Departamento de Doenças Infecciosas
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- 2014/2015 Influenza season in an inland portuguese regionPublication . Almeida, Sofia; Rodrigues, Débora; Gouveia, Paula; Paulo, Sandra; Faria, Conceição; Pechirra, Pedro; Costa, Inês; Cristóvão, Paula; Guiomar, RaquelInfluenza surveillance is an important tool to identify emerging/reemerging strains, and defining seasonality of the circulating strains. The aim of this work is to compare the circulating strains detected by Centro Hospitalar da Cova da Beira, EPE,(CHCB) from an inland north region of Portugal, with the strains circulating among Europe during2014/2015 Influenza season. In the present review, 249 nasofaringeal swabs received in were analized by real time PCR techniques, designed to amplify Influenza A and Influenza B virus. All the positive samples were sent to the Portuguese reference Laboratory in order to subtype influenza A virus and to perform genetic and antigenic characterization of the detected viruses. During 2014/2015 season, a total of 109 positive cases (62 Influenza A and 47 Influenza B) - were detected in the studied region. In the present season, all seasonal types/subtypes of influenza virus circulated, inspite of low level circulation of the Influenza A(H1)pdm strain (~5%of the positive samples, circulating between 6/2015-9/2015 weeks). A(H3) and B strains co-circulated between weeks 1/2015 and 11/2015 with peak activity in weeks 6 and 7/2015. Influenza A, excluding A(H1)pdm, was responsible for 47% of positive cases, mainly in the last 6 weeks. Influenza B strains were responsible for 42% of positive Influenza cases, mainly in the first 7 weeks of the year. All influenza B strains characterized by the Portuguese National Laboratory were from B/Yamagata lineage. 19% of influenza B strains wereselected for genetic characterization, all were similar to B/Phuket/3073/2013 (clade 3). At the date of submission of the abstract, only 8 Influenza A strains were genetically characterized, 5 belonged to genetic subgroup 3C.2a, represented by A/Hong Kong/5738/2014, dissimilar to the current A(H3N2) vaccine strain and 3 belonged to A/Samara/73/2013 (genetic group 3C.3), antigenically similar to the current A(H3N2) vaccine The co-circulation of influenza types/subtypes was similar to the one described in Europe, but in this Portuguese region, the Influenza B circulated in first part of the epidemic period, followed by A(H3) virus at the end of epidemic period.. The genetic characterization observed in Portugal was similar to the one from ECDC data for Influenza B. Relatively to Influenza A, the majority of detected viruses were dissimilar to the 2014/2015 A(H3) vaccine virus, being a higher proportion than the observed in Europe, but more data is needed to achieve any conclusion.
- 2015/16 I-MOVE/I-MOVE+ multicentre case control study in Europe: moderate vaccine effectiveness estimates against influenza A(H1N1)pdm09 and low estimates against lineage mismatched influenza B among childrenPublication . Kissling, Esther; Valenciano, Marta; Pozo, Francisco; Vilcu, Ana-Maria; Reuss, Annicka; Rizzo, Caterina; Larrauri, Amparo; Horváth, Judit Krisztina; Brytting, Mia; Domegan, Lisa; Korczyńska, Monika; Meijer, Adam; Machado, Ausenda; Ivanciuc, Alina; Višekruna Vučina, Vesna; van der Werf, Sylvie; Schweiger, Brunhilde; Bella, Antonino; Gherasim, Alin; Ferenczi, Annamária; Zakikhany, Katherina; O Donnell, Joan; Paradowska-Stankiewicz, Iwona; Dijkstra, Frederika; Guiomar, Raquel; Lazar, Mihaela; Kurečić Filipović, Sanja; Johansen, Kari; Moren, Alain; I-MOVE/I-MOVE+ study teamBackground:During the 2015/16 influenza season in Europe, the co-circulating influenza viruses were A(H1N1)pdm09 and B/Victoria, which was antigenically distinct from the B/Yamagata component in the trivalent influenza vaccine. Methods:We used the test negative design in a multicentre case–control study in twelve European countries to measure 2015/16 influenza vaccine effectiveness (VE) against medically-attended influenza-like illness (ILI) laboratory-confirmed as influenza. General practitioners swabbed a systematic sample of consulting ILI patients ainfluenza Vaccinend a random sample of influenza positive swabs were sequenced. We calculated adjusted VE against influenza A(H1N1)pdm09, A(H1N1)pdm09 genetic group 6B.1 and influenza B overall and by age group. Results: We included 11,430 ILI patients, of which 2272 were influenza A(H1N1)pdm09 and 2901 were influenza B cases. Overall VE against influenza A(H1N1)pdm09 was 32.9% (95% CI: 15.5-46.7). Among those aged 0–14, 15–64 and ≥65 years VE against A(H1N1)pdm09 was 31.9% (95% CI: -32.3-65.0), 41.4% (95%CI: 20.5-56.7) and 13.2% (95% CI: -38.0-45.3) respectively. Overall VE against influenza A(H1N1)pdm09 genetic group 6B.1 was 32.8% (95%CI: -4.1-56.7). Among those aged 0–14, 15–64 and ≥65 years VE against influenza B was -47.6% (95%CI: -124.9-3.1), 27.3% (95%CI: -4.6-49.4), and 9.3% (95%CI: -44.1-42.9) respectively. Conclusions: VE against influenza A(H1N1)pdm09 and its genetic group 6B.1 was moderate in children and adults, and low among individuals ≥65 years. VE against influenza B was low and heterogeneous among age groups. More information on effects of previous vaccination and previous infection are needed to understand the VE results against influenza B in the context of a mismatched vaccine.
