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Introduction: Exacerbations are common in individuals with alpha-1 antitrypsin deficiency (AATD)-related lung disease. This study intended to identify independent predictive factors for exacerbations in AATD using the Portuguese European Alpha-1 Research Collaboration (EARCO) registry. Methods: This study includes patients from the Portuguese EARCO registry, a prospective multicenter cohort (NCT04180319). From October 2020 to April 2023, this registry enrolled 137 patients, 14 of whom were excluded for analysis for either missing 12 months of follow-up or baseline pulmonary function. Results: Among the 123 AATD patients, 27 (22.0%) had at least one exacerbation in the last 12 months of follow-up. Patients with Pi*ZZ phenotype were three times more likely than the rest of the population to experience any exacerbation (32.7 vs. 14.1%, p = 0.014; OR 3.0). BODE index was significantly higher in exacerbators than in non-exacerbators (3.9 ± 2.4 vs. 1.3 ± 1.2; p < 0.001), including on multivariate analysis (p = 0.002). Similar results were found for BODEx (multivariate p < 0.001). DLCO was the only functional parameter independently associated with exacerbations (p = 0.024). Conclusions: DLCO, BODE, and BODEx were independent predictors of exacerbations at 12 months in AATD patients. Understanding these risk factors can aid decision-making on AATD-related lung disease management and improve patient outcomes. [ABSTRACT FROM AUTHOR]

Planning for biodiversity conservation and management requires understanding the underlying ecological and socio‐economic trade‐offs. In this study held in extensive grasslands of Southern Portugal, we investigated: (a) how pollinators, potential agricultural pests and natural enemies relate with yield (above‐ground vegetation biomass) and vegetation quality (crude protein content [CPC]), two important provisioning services provided by grasslands; and (b) how the abundance of target taxa can be favoured or controlled through farmland management. We expected to provide preliminary knowledge into the effects of annual weather variability on both modulating the association of the target taxa with vegetation biomass and CPC, thereby conditioning the management measures required to optimise those services. Vegetation and arthropods were sampled in May from 2012 to 2014. Linear mixed models were used to examine the relationship of arthropod abundance with yield, vegetation quality and management variables. Vegetation biomass better explained the abundance of bees, leafhoppers and ladybird beetles, whereas aphids and ichneumonid wasps were more associated to CPC (bees presented contrasting annual responses). Higher stocking rates favoured higher abundance of aphids, and contrasting annual responses were found for chalcid wasps and bees. Higher cultivation frequency was related with lower abundance of aphids, spiders, chalcid wasps and ladybird beetles. There was high annual variability in the relationship of target groups with vegetation biomass and CPC, as well as in the effects of management variables on target groups. Therefore, annual changes in trade‐offs between the potential for ecosystem services (pollination, biological control) and disservices (crop pest‐infestation) associated with these groups may be foreseen, according to yearly conditions. [ABSTRACT FROM AUTHOR]

Viral infections are known to be the main trigger for Chronic obstructive pulmonary disease (COPD) exacerbations. Face masks are acknowledged for effective viral aerosol shedding reduction. COVID-19 pandemic generated an opportunity to study the impact of face masks and confinement on droplet transmission diseases, usually implicated in acute exacerbations of COPD (AECOPD). We aimed to evaluate the variation on severe AECOPD (sAECOPD) rate in a Portuguese COPD cohort during the first COVID-19 lockdown and following months. This retrospective self-controlled study enrolled 322 adult patients followed at COPD-specialized consultation in a tertiary hospital from February 2016 to July 2020, of whom 286 met inclusion criteria. Severe AECOPD events were registered from March 2020 (beginning of state of emergency) until July 2020. From 2016 to 2019 there was a mean of 38 patients per year with sAECOPD. During 2020, 11 patients experienced sAECOPD. Over the course of 2020 there was a 73.4% (p < 0.001) decrease in sAECOPD events comparing with previous years' average. After the end of State of Emergency, the rate of sAECOPD events also declined by 74.6% (p < 0.001) comparing with the same timeline of previous years. Results were consistent and statistically significant when comparing 2020 with each of previous years for every period of analysis. Our findings suggest a sustained decrease in the rate of sAECOPD during confinement and in the following months. The widespread use of face mask and social distancing during COVID-19 pandemic may play an important role in preventing the transmission of respiratory infections and consequently reducing sAECOPD. [ABSTRACT FROM AUTHOR]

