Browsing by Issue Date, starting with "2018-10-31"
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- Population-level impact of Pneumococcal Conjugate Vaccines in older adults: Portuguese ReportPublication . Rodrigues, Ana Paula; Kislaya, Irina; Nunes, Baltazar; Gómez, Verónica; Gonçalves, PauloOverall objective: To estimate the population-level impact of pneumococcal conjugate vaccination on invasive pneumococcal disease (IPD), all-cause pneumonia (ACP) and pneumococcal pneumonia (PP) burden among adults 65 years of age and older. The impact measures we aimed to estimate were: The indirect effect of PCV7 given to children on IPD, ACP and PP burden among adults aged 65 years and more; The indirect effect of PCV13 (additional six serotypes) given to children on IPD, ACP and PP burden among adults aged 65 years and more. Specific objectives: To estimate the reduction of IPD, ACP and PP intra-hospital mortality among adults ≥65 years of age. Initially, in the Scientific Protocol, the reduction of intensive care unit (ICU) admission rate among adults aged 65 years or more hospitalized with IPD, ACP and PP associated with PCV7 and PCV13 introduction was considered. Nevertheless, given the variability of codes used between hospitals to identify ICU admissions, was not possible to achieve this objective. In addition, given the low number of annual hospitalizations due to pneumococcal sepsis and pneumococcal meningitis among adults aged 65 years and more the reduction of IPD hospitalization rate estimates by clinical presentation was not possible to perform.
- Severe RSV infections in children and elderly during 2017/2018 winter seasonPublication . Guiomar, Raquel; Pechirra, Pedro; Costa, Inês; Cristóvão, Paula; Conde, Patrícia; Nunes, Baltazar; Rodrigues, Ana Paula; Côrte-Real, Rita; Branquinho, Paula; Garcia, David; Conde, Sílvia; Rodrigues, Fernando; Pereira-Vaz, João; Alves, José; Ludivina, Freitas; Mota Vieira, Luísa; Cabral Veloso, Rita; Bruges Armas, Jácome; Couto, Ana Rita; Ribeiro, Carlos; Barreto, Rosário; Cunha, Mário; Martins, Luís; Almeida, Sofia; Peres, Maria João; Viseu, Regina; Mota, Paula; Lopes, Paulo; Soares, Vânia; Vale, Fátima; Fonseca, Patrícia; Toscano, Cristina; Dias, AnaBackground: Respiratory syncytial virus (RSV) is one of the most frequent and important respiratory viral agent that causes respiratory infection complications in younger children and elderly. RSV has an autumn / winter seasonality detected in cocirculation with influenza and other respiratory viruses. Material and Methods: During 2017/2018 season, 14 hospitals from Portugal mainland and Atlantic Island tested 4278 swabs for influenza, respiratory syncytial virus (RSV) and other respiratory viruses (oRV). Data on age and hospital service were recorded. Samples were collected from patients with mild to severe respiratory infections. Severity was correlated with the need for hospitalization. The study aimed to determine the age groups that had experienced severe RSV infections during the 2017/2018 season with the need of hospitalization, including in intensive care units (ICU). Results: Between October/2017-May/2018 were tested 4278 swabs for influenza, RSV and oRV (picornavirus, adenovirus, bocavirus, metapneumovirus, parainfluenzavirus, coronavirus). A total of 43%(1830) swabs were positive, from these 35%(639) were outpatients, 61%(1112) were hospitalized and 4% (79) were at ICU. The prevalence found were: Influenza 63%(1157), RSV 15%(266), oRV 13%(247) and 9%(160) of the cases were mixed infections. Influenza was detected in more than 70% of the positives swabs in patients aged above 15 years old. The oRV played a major role in respiratory infections in children, 0-4 and 5-14 years old, detected in 23% and 21% of the cases ,respectively. RSV was the predominant virus identified in toddlers, under 4 years old (29% of the positive samples and in 85% of codetection ). Among elderly 65+, RSV was confirmed in 13% of the respiratory infections. In hospitalized adults 65+, although influenza was detected in 80% of the positive swabs, RSV was 3.5 times more frequently detected than oRV, higher than the observed in outpatients (RSV 1.6 times more frequent than oRV). In hospitalized patients under 5 years old, RSV were detected in 31% of the positive swabs being 1.3 and 1.5 times more frequently than influenza and oRV, respectively. In ICU, 40%(32) of the cases were under 5 years old, influenza was confirmed in only 3% and RSV in 22% of the cases. 35%(28) ICU cases had 65+years old, influenza was confirmed in 57% and RSV in 14% of these patients. Conclusions: During 2017/2018, RSV was detected in severe respiratory infections. In young children (≤4 years old) RSV was the most frequently detected respiratory virus. In elderly 65+, besides influenza, RSV was frequently associated with severe respiratory infections. Prevention measures for RSV severe infections are essential not only in children but also among the elderly.