- 2015/16 seasonal vaccine effectiveness against hospitalisation with influenza A(H1N1)pdm09 and B among elderly people in Europe: results from the I-MOVE+ projectPublication . Rondy, Marc; Larrauri, Amparo; Casado, Itziar; Alfonsi, Valeria; Pitigoi, Daniela; Launay, Odile; Syrjänen, Ritva K; Gefenaite, Giedre; Machado, Ausenda; Vučina, Vesna Višekruna; Horváth, Judith Krisztina; Paradowska-Stankiewicz, Iwona; Marbus, Sierk D; Gherasim, Alin; Díaz-González, Jorge Alberto; Rizzo, Caterina; Ivanciuc, Alina E; Galtier, Florence; Ikonen, Niina; Mickiene, Aukse; Gomez, Veronica; Kurečić Filipović, Sanja; Ferenczi, Annamária; Korcinska, Monika R; van Gageldonk-Lafeber, Rianne; I-MOVE+ hospital working group; Valenciano, MartaWe conducted a multicentre test-negative case-control study in 27 hospitals of 11 European countries to measure 2015/16 influenza vaccine effectiveness (IVE) against hospitalised influenza A(H1N1)pdm09 and B among people aged ≥ 65 years. Patients swabbed within 7 days after onset of symptoms compatible with severe acute respiratory infection were included. Information on demographics, vaccination and underlying conditions was collected. Using logistic regression, we measured IVE adjusted for potential confounders. We included 355 influenza A(H1N1)pdm09 cases, 110 influenza B cases, and 1,274 controls. Adjusted IVE against influenza A(H1N1)pdm09 was 42% (95% confidence interval (CI): 22 to 57). It was 59% (95% CI: 23 to 78), 48% (95% CI: 5 to 71), 43% (95% CI: 8 to 65) and 39% (95% CI: 7 to 60) in patients with diabetes mellitus, cancer, lung and heart disease, respectively. Adjusted IVE against influenza B was 52% (95% CI: 24 to 70). It was 62% (95% CI: 5 to 85), 60% (95% CI: 18 to 80) and 36% (95% CI: -23 to 67) in patients with diabetes mellitus, lung and heart disease, respectively. 2015/16 IVE estimates against hospitalised influenza in elderly people was moderate against influenza A(H1N1)pdm09 and B, including among those with diabetes mellitus, cancer, lung or heart diseases.
- 4ª Reunião Vigilância Epidemiológica da Gripe em Portugal - época 2014/2015 : resumos das comunicações oraisPublication . Guiomar, Raquel; Falcão, Isabel; Rodrigues, Ana Paula; Rodrigues, Emanuel; Meneses de Almeida, Lúcio; Won, MiguelResumo das comunicações orais apresentadas na reunião da Vigilância Epidemiológica da Gripe em Portugal. Esta reunião pretende divulgar os resultados da vigilância clínica e laboratorial da época 2014/2015, incluindo informação sobre casos graves, mortalidade e severidade, sistemas de deteção precoce da epidemia de gripe, vacinação antigripal, bem como estratégias de intervenção em saúde pública em situações de baixa efetividade vacinal. Serão também apresentados temas relacionados com a vigilância da gripe aviária e a situação atual do Síndrome Respiratória do Médio oriente (MERS-CoV).