Background: Estimation of temporal changes in human immunodeficiency virus (HIV) transmission patterns can help to elucidate the impact of preventive strategies and public health policies.Methods: Portuguese HIV-1 subtype B and G pol genetic sequences were appended to global reference data sets to identify country-specific transmission clades. Bayesian birth-death models were used to estimate subtype-specific effective reproductive numbers (Re). Discrete trait analysis (DTA) was used to quantify mixing among transmission groups.Results: We identified 5 subtype B Portuguese clades (26-79 sequences) and a large monophyletic subtype G Portuguese clade (236 sequences). We estimated that major shifts in HIV-1 transmission occurred around 1999 (95% Bayesian credible interval [BCI], 1998-2000) and 2000 (95% BCI, 1998-2001) for subtypes B and G, respectively. For subtype B, Re dropped from 1.91 (95% BCI, 1.73-2.09) to 0.62 (95% BCI,.52-.72). For subtype G, Re decreased from 1.49 (95% BCI, 1.39-1.59) to 0.72 (95% BCI, .63-.8). The DTA suggests that people who inject drugs (PWID) and heterosexuals were the source of most (>80%) virus lineage transitions for subtypes G and B, respectively.Conclusions: The estimated declines in Re coincide with the introduction of highly active antiretroviral therapy and the scale-up of harm reduction for PWID. Inferred transmission events across transmission groups emphasize the importance of prevention efforts for bridging populations. [ABSTRACT FROM AUTHOR]

In recent years, haying has extended to Iberian Mediterranean dry grasslands potentially impacting on grassland bird ecology. We evaluated the impact of haying on a grassland bird community of South Portugal. Our main goals were: (1) to investigate the exposure of different species to haying, (2) to investigate potential removal of nests and dead birds from hayed fields by haying machinery using the ratio (REC) between the expected number of records and the number of records collected and (3) to link clutch destruction and bird mortality with haying management practices. Hayed fields were surveyed for signs of breeding and birds censused prior to mowing. Linear models were computed, linking the REC with haying machinery and sward properties. GLMs and model averaging were used to obtain models linking clutch destruction, bird mortality and haying management variables. Only 4 % of records evidenced successful nesting attempts ( N = 177). REC evaluation suggested high nest or dead bird removal by the machinery, particularly in fields with lower vegetation biomass prior to cutting. Sickle bar mowers and one-rotor rotary rakes returned higher REC but lower probability of found nests removed from the original nesting sites comparatively to discs mowers and wheel rakes. Higher probabilities of mortality events were found in fields mown earlier (but not in all years). On the other hand, lower mortality was found in fields raked with two-rotor rotary rakes. Delayed haying, silage production in temporary crops and the use haying machinery enabling simultaneously mowing and gathering hay in lines are discussed as management alternatives. [ABSTRACT FROM AUTHOR]

According to the EARS-Net surveillance data, Portugal has the highest prevalence of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) in Europe, but the information on MRSA in the community is very scarce and the links between the hospital and community are not known. In this study we aimed to understand the events associated to the recent sharp increase in MRSA frequency in Portugal and to evaluate how this has shaped MRSA epidemiology in the community. With this purpose, 180 nosocomial MRSA isolates recovered from infection in two time periods and 14 MRSA isolates recovered from 89 samples of skin and soft tissue infections (SSTI) were analyzed by pulsed-field gel electrophoresis (PFGE), staphylococcal chromosome cassette mec (SCCmec) typing, spa typing and multilocus sequence typing (MLST). All isolates were also screened for the presence of Panton Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) by PCR. The results showed that ST22-IVh, accounting for 72% of the nosocomial isolates, was the major clone circulating in the hospital in 2010, having replaced two previous dominant clones in 1993, the Iberian (ST247-I) and Portuguese (ST239-III variant) clones. Moreover in 2010, three clones belonging to CC5 (ST105-II, ST125-IVc and ST5-IVc) accounted for 20% of the isolates and may represent the beginning of new waves of MRSA in this hospital. Interestingly, more than half of the MRSA isolates (8/14) causing SSTI in people attending healthcare centers in Portugal belonged to the most predominant clones found in the hospital, namely ST22-IVh (n = 4), ST5-IVc (n = 2) and ST105-II (n = 1). Other clones found included ST5-V (n = 6) and ST8-VI (n = 1). None of the MRSA isolates carried PVL and only five isolates (ST5-V-t179) carried ACME type II. The emergence and spread of EMRSA-15 may be associated to the observed increase in MRSA frequency in the hospital and the consequent spillover of MRSA into the community. [ABSTRACT FROM AUTHOR]

