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- Vigilância Laboratorial da Tuberculose em Portugal: relatório 2023Publication . Laboratório Nacional de Referência de MicobactériasPor ocasião do Dia Mundial da Tuberculose que se celebra a 24 março, este ano dedicado ao tema "Sim! Nós podemos acabar com a TB!”, o Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) disponibiliza o relatório de Vigilância Laboratorial da Tuberculose em Portugal referente ao ano de 2023, elaborado pelo Laboratório Nacional de Referência de Micobactérias do seu Departamento de Doenças Infeciosas. Em 2019, e com a disseminação dos métodos de sequenciação genómica de nova geração, o Laboratório de Tuberculose e Micobactérias (atualmente, Laboratório Nacional de Referência de Micobactérias, LNR-TB), implementou metodologias baseadas em sequenciação do genoma total (WGS, whole genome sequencing) para efetuar, de forma sistemática e rotineira, a previsão de resistências e vigilância molecular dos casos de Tuberculose multirresistente (TB-RR/MR) em articulação com as Autoridades de Saúde. Em 2023, o LNR-TB publicou o seu primeiro relatório de vigilância molecular, que incluiu dados retrospetivos de 2020-2022, com informações genómicas das estirpes de MTC (complexo Mycobacterium tuberculosis) em circulação em Portugal, não só dos casos resistentes como também dos casos sensíveis. O presente relatório referente ao ano de 2023 pretende dar continuidade a este sistema de vigilância mais abrangente e robusto, fazendo a análise de possíveis relações filogenéticas de todas as estirpes de MTC isoladas no LNR-TB desde 2020, num contexto de confirmação diagnóstica inicial do caso de TB, enquadrando-as nas análises moleculares das estirpes que já se encontravam em vigilância desde 2013 (isto é, casos de TB- MR ou suspeitas de surtos). Do relatório apresentado, destacam-se os seguintes resultados: - A confirmação bacteriológica da TB é essencial para a monitorização da doença e para o conhecimento do perfil de suscetibilidade aos antimicrobianos, pelo que devem ser sempre solicitadas análises laboratoriais auxiliares ao diagnóstico. - Embora entre 2013 e 2022 se tenha assistido a uma tendência decrescente no número de casos de TB-RR/MR, com uma redução média de 2%/ano, em 2023 foram diagnosticados 20 novos casos de TB-RR/MR, correspondendo a um aumento de 50% relativamente a 2022. - No global, a maioria dos casos de TB-RR/MR continua a ocorrer na região de Lisboa e Vale do Tejo, seguido da região Norte, e com uma tendência crescente na região do Algarve que importa vigiar.
- Field evaluation of an automated mosquito surveillance system which classifies Aedes and Culex mosquitoes by genus and sexPublication . González-Pérez, María I.; Faulhaber, Bastian; Aranda, Carles; Williams, Mark; Villalonga, Pancraç; Silva, Manuel; Costa Osório, Hugo; Encarnaçao, Joao; Talavera, Sandra; Busquets, NúriaBackground: Mosquito-borne diseases are a major concern for public and veterinary health authorities, highlighting the importance of effective vector surveillance and control programs. Traditional surveillance methods are labor-intensive and do not provide high temporal resolution, which may hinder a full assessment of the risk of mosquito-borne pathogen transmission. Emerging technologies for automated remote mosquito monitoring have the potential to address these limitations; however, few studies have tested the performance of such systems in the field. Methods: In the present work, an optical sensor coupled to the entrance of a standard mosquito suction trap was used to record 14,067 mosquito flights of Aedes and Culex genera at four temperature regimes in the laboratory, and the resulting dataset was used to train a machine learning (ML) model. The trap, sensor, and ML model, which form the core of an automated mosquito surveillance system, were tested in the field for two classification purposes: to discriminate Aedes and Culex mosquitoes from other insects that enter the trap and to classify the target mosquitoes by genus and sex. The field performance of the system was assessed using balanced accuracy and regression metrics by comparing the classifications made by the system with those made by the manual inspection of the trap. Results: The field system discriminated the target mosquitoes (Aedes and Culex genera) with a balanced accuracy of 95.5% and classified the genus and sex of those mosquitoes with a balanced accuracy of 88.8%. An analysis of the daily and seasonal temporal dynamics of Aedes and Culex mosquito populations was also performed using the time-stamped classifications from the system. Conclusions: This study reports results for automated mosquito genus and sex classification using an optical sensor coupled to a mosquito trap in the field with highly balanced accuracy. The compatibility of the sensor with commercial mosquito traps enables the sensor to be integrated into conventional mosquito surveillance methods to provide accurate automatic monitoring with high temporal resolution of Aedes and Culex mosquitoes, two of the most concerning genera in terms of arbovirus transmission.