- In silico analysis of missense mutations as a first step in functional studies: examples from two sphingolipidosesPublication . Duarte, Ana Joana; Ribeiro, Diogo; Moreira, Luciana; Amaral, OlgaIn order to delineate a better approach to functional studies, we have selected 23 missense mutations distributed in different domains of two lysosomal enzymes, to be studied by in silico analysis. In silico analysis of mutations relies on computational modeling to predict their effects. Various computational platforms are currently available to check the probable causality of mutations encountered in patients at the protein and at the RNA levels. In this work we used four different platforms freely available online (Protein Variation Effect Analyzer- PROVEAN, PolyPhen-2, Swiss-model Expert Protein Analysis System-ExPASy, and SNAP2) to check amino acid substitutions and their effect at the protein level. The existence of functional studies, regarding the amino acid substitutions, led to the selection of the distinct protein mutants. Functional data were used to compare the results obtained with different bioinformatics tools. With the advent of next-generation sequencing, it is not feasible to carry out functional tests in all the variants detected. In silico analysis seems to be useful for the delineation of which mutants are worth studying through functional studies. Therefore, prediction of the mutation impact at the protein level, applying computational analysis, confers the means to rapidly provide a prognosis value to genotyping results, making it potentially valuable for patient care as well as research purposes. The present work points to the need to carry out functional studies in mutations that might look neutral. Moreover, it should be noted that single nucleotide polymorphisms (SNPs), occurring in coding and non-coding regions, may lead to RNA alterations and should be systematically verified. Functional studies can gain from a preliminary multi-step approach, such as the one proposed here.
- Differential self-report error by socioeconomic status in hypertension and hypercholesterolemia: INSEF 2015 studyPublication . Kislaya, Irina; Tolonen, Hanna; Rodrigues, Ana Paula; Barreto, Marta; Gil, Ana Paula; Gaio, Vânia; Namorado, Sónia; Santos, Ana João; Dias, Carlos Matias; Nunes, BaltazarBackground: This study aimed to compare self-reported and examination-based prevalence of hypertension and hypercholesterolemia in Portugal in 2015 and to identify factors associated with the measurement error in self-reports. Methods: We used data from the Portuguese National Health Examination Survey (n = 4911), that combines personal interview, blood collection and, physical examination. Sensitivity and specificity of self-reported hypertension and hypercholesterolemia were calculated. Poisson regression was used to estimate prevalence ratios (PRs) of underreport of hypertension and hypercholesterolemia according to sex, age, socioeconomic status (education and income) and general practitioner (GP) consultation in the past year. Results: Sensitivity of self-reports was 69.8% for hypertension and 38.2% for hypercholesterolemia. Underreport of hypertension was associated with male gender (PR = 1.54), lack of GP consultation (PR = 1.70) and being 25–44 years old (PR = 2.45) or 45–54 years old (PR = 2.37). Underreport of hypercholesterolemia was associated with lack of GP consultation (PR = 1.15), younger age (PR = 1.83 for 25–44 age group and PR = 1.52 for 45–54 age group), secondary (PR = 1.30) and higher (PR = 1.27) education. Conclusion: Self-reported data underestimate prevalence of hypertension and hypercholesterolemia. Magnitude of measurement error in self-reports varies by health conditions and population characteristics. Adding objective measurements to self-reported questionnaires improve data accuracy allowing better understanding of socioeconomic inequalities in health.