• GLMMs analysed weevil occurrence and abundance of each of its two annual generations. • Threshold for the positive effect of elevation was set at 360 m a.s.l. • Significant stand-level effects on weevil-induced defoliation. • Increased occurrence probability in large stands. • Higher abundances of both annual generations on 3–8 years-old trees. The weevil Gonipterus platensis is among the most important eucalypt (Eucalyptus spp.) pest species worldwide. In Portugal, weevil-induced damage has great economic significance and efforts are being taken to find adequate alternatives to the biological control of this defoliator by its parasitoid Anaphes nitens , which is ineffective at altitudes above 400 m. With the aim of improving current knowledge on the ecology of G. platensis , we evaluated its interactions with local and landscape factors through the application of generalized linear mixed models for (1) the probability of weevil occurrence in sampling points, and (2) the relative abundance of each of its two annual generations on eucalypt trees. Our models confirmed the significant positive effect of elevation, here found to come off just above 360 m a.s.l., on both the occurrence and the abundance of G. platensis. Moreover, our results denoted that stand-level variables can likewise affect this pest. Points located more than 400 m inside the stands and, to a lesser extent, those comprising smaller (yet mature) eucalypt trees and where trees of other species were absent, showed an increased probability of G. platensis occurrence. Concordantly, significantly higher abundances of both weevil generations were observed on 3–8 years-old eucalypt trees. In addition, there was a negative effect of coppiced stands on G. platensis abundance which was only significant for the first annual generation and probably was related with weevil's recent colonization of stands ravaged by wildfires two years before our field surveys. Weevil populations were not influenced by the density of stand canopy, neither by understory structure and composition, nor by bare soil cover, hence it is not expected that thinning, shrub removal and soil scarification practices can affect G. platensis attacks in eucalypt stands. Overall, our study provides key knowledge on the ecology of G. platensis and its response to local and landscape features, paving the way for enhanced management of eucalypt plantations. [ABSTRACT FROM AUTHOR]

• In South Portugal we linked extensive agriculture, bird richness and cultural ES. • Bird richness decreased when increasing stocking rates. • The peak of biomass production does not correspond to the peak of bird richness. • Agri-enviroment payments do not return profit for farmers in large contracted areas. • Mediterranean drylands can be managed to favour birds, farmers and cultural ES. Agri-environment schemes directly focused on bird conservation have been implemented in agropastoral Mediterranean drylands aiming to guide the design of agricultural landscapes to enhance biodiversity and associated ecosystem services. In this study, by linking agricultural intensification indicators with the richness of grassland specialist birds (RGSB), we aimed to perform a preliminary assessment on the sustainability of the agri-environmental measure "Maintenance of the cereal-fallow dryland rotation" evaluating for potential ecosystem service trade-offs resulting from the application of this measure in Southern Portugal. Our approach is novel by considering simultaneously three major drivers of farmland management ecology (grazing, cropping and haying) in an assessment performed at field level. During the 2012 to 2016 breeding seasons, bird and vegetation samplings were carried to obtain RGSB, and above-ground biomass and crude protein content, which were analysed using Linear Mixed Models (LMM) in relation to grazing, cultivation and haying intensity. Further, a cost-benefit analysis for farmers of the agri-environmental measure was performed. Mixed models indicated a decrease on RGSB when increasing stocking rates and, in a lesser extent, cropping intensity or haying frequency. Vegetation biomass and RGSB (as an indicator of grassland management) were non-linearly associated indicating that the peak of biomass production does not correspond to the peak of bird richness. Crude protein content was negatively associated with RGSB. Cost-benefit analysis showed that agri-enviroment payments can hardly return profit for farmers when contracted areas are higher than 250 ha. Farmers' profits can be maximized by increasing the contracted crop area. We conclude that the management of drylands to maintain these biodiversity-rich Iberian cultural landscapes can be adjusted to favour both bird conservation and farmers and therefore, cultural services linked to species richness such as the potential for ornithological tourism. [ABSTRACT FROM AUTHOR]

