Browsing by Author "Nogueira, Paulo Jorge"
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- Attributable deaths and disability-adjusted life-years caused by infections with antibiotic-resistant bacteria in the EU and the European Economic Area in 2015: a population-level modelling analysisPublication . Cassini, Alessandro; Högberg, Liselotte Diaz; Plachouras, Diamantis; Quattrocchi, Annalisa; Hoxha, Ana; Simonsen, Gunnar Skov; Colomb-Cotinat, Mélanie; Kretzschmar, Mirjam E.; Devleesschauwer, Brecht; Cecchini, Michele; Ouakrim, Driss Ait; Oliveira, Tiago Cravo; Struelens, Marc J.; Suetens, Carl; Monnet, Dominique L.; Strauss, Reinhild; Mertens, Karl; Struyf, Thomas; Catry, Boudewijn; Latour, Katrien; Ivanov, Ivan N.; Dobreva, Elina G.; Tambic Andraševic, Arjana; Soprek, Silvija; Budimir, Ana; Paphitou, Niki; Žemlicková, Helena; Schytte Olsen, Stefan; Wolff Sönksen, Ute; Märtin, Pille; Ivanova, Marina; Lyytikäinen, Outi; Jalava, Jari; Coignard, Bruno; Eckmanns, Tim; Abu Sin, Muna; Haller, Sebastian; Daikos, George L.; Gikas, Achilleas; Tsiodras, Sotirios; Kontopidou, Flora; Tóth, Ákos; Hajdu, Ágnes; Guólaugsson, Ólafur; Kristinsson, Karl G.; Murchan, Stephen; Burns, Karen; Pezzotti, Patrizio; Gagliotti, Carlo; Dumpis, Uga; Liuimiene, Agne; Perrin, Monique; Borg, Michael A.; de Greeff, Sabine C.; Monen, Jos C.M.; Koek, Mayke B.G.; Elstrøm, Petter; Zabicka, Dorota; Deptula, Aleksander; Hryniewicz, Waleria; Caniça, Manuela; Nogueira, Paulo Jorge; Fernandes, Paulo André; Manageiro, Vera; Popescu, Gabriel A.; Serban, Roxana I.; Schréterová, Eva; Litvová, Slavka; Štefkovicová, Mária; Kolman, Jana; Klavs, Irena; Korošec, Aleš; Aracil, Belén; Asensio, Angel; Pérez-Vázquez, María; Billström, Hanna; Larsson, Sofie; Reilly, Jacqui S.; Johnson, Alan; Hopkins, SusanBackground: Infections due to antibiotic-resistant bacteria are threatening modern health care. However, estimating their incidence, complications, and attributable mortality is challenging. We aimed to estimate the burden of infections caused by antibiotic-resistant bacteria of public health concern in countries of the EU and European Economic Area (EEA) in 2015, measured in number of cases, attributable deaths, and disability-adjusted life-years (DALYs). Methods: We estimated the incidence of infections with 16 antibiotic resistance–bacterium combinations from European Antimicrobial Resistance Surveillance Network (EARS-Net) 2015 data that was country-corrected for population coverage. We multiplied the number of bloodstream infections (BSIs) by a conversion factor derived from the European Centre for Disease Prevention and Control point prevalence survey of health-care-associated infections in European acute care hospitals in 2011–12 to estimate the number of non-BSIs. We developed disease outcome models for five types of infection on the basis of systematic reviews of the literature. Findings: From EARS-Net data collected between Jan 1, 2015, and Dec 31, 2015, we estimated 671 689 (95% uncertainty interval [UI] 583 148–763 966) infections with antibiotic-resistant bacteria, of which 63·5% (426 277 of 671 689) were associated with health care. These infections accounted for an estimated 33 110 (28 480–38 430) attributable deaths and 874 541 (768 837–989 068) DALYs. The burden for the EU and EEA was highest in infants (aged <1 year) and people aged 65 years or older, had increased since 2007, and was highest in Italy and Greece. Interpretation: Our results present the health burden of five types of infection with antibiotic-resistant bacteria expressed, for the first time, in DALYs. The estimated burden of infections with antibiotic-resistant bacteria in the EU and EEA is substantial compared with that of other infectious diseases, and has increased since 2007. Our burden estimates provide useful information for public health decision-makers prioritising interventions for infectious diseases.