- Changes in environmental exposures over decades may influence the genetic architecture of severe spermatogenic failurePublication . Cerván-Martín, Miriam; González-Muñoz, Sara; Guzmán-Jiménez, Andrea; Higueras-Serrano, Inmaculada; Castilla, José A.; Garrido, Nicolás; Luján, Saturnino; Bassas, Lluís; Seixas, Susana; Gonçalves, João; Lopes, Alexandra M; Larriba, Sara; Palomino-Morales, Rogelio J.; Bossini-Castillo, Lara; Carmona, F. DavidStudy question: Do the genetic determinants of idiopathic severe spermatogenic failure (SPGF) differ between generations? Summary answer: Our data support that the genetic component of idiopathic SPGF is impacted by dynamic changes in environmental exposures over decades. What is known already: The idiopathic form of SPGF has a multifactorial etiology wherein an interaction between genetic, epigenetic, and environmental factors leads to the disease onset and progression. At the genetic level, genome-wide association studies (GWASs) allow the analysis of millions of genetic variants across the genome in a hypothesis-free manner, as a valuable tool for identifying susceptibility risk loci. However, little is known about the specific role of non-genetic factors and their influence on the genetic determinants in this type of conditions. Study design, size, duration: Case-control genetic association analyses were performed including a total of 912 SPGF cases and 1360 unaffected controls. Participants/materials, setting, methods: All participants had European ancestry (Iberian and German). SPGF cases were diagnosed during the last decade either with idiopathic non-obstructive azoospermia (n = 547) or with idiopathic non-obstructive oligozoospermia (n = 365). Case-control genetic association analyses were performed by logistic regression models considering the generation as a covariate and by in silico functional characterization of the susceptibility genomic regions. Main results and the role of chance: This analysis revealed 13 novel genetic association signals with SPGF, with eight of them being independent. The observed associations were mostly explained by the interaction between each lead variant and the age-group. Additionally, we established links between these loci and diverse non-genetic factors, such as toxic or dietary habits, respiratory disorders, and autoimmune diseases, which might potentially influence the genetic architecture of idiopathic SPGF. Large scale data: GWAS data are available from the authors upon reasonable request. Limitations, reasons for caution: Additional independent studies involving large cohorts in ethnically diverse populations are warranted to confirm our findings. Wider implications of the findings: Overall, this study proposes an innovative strategy to achieve a more precise understanding of conditions such as SPGF by considering the interactions between a variable exposome through different generations and genetic predisposition to complex diseases.
- Anomalias Congénitas: Defeitos do Tubo NeuralPublication . Equipa do Registo Nacional de Anomalias CongénitasO infográfico Anomalias Congénitas: Defeitos do Tubo Neural (DTN) evidencia o facto da prevenção primária dos DNT em Portugal estar comprometida, devido à baixa proporção de mulheres que inicia a toma de ácido fólico antes da gravidez. O infográfico apresentado abrange o período 2017-2018 e tem como fonte de dados o Registo Nacional de Anomalias Congénitas – RENAC (dados de mulheres com nascimentos com AC) e a Rede Médicos-Sentinela – RMS (dados de mulheres com nascimentos sem AC).
- Anomalias Congénitas: Fatores de Risco – Idade maternaPublication . Equipa do Registo Nacional de Anomalias CongénitasO infográfico Anomalias Congénitas: Fatores de Risco – Idade materna demonstra que em Portugal tem aumentado a proporção de nascimentos com anomalias congénitas nas idades maternas mais tardias. A análise apresentada tem como fonte de dados o RENAC e abrange o período compreendido entre 2011 e 2019.