The decline of the White Stork (Ciconia ciconia) in the Iberian Peninsula was averted within the last 30 years, partially due to an increase in food availability in landfills. In this study, we compared 2 colonies located at different distances from a landfill in southern Portugal, with the aim of assessing differences in stork diets. We also compared our current results with data from the same colonies before the landfill was built. Additionally, we studied storks' exposure to kleptoparasitism by Black Kites (Milvus migrans) as a potential factor affecting their feeding behavior in landfills. We analyzed 182 pellets collected in 2005 and 2010 in non-landfill colonies and from landfills only in 2010. We carried out >47 h of focal observations of storks feeding at the landfill. Pellet contents are primarily insects (15 families from 5 orders) as well as unidentified and inorganic materials. Our analyses of variance revealed significant local, seasonal, and annual differences in Coleoptera, Orthoptera, Hymenoptera, and total number of insects. Our observations at the landfill showed that storks feed on large amounts of organic material, mostly fresh meat and fish, which means that observational data differs from pellet data. Black Kites kleptoparasitize White Storks mainly at the beginning and end of the morning limiting their food intake and increasing the amount of time storks spend at the landfill. We conclude that foraging in landfills has provoked an important shift in the White Stork's diet, partially replacing these birds' natural food items and exposing them to potential new threats such as the ingestion of inorganic material and exposure to kleptoparasitism by kites. [ABSTRACT FROM AUTHOR]

Conservation agriculture (CA) gained recently some visibility in the Mediterranean region. By affecting soil and plant ecology, CA is expected to influence other biological groups, notably farmland birds. This study aims to assess (1) the importance of tillage regime (conventional vs. no-tillage) and frequency of cultivation under these two regimes in determining the richness and abundance of birds in extensive grasslands originated within rotational cropping systems, and (2) how tillage systems contribute to changes in bird richness and abundance, comparatively to other drivers of bird ecology in Mediterranean farmland. We conducted bird censuses (point counts) from 2012 to 2016 in 34-52 fields per year of 15 farms in Évora region (Southern Portugal). Generalized Linear Mixed Models were used to link bird abundance/richness with agricultural descriptors. Both tillage regime and cultivation frequency showed weak effects on Species richness and Total bird abundance. However, a strong variability in the response to tillage descriptors was found between species. For the little bustard and the Iberian grey shrike, a strong interaction with the annual weather regime and opposite trends for the effect of tillage regime were detected. Despite its moderate influence on bird assemblages comparatively to other major drivers of bird richness and abundance (i.e. grazing and annual weather regime), CA could constitute a potential complementary "greening measure" to manage extensive grasslands within rotational cropping systems, particularly in areas where soil erosion is a problem, although some species may not benefit from its implementation., (Copyright © 2018 Elsevier Ltd. All rights reserved.)

Portugal is the European country with the highest prevalence of methicillin resistant Staphylococcus aureus (MRSA), in which EMRSA-15 (ST22-IVh) has been the dominant clone since soon after its introduction in Portuguese hospitals in 2001. In this study, we intend to not only, assess the evolution of the invasive MRSA in Portuguese hospitals, but also to evaluate the invasive methicillin susceptible S. aureus (MSSA) population and the relationship between both populations. In the current study, two major MRSA clones were identified: EMRSA-15 that has been dominant for more than 10 years and accounts for 75% of the MRSA isolates, and ST105-II, a clone related with the New York/Japan clone (ST5-II). In contrast, among MSSA, several clonal backgrounds were identified. Despite of the massive predominance of EMRSA-15 in the last decade, an increase in spa diversity has been observed in the last few years, which suggests a recent and local diversification of this clone. Interestingly, MRSA and MSSA populations with related clonal backgrounds appear to have increased as a result of the dissemination of MRSA to the community environment.