- Challenging measles case definition: three measles outbreaks in three Health Regions of Portugal, February to April 2018Publication . Augusto, Gonçalo Figueiredo; Cruz, Diogo; Silva, Andreia; Pereira, Natália; Aguiar, Bárbara; Leça, Ana; Serrada, Elisabete; Valente, Paula; Fernandes, Teresa; Guerra, Fernando; Palminha, Paula; Vinagre, Elsa; Lopo, Sílvia; Cordeiro, Rita; Sáez-López, Emma; Neto, Maria; Nogueira, Paulo Jorge; Freitas, GraçaWe report three simultaneous measles outbreaks with 112 confirmed cases in three Health Regions of Portugal, from February to April 2018. The mean age of cases was 30 years, 79% worked in a healthcare setting and 87% were vaccinated. Genotype B3 was identified in 84 cases from the three outbreaks. Primary cases in each outbreak were imported. Several cases presented with modified measles, highlighting the importance of rethinking the measles case definition for vaccinated cases.
- Excess Mortality Estimation During the COVID-19 Pandemic: Preliminary Data from PortugalPublication . Nogueira, Paulo Jorge; De Araújo Nobre, Miguel; Nicola, Paulo Jorge; Furtado, Cristina; Vaz Carneiro, AntónioIntroduction: Portugal is experiencing the effects of the COVID-19 pandemic since March 2020. All-causes mortality in Portugal increased during March and April 2020 compared to previous years, but this increase is not explained by COVID-19 reported deaths. The aim of this study was to analyze and consider other criteria for estimating excessive all-causes mortality during the early COVID-19pandemic period. Material and Methods: Public data was used to estimate excess mortality by age and region between March 1 and April 22, proposing baselines adjusted for the lockdown period. Results: Despite the inherent uncertainty, it is safe to assume an observed excess mortality of 2400 to 4000 deaths. Excess mortality was associated with older age groups (over age 65). Discussion: The data suggests a ternary explanation for early excess mortality: COVID-19, non-identified COVID-19 and decrease in access to healthcare. The estimates have implications in terms of communication of non-pharmaceutical actions, for research, and to healthcare professionals. Conclusion: The excess mortality occurred between March 1 and April 22 was 3.5- to 5-fold higher than what can be explained by the official COVID-19 deaths.
- Gripe - Cenários para uma eventual pandemia. Actualização de Julho de 2006Publication . Nunes, Baltazar; Falcão, Isabel; Machado, Ausenda; Nogueira, Paulo Jorge; Rodrigues, Emanuel; Paixão, Eleonora; Falcão, José MarinhoObjectivo: Actualização dos «Cenários preliminares para uma eventual pandemia de gripe», elaborados em 2005, a pedido do Grupo Gestor do Plano de Contingência para a Gripe. Metodologia: A actualização dos cenários centrou-se em três aspectos principais: A inclusão de resultados relacionados com a necessidade de internamento em unidades de cuidados intensivos e de utilização de ventilação assistida, que não constavam nos cenários de 2005; A introdução do efeito do oseltamivir, fármaco ainda não disponível em 2005 para aplicação generalizada; A revisão de alguns valores dos parâmetros usados para cálculo dos cenários de 2005, tendo, já, como base, valores obtidos para a população portuguesa nos últimos anos. Resultados: Em termos gerais, o cenário mais grave foi condicionado por uma taxa de ataque de 40%, de uma percentagem de hospitalização de 5,5% e de uma letalidade de 1,5%, valores estes superiores aos utilizados em 2005. Sem intervenção farmacológica, este cenário seria mais severo que os de 2005. Por outro lado, incorporaram-se também os efeitos esperados com a utilização de oseltamivir como tratamento que, ao contrário do que aconteceu em 2005, estaria, brevemente, disponível. Esse efeito gerou uma diminuição da gravidade de todos os cenários no que respeita ao número de internamentos e ao número de óbitos. Saliente-se que, neste relatório, são apresentados cenários referentes apenas à população nacional e a cada uma das Regiões Autónomas e Regiões do Continente