- Abundance and Updated Distribution of Aedes aegypti (Diptera: Culicidae) in Cabo Verde Archipelago: A Neglected Threat to Public HealthPublication . Da Veiga Leal, S.; Varela, I. B. F.; Gonçalves, A. A. L.; Monteiro, D. D. S.; Ramos de Sousa, C. M.; Mendonça, M. L. L.; De Pina, A. J.; Alves, M. J.; Osório, H. C.Background: Mosquito-borne viruses, such as Zika, dengue, yellow fever, and chikungunya, are important causes of human diseases nearly worldwide. The greatest health risk for arboviral disease outbreaks is the presence of the most competent and highly invasive domestic mosquito, Aedes aegypti. In Cabo Verde, two recent arbovirus outbreaks were reported, a dengue outbreak in 2009, followed by a Zika outbreak in 2015. This study is the first entomological survey for Ae. aegypti that includes all islands of Cabo Verde archipelago, in which we aim to evaluate the actual risk of vector-borne arboviruses as a continuous update of the geographical distribution of this species. Methods: In order to assess its current distribution and abundance, we undertook a mosquito larval survey in the nine inhabited islands of Cabo Verde from November 2018 to May 2019. Entomological larval survey indices were calculated, and the abundance analyzed. We collected and identified 4045 Ae. aegypti mosquitoes from 264 positive breeding sites in 22 municipalities and confirmed the presence of Ae. aegypti in every inhabited island. Results: Water drums were found to be the most prevalent containers (n = 3843; 62.9%), but puddles (n = 27; 0.4%) were the most productive habitats found. The overall average of the House, Container, and Breteau larval indices were 8.4%, 4.4%, and 10.9, respectively. However, 15 out of the 22 municipalities showed that the Breteau Index was above the epidemic risk threshold. Conclusion: These results suggest that if no vector control measures are considered to be in place, the risk of new arboviral outbreaks in Cabo Verde is high. The vector control strategy adopted must include measures of public health directed to domestic water storage and management.
- Accessing indoor fungal contamination by Aspergillus fumigatus complex using conventional and molecular methods in portuguese poultriesPublication . Viegas, C.; Malta-Vacas, J.; Sabino, R.; Viegas, S.; Veríssimo, C.Epidemiological studies showed increased prevalence of respiratory symptoms and adverse changes in pulmonary function parameters in poultry workers, corroborating the increased exposure to risk factors, such as fungal load and their metabolites. This study aimed to determine the occupational exposure threat due to fungal contamination caused by the toxigenic isolates belonging to the complex of the species of Aspergillus flavus and also isolates from Aspergillus fumigatus species complex. The study was carried out in seven Portuguese poultries, using cultural and molecular methodologies. For conventional/cultural methods, air, surfaces, and litter samples were collected by impaction method using the Millipore Air Sampler. For the molecular analysis, air samples were collected by impinger method using the Coriolis μ air sampler. After DNA extraction, samples were analyzed by real-time PCR using specific primers and probes for toxigenic strains of the Aspergillus flavus complex and for detection of isolates from Aspergillus fumigatus complex. Through conventional methods, and among the Aspergillus genus, different prevalences were detected regarding the presence of Aspergillus flavus and Aspergillus fumigatus species complexes, namely: 74.5 versus 1.0 % in the air samples, 24.0 versus 16.0 % in the surfaces, 0 versus 32.6 % in new litter, and 9.9 versus 15.9 % in used litter. Through molecular biology, we were able to detect the presence of aflatoxigenic strains in pavilions in which Aspergillus flavus did not grow in culture. Aspergillus fumigatus was only found in one indoor air sample by conventional methods. Using molecular methodologies, however, Aspergillus fumigatus complex was detected in seven indoor samples from three different poultry units. The characterization of fungal contamination caused by Aspergillus flavus and Aspergillus fumigatus raises the concern of occupational threat not only due to the detected fungal load but also because of the toxigenic potential of these species.
- Accessing occupational exposure to fungi in a cork industryPublication . Viegas, C.; Clérigo, A.; Faria, T.; Sabino, Raquel; Veríssimo, Cristina; Quintal-Gomes, A.; Viegas, S.In this study we aimed to access fungal exposure in workers from one cork industry through the mycological analysis of their nasal exudate and the environmental fungal contamination of their surroundings as well. Nasal mucous samples from 127 workers were taken with sterilized cotton swabs.The fungal species identified in the collected nose swabs were shown to be correlated with the results obtained in the environment. Eighty workers (63.0%) presented contamination of their nose nostril with Chrysonilia sitophila, which number of colonies was countless. Within the Aspergillus genus, the complexes Fumigati, Circumdati, Versicolores and Candidi were isolated. No azole-resistant Aspergillus isolates grew in the selective media used (screened itraconazole and voriconazole resistance).This approach allowed us to estimate the risk associated with these tasks performance. Moreover, the cork industry is related to high dust contamination and this can promote exposure to fungi since dust particles can act as carriers of fungi to the worker’s nose. Assessment by molecular tools will ensure the specific targeting of DNA from P. glabrum complex in workers nose.