- Insights into the population structure and pan-genome of Haemophilus influenzaePublication . Pinto, M.; González-Díaz, A.; Machado, M.P.; Duarte, S.; Vieira, L.; Carriço, J.A.; Marti, S.; Bajanca-Lavado, M.P.; Gomes, J.P.The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies. Here, we aimed to study the population structure of H. influenzae and to get some insights into its pan-genome. We studied 305H. influenzae strains, enrolling 217 publicly available genomes, as well as 88 newly sequenced H. influenzae invasive strains isolated in Portugal, spanning a 24-year period. NTHi isolates presented a core-SNP-based genetic diversity about 10-fold higher than the one observed for Hib. The analysis of key factors involved in pathogenesis, such as lipooligosaccharides, hemagglutinating pili and High Molecular Weight-adhesins, suggests that NTHi shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion and persistence. Discreet NTHi subpopulations structures are proposed based on core-genome supported with 17 candidate genetic markers identified in the accessory genome. Additionally, this study provides two bioinformatics tools for in silico rapid identification of H. influenzae serotypes and NTHi clades previously proposed, obviating laboratory-based demanding procedures. The present study constitutes an important genomic framework that could lay way for future studies on the genetic determinants underlying invasiveness and disease and population structure of H. influenzae.
- RSV attributable mortality in Portugal between 2014 and 2018Publication . Rodrigues, Ana Paula; Silva, Susana; Guiomar, Raquel; Pechirra, Pedro; Cristóvão, Paula; Nunes, BaltazarBackground: RSV has been recognized as a serious pathogen in at-risk adult populations (long-term care facilities, immunocompromised). In adults, RSV infection is usually mild, but its effects on morbidity and mortality in adults can be substantial as has been previously reported. Given that RSV has a similar seasonality pattern as influenza it is plausible that RSV circulation had contributed to excess all-cause mortality observed during previous winters in Portugal. This study aimed to estimate RSV attributable all-cause mortality between 2014/15 and 2017/18 seasons in Portugal. Methods: Influenza and RSV data (as Goldstein index) was collected by National Influenza Surveillance System and mortality from Portuguese Mortality Surveillance System. Both systems are under coordination of National Health Institute Doutor Ricardo Jorge. Temperatures were downloaded from the National Oceanic and Atmospheric Administration Online Climate Data Directory. An adaptation of FluMOMO model, developed on EuroMOMO network, was used to estimate RSV attributable mortality on studied seasons using data between W40/2014 and W20/2018. Analysis was performed for total (all ages) and specifically for 0-4 years, 5-14 years, 15-64 years and 65 and more years. Non-disaggregated data on Influenza and RSV were used for all age groups. Results: All-cause excess mortality was observed during 2014/15, 2016/17 and 2017/18 winter seasons in Portugal. RSV explained, in those seasons and on total strata, respectively, 12%, 8% and 9% of the observed mortality above the expected during the referred periods.For all age groups under 65 years old RSV attributed mortality was higher than influenza attributable mortality in almost all seasons, although for the 5-14 years old age-group this attributable mortality was not statistically significant. Above 65 years RSV had impact in all-cause mortality in all studied seasons, although with low magnitude than Influenza. Only in 2015/16 when influenza activity was very low with A(H1) dominance, RSV attributable mortality was higher than Influenza attributable mortality. Conclusions: During autumn and winter seasons RSV infections have impacts in all-cause mortality in Portugal. Those findings should be accounted on mortality surveillance systems during the winter season.
- Measuring influenza vaccine effectiveness against pneumococcal pneumonia using the screening methodPublication . Rodrigues, Ana Paula; Kislaya, Irina; Machado, Ausenda; Gómez, Verónica; Gonçalves, Paulo; Nunes, BaltazarThe main objective was to measure in the community dwelling elderly population (aged ≥65 years) the direct effect (effectiveness) of influenza vaccine against: i. Pneumococcal pneumonia (PP); ii. Invasive pneumococcal disease (IPD).