- Hepatitis C antibody prevalence and behavioral correlates in people who inject drugs attending harm reduction services in Lisbon, PortugalPublication . Curado, Adriana; Nogueira, Paulo Jorge; Virgolino, Ana; Santa Maria, João; Mendão, Luís; Furtado, Cristina; Antunes, FranciscoThe hepatitis C virus (HCV) infection is an important public health problem, affecting millions of people worldwide. People who inject drugs (PWID) are at increased risk of HCV infection due to, among other factors, widespread unsafe injecting practices, such as sharing of infected equipment or unprotected sexual practices. In Portugal, there is a lack of data regarding the proportion of infected persons through injecting drug use. This study aimed to evaluate the anti-HCV prevalence and behavioral correlates of infection in PWID attending harm reduction services in the Metropolitan Area of Lisbon, Portugal. A cross-sectional study with a purposive sample of PWID was undertaken between March 2018 and March 2020. Participants were recruited through the harm-reduction services of a nongovernmental organization. A rapid diagnostic test for anti-HCV screening was performed. Data on drug consumption history and current practices, past HCV testing, care and treatment history, and knowledge regarding hepatitis C were also collected through a questionnaire applied by trained inquirers. A total of 176 PWID participated in this study. An overall prevalence of 70.5% of anti-HCV positive in this population was found. Those with an anti-HCV positive testing result tended to start consuming at a younger age and have a higher consumption of benzodiazepines in the last 30 days. Sharing needles and other injecting material is a frequent risk behavior among this group. Also, they are more likely to have attended an opioid agonist treatment and to have undertaken previous hepatitis C and HIV tests in the past. This study represents an important effort to better understand the HCV prevalence and behavioral correlates of infection among PWID in Portugal, as well as to better estimate those in need of HCV treatment.
- Impact of Loci Nature on Estimating Recombination and Mutation Rates in Chlamydia trachomatisPublication . Ferreira, Rita; Borges, Vitor; Nunes, Alexandra; Nogueira, Paulo Jorge; Borrego, Maria José; Gomes, João PauloThe knowledge of the frequency and relative weight of mutation and recombination events in evolution is essential for understanding how microorganisms reach fitted phenotypes. Traditionally, these evolutionary parameters have been inferred by using data from multilocus sequence typing (MLST), which is known to have yielded conflicting results. In the near future, these estimations will certainly be performed by computational analyses of full-genome sequences. However, it is not known whether this approach will yield accurate results as bacterial genomes exhibit heterogeneous representation of loci categories, and it is not clear how loci nature impacts such estimations. Therefore, we assessed how mutation and recombination inferences are shaped by loci with different genetic features, using the bacterium Chlamydia trachomatis as the study model. We found that loci assigning a high number of alleles and positively selected genes yielded nonconvergent estimates and incongruent phylogenies and thus are more prone to confound algorithms. Unexpectedly, for the model under evaluation, housekeeping genes and noncoding regions shaped estimations in a similar manner, which points to a nonrandom role of the latter in C. trachomatis evolution. Although the present results relate to a specific bacterium, we speculate that microbe-specific genomic architectures (such as coding capacity, polymorphism dispersion, and fraction of positively selected loci) may differentially buffer the effect of the confounding factors when estimating recombination and mutation rates and, thus, influence the accuracy of using full-genome sequences for such purpose. This putative bias associated with in silico inferences should be taken into account when discussing the results obtained by the analyses of full-genome sequences, in which the "one size fits all" approach may not be applicable.
