mortality decreased from seven cases in 2003 (0.27/10,000 patient-days) to zero cases in 2016 (0.00/10,000 patient-days).

CONCLUSIONS

Surveillance, implementation of a multi-modal strategy and periodical assessment of healthcare workers' adherence to hospital guidelines led to a sustained reduction in PVCR-BSIs. This reduction had a major impact on S. aureus BSI rates and associated mortality.

Understanding the temporal dimension of the red-edge spectral region for forest decline detection using high-resolution hyperspectral and Sentinel-2a imagery

The operational monitoring of forest decline requires the development of remote sensing methods that are sensitive to the spatiotemporal variations of pigment degradation and canopy defoliation. In this context, the red-edge spectral region (RESR) was proposed in the past due to its combined sensitivity to chlorophyll content and leaf area variation. In this study, the temporal dimension of the RESR was evaluated as a function of forest decline using a radiative transfer method with the PROSPECT and 3D FLIGHT models. These models were used to generate synthetic pine stands simulating decline and recovery processes over time and explore the temporal rate of change of the red-edge chlorophyll index (CI) as compared to the trajectories obtained for the structure-related Normalized Difference Vegetation Index (NDVI). The temporal trend method proposed here consisted of using synthetic spectra to calculate the theoretical boundaries of the subspace for healthy and declining pine trees in the temporal domain, defined by CI_time=n/CI_time=n+1 vs. NDVI_time=n/NDVI_time=n+1. Within these boundaries, trees undergoing decline and recovery processes showed different trajectories through this subspace. The method was then validated using three high-resolution airborne hyperspectral images acquired at 40 cm resolution and 260 spectral bands of 6.5 nm full-width half-maximum (FWHM) over a forest with widespread tree decline, along with field-based monitoring of chlorosis and defoliation (i.e., 'decline' status) in 663 trees between the years 2015 and 2016. The temporal rate of change of chlorophyll vs. structural indices, based on reflectance spectra extracted from the hyperspectral images, was different for trees undergoing decline, and aligned towards the decline baseline established using the radiative transfer models. By contrast, healthy trees over time aligned towards the theoretically obtained healthy baseline. The applicability of this temporal trend method to the red-edge bands of the MultiSpectral Imager (MSI) instrument on board Sentinel-2a for operational forest status monitoring was also explored by comparing the temporal rate of change of the Sentinel-2-derived CI over areas with declining and healthy trees. Results demonstrated that the Sentinel-2a red-edge region was sensitive to the temporal dimension of forest condition, as the relationships obtained for pixels in healthy condition deviated from those of pixels undergoing decline.

Mortality risk factors among non-ICU patients with nosocomial vascular catheter-related bloodstream infections: a prospective cohort study

BACKGROUND

Vascular catheter-related bloodstream infections (CRBSIs) are highly preventable hospital-acquired infections and a major threat to patient safety. While there is significant information regarding CRBSI outcome among intensive care unit (ICU) patients, data regarding non-ICU patients are scarce.

AIM

To determine the risk factors associated with 30-day mortality among non-ICU patients with nosocomial CRBSIs.

METHODS

Prospective cohort study of non-ICU patients with nosocomial CRBSIs in a tertiary care centre between January 2004 and December 2014. The primary outcome was 30-day mortality, defined as death from any cause within 30 days of CRBSI. Follow-up was performed 30 days after CRBSI onset. Time until death was the dependent variable in Cox regression analysis.

FINDINGS

In total, 546 cases of CRBSI were identified. The mean age of patients was 64.5 years [interquartile range (IQR) 55-75 years], 66% were male, and the mean Charlson score was 3.59 (IQR 2-5). Of the 546 cases, 58.4% resulted from central venous catheters and 41.6% from peripheral venous catheters. The causative agents were Gram-positive cocci (70.1% of cases), Gram-negative bacilli (31.1%) and Candida spp. (1%). Mortality within 30 days was 13.9%, with no significant changes over the study period. Independent risk factors for 30-day mortality were Charlson score ≥4 [hazard ratio (HR) 1.80, 95% confidence interval (CI) 1.19-2.73], Staphylococcus aureus infection (HR 2.67, 95% CI 1.61-4.43) and Candida spp. infection (HR 6.1, 95% CI 2.08-18.04). Age; area of admission; type, use and site of vascular catheter; and administration of appropriate empirical antibiotic treatment were not independent risk factors for 30-day mortality.

CONCLUSION

Nosocomial CRBSIs outside ICUs are associated with high risk of mortality, particularly among patients with a higher Charlson score and bloodstream infections caused by Staphylococcus aureus and Candida spp.