- Accessing the molecular basis of transferable quinolone resistance in Escherichia coli and Salmonella spp from food-producing animals and productsPublication . Caniça, Manuela; Jones-Dias, Daniela; Francisco, Ana Patrícia; Manageiro, Vera; Ferreira, EugéniaBackground: Salmonella and Escherichia coli resistant to quinolones frequently arise in animals, being easily transferred to humans through the food chain, which can ultimately lead to the development of untreatable infectious diseases. The aim of the present study was to investigate the presence of PMQR determinants among Salmonella spp and E. coli from food-producing animals and derivative food products. Methods: Salmonella spp (n=183) and E. coli (n=182) isolates were collected from food-producing animals (n=274) and derivative food products (n=91). Antimicrobial susceptibility testing was performed by standard disk diffusion method, according to the CA-SFM veterinary guidelines. PCR and sequencing were used to detect PMQR- (qnrA, qnrB, qnrC, qnrD, qnrS, aac(6’)-Ib-cr, and qepA) and β-lactamase-encoding genes (blaTEM, blaSHV, blaOXA and ampC) and to examine the QRDR of gyrA, gyrB, parC and parE genes in PMQR positive isolates. Plasmid characterization was accessed by conjugation followed by replicon-typing. Genetic relatedness of PMQR positive E. coli was examined by MLST and Salmonella isolates were serotyped according to the Kauffmann-White scheme. Mobile genetic elements were also investigated through PCR mapping assays. Results: Overall, 4.7% (17/365) harbored Qnr-encoding genes from qrnB and qnrS families, specifically qnrB2 (n=3), qrnB19 (n=3), and qnrS1 (n=11). All but one isolate presented at least one mutation in QRDR region of genes gyrA, parC or parE genes. 35.3% of Qnr-producing isolates presented resistance to β-lactam antibiotics that were justified by the presence of β-lactamases from TEM (TEM-1, n=10; and TEM-135, n=1) and SHV (SHV-108, n=1) families in QnrB19- and QnrS1-harbouring isolates. All but one Qnr-producing isolates were positively typed by replicon-typing, varying among IncN (n=2), IncFIB (n=11), IncFIC (n=3), IncI1 (n=2), IncHI2 (n=5), IncY (n=1) and IncL/M (n=3) and were, mostly, genetic unrelated. Qnr genes were detected nearby several mobile elements like ISEcl2, IS26 and ISCR1. Conclusions: This study illustrated the existence of Qnr-producing E. coli and Salmonella from food-producing animals, associated to specific mobile elements that can mediate their transference between species and among distinct settings. Epidemiology of PMQR mechanisms and the dissemination of plasmids carrying Qnr-encoding genes in veterinary isolates can compromise the efficacy of fluroquinolone treatments in both animals and humans.
- Accuracy of prenatal culture in predicting intrapartum group B streptococcus colonization statusPublication . Florindo, C.; Damião, V.; Lima, J.; Nogueira, I.; Rocha, I.; Caetano, P.; Ribeiro, L.; Viegas, S.; Gomes, João Paulo; Borrego, M.J.Objective: To evaluate the positive predictive value (PPV) of group B Streptococcus (GBS) cultures at 35–37 weeks of gestation relative to GBS colonization status at delivery. Methods: Rectovaginal swabs from 221 women at labor in four Lisbon hospitals were collected for GBS screening according to the CDC guidelines. Results: The PPV was 24.4%. IAP was administered to 100% of prenatally GBS positive women. There was no case of early onset GBS disease (EOD). Conclusions: Poor accuracy of prenatal cultures in identifying true candidates for IAP highlights the need for Portuguese clinical and laboratory guidelines to prevent EOD and antibiotic overtreatment of pregnant women.
- Acquired antibiotic resistance among wild animals: the case of Iberian Lynx (Lynx pardinus)Publication . Sousa, M.; Gonçalves, A.; Silva, N.; Serra, R.; Alcaide, E.; Zorrilla, I.; Torres, C.; Caniça, Manuela; IgrejaS, G.; Poeta, P.The selective pressure generated by the clinical misuse of antibiotics has been the major driving force leading to the emergence of antibiotic resistance among bacteria. Antibiotics or even resistant bacteria are released into the environment and contaminate the surrounding areas. Human and animal populations in contact with these sources are able to become reservoirs of these resistant organisms. Then, due to the convergence between habitats, the contact of wild animals with other animals, humans, or human sources is now more common and this leads to an increase in the exchange of resistance determinants between their microbiota. Indeed, it seems that wildlife populations living in closer proximity to humans have higher levels of antibiotic resistance. Now, the Iberian Lynx (Lynx pardinus) is a part of this issue, being suggested as natural reservoir of acquired resistant bacteria. The emerging public health concern regarding microbial resistance to antibiotics is becoming true: the bacteria are evolving and are now affecting unintentional hosts.