- A large outbreak of Legionnaires’ Disease in an industrial town in PortugalPublication . George, Francisco; Shivaji, Tara; Pinto, Catia Sousa; Serra, Luis Antonio Oliveira; Valente, João; Albuquerque, Maria João; Vicêncio, Paula Cristina Olivença; San-Bento, Ana; Diegues, Paulo; Nogueira, Paulo Jorge; Marques, Teresa; Rebelo, Helena; Costa, Filipa; Rodrigues, Raquel; Nunes, Alexandra; Borges, Vitor; Gomes, João Paulo; Sampaio, Daniel; Barreiro, Paula; Duarte, Silvia; Carpinteiro, Dina; Mendonça, Joana; Silva, Catarina; Vieira, Luís; Simões, Maria Joao; Gonçalves, Paulo; Nunes, Baltazar; Dias, Carlos; Machado, Jorge; Almeida, Fernando; Goncalves, Elsa A; Carvalho, Lucilia; Viterbo, Pedro; Jardim, Dilia; Lacasta, Nuno; Boavida, Filomena; Perez, Ana; Santana, Isabel; Matias, Paula; Banza, Nuno; Rabacal, CarlosBackground: We describe the investigation and control of an outbreak of Legionnaires’ disease in Portugal in October, November and December 2014. Methods: Confirmed cases were individuals with pneumonia, laboratory evidence of Legionella pneumophila serogroup 1 and exposure, by residence, occupational or leisure to the affected municipalities. 49 possible sources were reduced to four potential sources, all industries with wet cooling system, following risk assessment. We geo-referenced cases’ residences and the location of cooling towers defining four study areas 10km buffer centered on each cooling tower system. We compared the number of cases with expected numbers, calculated from the outbreak's attack rates applied to 2011 census population. Using Stones’ Test, we tested observed to expected ratios for decline in risk, with distance up to 10km four directions. Isolates of Legionella pneumophila were compared using molecular methods. Results: We identified 403 cases, 377 of which were confirmed, 14 patients died. Patients became ill between 14 October and 2 December. A NE wind and thermal inversion were recorded during the estimated period of exposure. Disease risk was highest in people living south west from all of the industries identified and decreased with distance (p<0.001). 71 clinical isolates demonstrated an identical SBT profile to an isolate from a cooling tower. Whole genome sequencing identified an unusual L. pneumophila subsp. fraseri serogroup 1 as the outbreak causative strain, and confirmed isolates’ relatedness. Conclusions: Industrial wet cooling systems, bacteria with enhanced survival characteristics and a combination of climatic conditions contributed to the second largest outbreak of Legionnaires’ disease recorded internationally.
- Uma observação sobre estimativas da prevalência de algumas doenças crónicas, em Portugal ContinentalPublication . Branco, Maria João; Nogueira, Paulo Jorge; Contreiras, TeresaObjectivo: O Observatório Nacional de Saúde realizou um estudo com o objectivo de estimar a prevalência auto-declarada de algumas doenças crónicas na população residente em unidades de alojamento do Continente, com telefone fixo. Metodologia: O estudo, descritivo transversal, constou de um inquérito realizado por entrevista telefónica, no último trimestre de 2004, a um elemento de 18 e mais anos, residente nas unidades de alojamento (UA) que integram a amostra de famílias ECOS. Este respondente deu informação sobre a ocorrência de doenças crónicas noutros elementos do agregado. Esta amostra é aleatória e constituída por 1211 UA, com telefone fixo, com alocação homogénea, estratificada por Região de Saúde do Continente. Nestas unidades de alojamento existem 3434 indivíduos. As variáveis colhidas contemplaram idade, nível de instrução, ocupação e Região de Saúde de residência, peso, altura, ocorrência de sensação de ardor/queimadura retroesternal, tensão arterial elevada, diabetes, asma/bronquite asmática, doenças reumáticas, cancro, doença da tiróide, doença de Alzheimer; doença bipolar, doença de Parkinson, doença de Crohn e psoríase. Resultados: Obtiveram-se 975 questionários válidos que incluíram respostas referentes a 2820 indivíduos. As prevalências, auto declaradas, estimadas na amostra de indivíduos em estudo (2820) foram as seguintes: Hipertensão arterial, 18%. Diabetes, 5%. Asma/bronquite asmática, 9%. Doenças reumáticas, 24%. Qualquer tipo de cancro com confirmação médica, 2%. Doença da tiróide com confirmação médica, 4%. Doença de Alzheimer com confirmação médica, 0,1%. Doença Bipolar com confirmação médica, 0,4%. Doença de Parkinson com confirmação médica, 0,3%. Doença de Crohn com confirmação médica, 0,3%. As prevalências, auto declaradas, estimadas apenas na amostra de respondentes de 18 e mais anos (975) foram as seguintes: Sintomatologia sugestiva de Doença do Refluxo Gastro-Esofágico (sensação de ardor/queimadura retroesternal), 35%. Psoríase, 1,8%. Obesidade, 15,4%. Apesar das limitações metodológicas e da eventual imprecisão de alguns valores, estes resultados podem constituir valores de referência, úteis na fundamentação de programas de prevenção/intervenção.