A Novel Remote Sensing Approach for Prediction of Maize Yield Under Different Conditions of Nitrogen Fertilization

Maize crop production is constrained worldwide by nitrogen (N) availability and particularly in poor tropical and subtropical soils. The development of affordable high-throughput crop monitoring and phenotyping techniques is key to improving maize cultivation under low-N fertilization. In this study several vegetation indices (VIs) derived from Red-Green-Blue (RGB) digital images at the leaf and canopy levels are proposed as low-cost tools for plant breeding and fertilization management. They were compared with the performance of the normalized difference vegetation index (NDVI) measured at ground level and from an aerial platform, as well as with leaf chlorophyll content (LCC) and other leaf composition and structural parameters at flowering stage. A set of 10 hybrids grown under five different nitrogen regimes and adequate water conditions were tested at the CIMMYT station of Harare (Zimbabwe). Grain yield and leaf N concentration across N fertilization levels were strongly predicted by most of these RGB indices (with R (2)~ 0.7), outperforming the prediction power of the NDVI and LCC. RGB indices also outperformed the NDVI when assessing genotypic differences in grain yield and leaf N concentration within a given level of N fertilization. The best predictor of leaf N concentration across the five N regimes was LCC but its performance within N treatments was inefficient. The leaf traits evaluated also seemed inefficient as phenotyping parameters. It is concluded that the adoption of RGB-based phenotyping techniques may significantly contribute to the progress of plant breeding and the appropriate management of fertilization.

Unmanned aerial platform-based multi-spectral imaging for field phenotyping of maize

BACKGROUND

Recent developments in unmanned aerial platforms (UAP) have provided research opportunities in assessing land allocation and crop physiological traits, including response to abiotic and biotic stresses. UAP-based remote sensing can be used to rapidly and cost-effectively phenotype large numbers of plots and field trials in a dynamic way using time series. This is anticipated to have tremendous implications for progress in crop genetic improvement.

RESULTS

We present the use of a UAP equipped with sensors for multispectral imaging in spatial field variability assessment and phenotyping for low-nitrogen (low-N) stress tolerance in maize. Multispectral aerial images were used to (1) characterize experimental fields for spatial soil-nitrogen variability and (2) derive indices for crop performance under low-N stress. Overall, results showed that the aerial platform enables to effectively characterize spatial field variation and assess crop performance under low-N stress. The Normalized Difference Vegetation Index (NDVI) data derived from spectral imaging presented a strong correlation with ground-measured NDVI, crop senescence index and grain yield.

CONCLUSION

This work suggests that the aerial sensing platform designed for phenotyping studies has the potential to effectively assist in crop genetic improvement against abiotic stresses like low-N provided that sensors have enough resolution for plot level data collection. Limitations and future potential uses are also discussed.

[Programs for optimizing the use of antibiotics (PROA) in Spanish hospitals: GEIH-SEIMC, SEFH and SEMPSPH consensus document]

The antimicrobial agents are unique drugs for several reasons. First, their efficacy is higher than other drugs in terms of reduction of morbidity and mortality. Also, antibiotics are the only group of drugs associated with ecological effects, because their administration may contribute to the emergence and spread of microbial resistance. Finally, they are used by almost all medical specialties. Appropriate use of antimicrobials is very complex because of the important advances in the management of infectious diseases and the spread of antibiotic resistance. Thus, the implementation of programs for optimizing the use of antibiotics in hospitals (called PROA in this document) is necessary. This consensus document defines the objectives of the PROA (namely, to improve the clinical results of patients with infections, to minimise the adverse events associated to the use of antimicrobials including the emergence and spread of antibiotic resistance, and to ensure the use of the most cost-efficacious treatments), and provides recommendations for the implementation of these programs in Spanish hospitals. The key aspects of the recommendations are as follows. Multidisciplinary antibiotic teams should be formed, under the auspices of the Infection Committees. The PROA need to be considered as part of institutional programs and the strategic objectives of the hospital. The PROA should include specific objectives based on measurable indicators, and activities aimed at improving the use of antimicrobials, mainly through educational activities and interventions based more on training activities directed to prescribers than just on restrictive measures.