According to the EARS-Net surveillance data, Portugal has the highest prevalence of nosocomial methicillin-resistant Staphylococcus aureus (MRSA) in Europe, but the information on MRSA in the community is very scarce and the links between the hospital and community are not known. In this study we aimed to understand the events associated to the recent sharp increase in MRSA frequency in Portugal and to evaluate how this has shaped MRSA epidemiology in the community. With this purpose, 180 nosocomial MRSA isolates recovered from infection in two time periods and 14 MRSA isolates recovered from 89 samples of skin and soft tissue infections (SSTI) were analyzed by pulsed-field gel electrophoresis (PFGE), staphylococcal chromosome cassette mec (SCCmec) typing, spa typing and multilocus sequence typing (MLST). All isolates were also screened for the presence of Panton Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) by PCR. The results showed that ST22-IVh, accounting for 72% of the nosocomial isolates, was the major clone circulating in the hospital in 2010, having replaced two previous dominant clones in 1993, the Iberian (ST247-I) and Portuguese (ST239-III variant) clones. Moreover in 2010, three clones belonging to CC5 (ST105-II, ST125-IVc and ST5-IVc) accounted for 20% of the isolates and may represent the beginning of new waves of MRSA in this hospital. Interestingly, more than half of the MRSA isolates (8/14) causing SSTI in people attending healthcare centers in Portugal belonged to the most predominant clones found in the hospital, namely ST22-IVh (n = 4), ST5-IVc (n = 2) and ST105-II (n = 1). Other clones found included ST5-V (n = 6) and ST8-VI (n = 1). None of the MRSA isolates carried PVL and only five isolates (ST5-V-t179) carried ACME type II. The emergence and spread of EMRSA-15 may be associated to the observed increase in MRSA frequency in the hospital and the consequent spillover of MRSA into the community.

This two-year study investigated the epidemiology of nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) among patients and healthcare workers (HCWs) in two wards with a high frequency of MRSA isolation, at Hospital Geral de Santo António (HGSA), Portugal. Three point-prevalence surveys per year were carried out. A case-control approach was used to identify potential risk factors associated with MRSA carriage among patients. Incidence rates and risk factors of MRSA carriage among HCWs who were negative at the baseline observation were estimated. Prevalence of MRSA carriage among 276 patients screened was 5.1%. Admission to HGSA or attendance to the Diabetic Foot Outpatient Unit (DFOU) of HGSA within the past 12 months, and previous MRSA isolation were significant risk factors for MRSA carriage. Among HCWs (n = 126), the prevalence of MRSA carriage was 4.8% and the incidence rate was 61/1000 person-years. Nurses and nurse aids were the HCW categories with the highest risk of becoming colonized with MRSA over time (p = 0.01). One HCW chronically colonized was detected. Molecular typing revealed a clonal identity for isolates recovered from patients and HCWs of the same wards, with 88.6% of isolates belonging to the EMRSA-15 (ST22-MRSA-IV) clone.

Six clinical isolates of Enterobacter cloacae isolated in a Portuguese hospital, between April 1999 and November 2000, demonstrated resistance to almost all broad-spectrum cephalosporins, except to cefepime. These isolates were susceptible to quinolones and to aminoglycosides. Isoelectric focusing demonstrated production of beta-lactamases with pIs > 8.0 and by all six isolates, exhibiting a cephalosporinase phenotype. The results of pulsed field gel electrophoresis revealed that these isolates were genetically unrelated. The amino acid sequence of six AmpC beta-lactamases (Eclo1FF, Eclo6FF, Eclo9FF, Eclo10FF, Eclo11FF and Eclo15FF) shared 97-99% homology with the chromosomal AmpC beta-lactamase from E. cloacae P99 and 86-87% homology with those of two plasmid-mediated AmpC beta-lactamases, MIR-1 and ACT-1. This is the first report of chromosomal AmpC beta-lactamase production by E. cloacae isolates in a Portuguese hospital.