- Report of simultaneous measles outbreaks in two different health regions in Portugal, February to May 2017: lessons learnt and upcoming challengesPublication . Augusto, Gonçalo Figueiredo; Silva, Andreia; Pereira, Natália; Fernandes, Teresa; Leça, Ana; Valente, Paula; Calé, Etelvina; Aguiar, Bárbara Andreia; Martins, António; Palminha, Paula; Vinagre, Elsa; Cordeiro, Rita; Lopo, Sílvia; Nogueira, Paulo JorgeIn Portugal, measles vaccination coverage and population immunity are high, and no endemic measles cases had been reported since 2004. The World Health Organization classified measles as eliminated in the country in 2015 and 2016, based on data from the previous 3 years. However, in a context of increasing incidence in several European countries in 2016 and 2017, Portugal experienced two simultaneous measles outbreaks with a total of 27 laboratory-confirmed cases (0.3 cases/100,000 population) in two health regions between February and May 2017. Nineteen cases (70.1%) were adults, of whom 12 were healthcare workers. Overall, 17 cases (63.0%) were not vaccinated, of whom five were infants younger than 12 months of age. One unvaccinated teenager died. Genotype B3 was identified in 14 cases from both regions. Measles virus sequencing identified different possible origins of the virus in each region affected. Although measles transmission was stopped in less than 2 months from the first case being notified, these outbreaks represent an opportunity to reinforce awareness of measles diagnosis. We highlight the intensity of the control measures taken and their impact on the rapid control of the outbreaks and also the fact that high vaccination coverage was crucial to stop transmission.
- The Role of Health Preconditions on COVID-19 Deaths in Portugal: Evidence from Surveillance Data of the First 20293 Infection CasesPublication . Nogueira, Paulo Jorge; de Araújo Nobre, Miguel; Costa, Andreia; Ribeiro, Ruy M.; Furtado, Cristina; Bacelar Nicolau, Leonor; Camarinha, Catarina; Luís, Márcia; Abrantes, Ricardo; Vaz Carneiro, AntónioBackground: It is essential to study the effect of potential co-factors on the risk of death in patients infected by COVID-19. The identification of risk factors is important to allow more efficient public health and health services strategic interventions with a significant impact on deaths by COVID-19. This study aimed to identify factors associated with COVID-19 deaths in Portugal. Methods: A national dataset with the first 20,293 patients infected with COVID-19 between 1 January and 21 April 2020 was analyzed. The primary outcome measure was mortality by COVID-19, measured (registered and confirmed) by Medical Doctors serving as health delegates on the daily death registry. A logistic regression model using a generalized linear model was used for estimating Odds Ratio (OR) with 95% confidence intervals (95% CI) for each potential risk indicator. Results: A total of 502 infected patients died of COVID-19. The risk factors for increased odds of death by COVID-19 were: sex (male: OR = 1.47, ref = female), age ((56-60) years, OR = 6.01; (61-65) years, OR = 10.5; (66-70) years, OR = 20.4; (71-75) years, OR = 34; (76-80) years, OR = 50.9; (81-85) years, OR = 70.7; (86-90) years, OR = 83.2; (91-95) years, OR = 91.8; (96-104) years, OR = 140.2, ref = (0-55)), Cardiac disease (OR = 2.86), Kidney disorder (OR = 2.95), and Neuromuscular disorder (OR = 1.58), while condition (None (absence of precondition); OR = 0.49) was associated with a reduced chance of dying after adjusting for other variables of interest. Conclusions: Besides age and sex, preconditions justify the risk difference in mortality by COVID-19.