Methicillin-susceptible Staphylococcus aureus clone related to the early pandemic phage type 80/81 causing an outbreak among residents of three occupational centres in Barcelona, Spain

In the 1950s an unusually virulent and transmissible penicillin-resistant Staphylococcus aureus clone harbouring Panton-Valentine leukocidin (PVL) genes, known as phage type 80/81 and subsequently identified as multilocus sequence type (ST) 30, emerged and caused serious infections in hospitals and the community. We describe an outbreak of skin infections caused by a PVL-positive, methicillin-susceptible S. aureus (MSSA) strain of ST1472, related to phage type 80/81, in three associated occupational centres. After identification of the first patient an active case-finding strategy was initiated among the three centres. Epidemiological and clinical features were indistinguishable from outbreaks currently caused by community-acquired methicillin-resistant S. aureus. The S. aureus was cultured and identified from nasal swabs and skin lesions by conventional methods; PVL was detected using a PCR assay. Pulsed-field gel electrophoresis and DNA-array-based genotyping were applied to MSSA isolates. MSSA was identified in nasal swabs from 49 of 133 individuals (37%). A single pulsed-field gel electrophoresis pattern, belonging to ST1472 (CC30) and PVL positivity, were detected in 20 individuals, including eight of 18 skin cultures, i.e. 15% of the screened individuals were colonized by the epidemic strain. Nasal and cutaneous decontamination with 5% nasal mupirocin ointment and 2% aqueous chlorhexidine was implemented for all individuals. Patients with active skin infections were treated with a first-generation cephalosporin. General recommendations were made to prevent cross-transmission. No new cases were reported over the following 90 days.

Clinical epidemiology and outcomes of peripheral venous catheter-related bloodstream infections at a university-affiliated hospital

Despite enormous clinical experience of using peripheral vascular catheters, there is still controversy over the incidence and clinical relevance of bloodstream infections caused by these devices and the measures for preventing them. We performed a prospective study to determine the clinical epidemiology and outcomes of nosocomial bloodstream infections caused by short- and mid-line peripheral venous catheters among a group of non-intensive care unit patients. Cases of peripheral venous catheter-related bloodstream infections (PVC-BSIs) were compared to cases of central venous catheter-related bloodstream infections (CVC-BSIs). From October 2001 to March 2003, 150 cases of vascular catheter-related bloodstream infections were identified among 147 patients. Seventy-seven episodes (0.19 cases/1000 patient-days) were PVC-BSIs and 73 episodes (0.18 cases/1000 patient-days) were CVC-BSIs. Compared with CVC-BSIs, patients with PVC-BSIs more often had the catheter inserted in the emergency department (0 vs 42%), had a shorter duration from catheter insertion to bacteraemia (mean: 15.4 vs 4.9 days) and had Staphylococcus aureus (33 vs 53%) more frequently as the causative pathogen. Among patients with PVC-BSIs, catheters inserted in the emergency department had a significantly shorter duration in situ compared with those inserted on hospital wards (mean: 3.7 vs 5.7 days). Patients with PVC-BSIs caused by S. aureus had a higher rate of complicated bacteraemia (7%) and higher overall mortality (27%) than patients with PVC-BSIs caused by other pathogens (0 and 11%, respectively). Bloodstream infections remain underestimated and potentially serious complications of peripheral vascular catheterisation. Targeted interventions should be introduced to minimise this complication.

Predictive factors of meticillin resistance among patients with Staphylococcus aureus bloodstream infections at hospital admission

Meticillin-resistant Staphylococcus aureus (MRSA) is prevalent throughout the healthcare system in Spain, particularly in long-term care facilities (LTCF) and the incidence of MRSA bloodstream infection (MRSA-BSI) at hospital admission is increasing. This study aimed to determine factors that predict meticillin resistance among patients who require hospitalization for S. aureus BSI. We performed a case-control study comparing patients with S. aureus at hospital admission from January 1991 to December 2003. Case patients with MRSA-BSI at hospital admission (N=50) were compared with control patients with meticillin-susceptible S. aureus bloodstream infection (MSSA-BSI) at hospital admission (N=98). The incidence of MRSA-BSI at hospital admission increased significantly from 0.08 cases/1000 hospital admissions in 1991 to 0.37 cases in 2003 (P<0.001). Univariate analysis comparing patients with MRSA- and MSSA-BSI found a significant association between meticillin resistance and age >60 years, female sex, prior MRSA isolation and healthcare-related BSI. No differences were found in underlying conditions such as diabetes, haemodialysis, immunosuppression, source of infection or mortality between the two groups. Multivariate analyses identified prior MRSA isolation [odds ratio (OR): 41; 95% confidence interval (CI): 4-350] and admission from long-term care facilities (OR: 37; 95% CI: 4.5-316) as independent risk factors for MRSA-BSI.