- Interventions for increasing energy efficiency in hospitals (Protocol)Publication . Chen-Xu, José; Kislaya, Irina; Fernandes, Ricardo M; Carvalho, Joana; Blanco-Rojas, Beatriz J; El-Omrani, Omnia; Miotto, Edoardo; Čič, Katja; Boto, Paulo; Viegas, Susana; Cochrane Central Editorial ServiceThis is a protocol for a Cochrane Review (intervention). The objectives are as follows: The main objective is to assess the effectiveness of interventions designed to increase energy efficiency in hospitals.
- Firefighters’ Occupational Exposure in Preparation for Wildfire Season: Addressing Biological ImpactPublication . Esteves, Filipa; Slezakova, Klara; Madureira, Joana; Vaz, Josiana; Fernandes, Adília; Morais, Simone; Pereira, Maria do Carmo; Teixeira, João Paulo; Costa, SolangeThe characterization of wildland firefighters’ occupational exposure must consider different exposures, including those at the fire station. The present study aimed to characterize the occupational exposure of 172 Northern Portuguese wildland firefighters in fire stations during the pre-wildfire season of 2021. The biological impact of estimated inhaled doses of PM10 and PM2.5 (indoor/outdoor) was accessed through a buccal micronucleus cytome (BMCyt) assay in exfoliated buccal cells of a subgroup of 80 firefighters. No significant association was found between estimated inhaled doses of PM10 and PM2.5 (mean 1.73 ± 0.43 µg kg−1 and 0.53 ± 0.21 µg kg−1, respectively) and biological endpoints. However, increased frequencies of cell death parameters were found among subjects of the Permanent Intervention Teams (full-time firefighters). The intake of nutritional supplements was associated with a significant decrease in micronucleus frequencies (i.e., DNA damage or chromosome breakage). In addition, our findings showed a significantly increased frequency of cell death endpoints (i.e., nuclear fragmentation) with coffee consumption, while daily consumption of vegetables significantly decreased it (i.e., nuclear shrinkage). Our results provide data on the occupational exposure of wildland firefighters while working in fire stations during the pre-wildfire season, providing the essential baseline for further studies throughout the wildfire season.
- Baseline data and associations between urinary biomarkers of polycyclic aromatic hydrocarbons, blood pressure, hemogram, and lifestyle among wildland firefightersPublication . Barros, Bela; Paiva, Ana Margarida; Oliveira, Marta; Alves, Sara; Esteves, Filipa; Fernandes, Adília; Vaz, Josiana; Slezakova, Klara; Costa, Solange; Teixeira, João Paulo; Morais, SimoneIntroduction: Available literature has found an association between firefighting and pathologic pathways leading to cardiorespiratory diseases, which have been linked with exposure to polycyclic aromatic hydrocarbons (PAHs). PAHs are highlighted as priority pollutants by the European Human Biomonitoring Initiative in occupational and non-occupational contexts. Methods: This cross-sectional study is the first to simultaneously characterize six creatinine-adjusted PAHs metabolites (OHPAHs) in urine, blood pressure, cardiac frequency, and hemogram parameters among wildland firefighters without occupational exposure to fire emissions (> 7 days), while exploring several variables retrieved via questionnaires. Results: Overall, baseline levels for total OHPAHs levels were 2 to 23-times superior to the general population, whereas individual metabolites remained below the general population median range (except for 1-hydroxynaphthalene+1-hydroxyacenaphtene). Exposure to gaseous pollutants and/or particulate matter during work-shift was associated with a 3.5-fold increase in total OHPAHs levels. Firefighters who smoke presented 3-times higher total concentration of OHPAHs than non-smokers (p < 0.001); non-smoker females presented 2-fold lower total OHPAHs (p = 0.049) than males. 1-hydroxypyrene was below the recommended occupational biological exposure value (2.5 μg/L), and the metabolite of carcinogenic PAH (benzo(a)pyrene) was not detected. Blood pressure was above 120/80 mmHg in 71% of subjects. Firefighters from the permanent intervention team presented significantly increased systolic pressure than those who performed other functions (p = 0.034). Tobacco consumption was significantly associated with higher basophils (p = 0.01–0.02) and hematocrit (p = 0.03). No association between OHPAHs and blood pressure was found. OHPAHs concentrations were positively correlated with monocyte, basophils, large immune cells, atypical lymphocytes, and mean corpuscular volume, which were stronger among smokers. Nevertheless, inverse associations were observed between fluorene and pyrene metabolites with neutrophils and eosinophils, respectively, in non-smokers. Hemogram was negatively affected by overworking and lower physical activity. Conclusion: This study suggests possible associations between urinary PAHs metabolites and health parameters in firefighters, that should be further assessed in larger groups.
- ReporType: A Flexible Bioinformatics Tool for Targeted Loci Screening and Typing of Infectious AgentsPublication . Cruz, Helena; Pinheiro, Miguel; Borges, VítorIn response to the pressing need for continuous monitoring of emergence and circulation of pathogens through genomics, it is imperative to keep developing bioinformatics tools that can help in their rapid characterization and classification. Here, we introduce ReporType, a versatile bioinformatics pipeline designed for targeted loci screening and typing of infectious agents. Developed using the snakemake workflow manager, ReporType integrates multiple software for read quality control and de novo assembly, and then applies ABRicate for locus screening, culminating in the production of easily interpretable reports for the identification of pathogen genotypes and/or screening of specific genomic loci. The pipeline accommodates a range of input formats, from Illumina or Oxford Nanopore Technology (ONT) reads (FASTQ) to Sanger sequencing files (AB1), or FASTA files, making it flexible for application in multiple pathogens and with different purposes. ReporType is released with pre-prepared databases for some viruses and bacteria, yet it remains easily configurable to handle custom databases. ReporType performance and functionality were validated through proof-of-concept exercises, encompassing diverse pathogenic species, including viruses such as measles, Newcastle disease virus (NDV), Dengue virus (DENV), influenza, hepatitis C virus (HCV) and Human T-Cell Lymphotropic virus type 1 (HTLV-1), as well as bacteria like and . In summary, ReporType emerges as a simple, dynamic and pan-pathogen tool, poised to evolve in tandem with the ever-changing needs of the fields of pathogen genomics, infectious disease epidemiology, and one health bioinformatics. ReporType is freely available at GitHub.
- Safety and efficacy of a feed additive consisting of 6‐phytase produced by Aspergillus oryzae DSM 33737 (HiPhorius™) for all poultry, all Suidae and all fin fish (DSM Nutritional Products Ltd)Publication . Bampidis, Vasileios; Azimonti, Giovanna; Bastos, Maria de Lourdes; Christensen, Henrik; Dusemund, Birgit; Durjava, Mojca; Kouba, Maryline; López‐Alonso, Marta; López Puente, Secundino; Marcon, Francesca; Mayo, Baltasar; Pechová, Alena; Petkova, Mariana; Ramos, Fernando; Villa, Roberto Edoardo; Woutersen, Ruud; Dierick, Noël; Louro, Henriqueta; Martelli, Giovanna; Tosti, Luca; Anguita, Montserrat; Firmino, Joana P.; Innocenti, Matteo L.; Petenatti, Elisa; Pizzo, Fabiola; Ortuño, Jordi; EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP)Following a request from the European Commission, the EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) was asked to deliver a scientific opinion on the safety and efficacy of 6‐phytase produced by the genetically modified strain Aspergillus oryzae DSM 33737 (HiPhorius™ 10, 40, 20L and 50L) as a zootechnical feed additive for all poultry, all Suidae and all fin fish. The FEEDAP Panel concluded that the genetic modification of the production strain does not give rise to safety concerns. Based on the no observed adverse effect level identified in a subchronic oral toxicity study in rats, the additive was considered safe for all poultry, all Suidae and all fin fish at the proposed conditions of use. The Panel also concluded that the use of the product as a feed additive is of no concern for the consumers and the environment. The liquid formulations of the additive are not skin or eye irritants. The two solid ones are not skin irritants but are eye irritants. Owing to the lack of data, the Panel cannot conclude on the skin sensitisation of the final formulations of the additive. Due to the proteinaceous nature of the active substance (6‐phytase), the additive is considered a respiratory sensitiser. The Panel concludes that the additive is efficacious when included in the diet of poultry for fattening or reared for laying/breeding, reproductive Suidae, and all fin fish. Due to the lack of sufficient data, the Panel could not conclude on the efficacy for laying and reproductive poultry and growing Suidae.