Browsing by Author "Barreiro, Paula"
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- Accreditation under the International Standard ISO 15189: Experience of a Genetics Laboratory in DNA SequencingPublication . Silva, Catarina; Cardoso, Ana; A Sampaio, Daniel; Carpinteiro, Dina; Mendonça, Joana; Duarte, Sílvia; Barreiro, Paula; Torgal, Helena; Isidro, Glória; Vieira, LuísIntroduction: Health care is to some extent influenced by the results of laboratory tests. In order to provide the best care for the patient, laboratories must seek to achieve high levels of quality and competence. International Standard ISO 15189 specifies these requirements and may be used by laboratories to perform accredited genetic tests of materials derived from the human body. Here we describe the procedures to establish Accreditation of DNA sequencing in our laboratory and the first Accreditation of its kind in Portugal. Methods: Our laboratory started to prepare to comply with ISO 15189 Accreditation requirements for DNA sequencing in 2010. Documents describing administrative and technical procedures of the sequencing workflow including sample registries, laboratory protocols, operation and maintenance of equipments, as well as preparation and use of reagents were produced. Regular examination of laboratory equipments by an external entity was implemented to confirm compliance with working requirements. Requisites for personnel training and demonstration of competence were also implemented. The laboratory participated regularly in the DNA sequencing scheme organized by the European Molecular Genetics Quality Network (EMQN). Results: The laboratory obtained formal recognition by Instituto Português de Acreditação (IPAC) in May 2014. A maximum genotyping score for DNA sequencing has been obtained in the external quality assessment scheme since 2010. Sequencing quality measured in terms of the quality read overlap metrics is currently of approximately 96% according to the EMQN scheme. The laboratory processes and analyzes an average of 28.750 samples per year. Discussion: Accreditation of a genetic test under ISO 15189 is a highly demanding and laborious task for a genetic laboratory. However, it is an important step in order to guarantee the highest quality and reproducibility of genetic test results.
- Architecture of Class 1, 2, and 3 Integrons from Gram Negative Bacteria Recovered among Fruits and VegetablesPublication . Jones-Dias, Daniela; Manageiro, Vera; Ferreira, Eugénia; Barreiro, Paula; Vieira, Luís; Moura, Inês B; Caniça, ManuelaThe spread of antibiotic resistant bacteria throughout the food chain constitutes a public health concern. To understand the contribution of fresh produce in shaping antibiotic resistance bacteria and integron prevalence in the food chain, 333 antibiotic resistance Gram negative isolates were collected from organic and conventionally produced fruits (pears, apples, and strawberries) and vegetables (lettuces, tomatoes, and carrots). Although low levels of resistance have been detected, the bacterial genera identified in the assessed fresh produce are often described not only as environmental, but mostly as commensals and opportunistic pathogens. The genomic characterization of integron-harboring isolates revealed a high number of mobile genetic elements and clinically relevant antibiotic resistance genes, of which we highlight the presence of as mcr-1, qnrA1, bla GES-11, mphA, and oqxAB. The study of class 1 (n = 8), class 2 (n = 3) and class 3 (n = 1) integrons, harbored by species such as Morganella morganii, Escherichia coli, Klebsiella pneumoniae, led to the identification of different integron promoters (PcW, PcH1, PcS, and PcWTNG-10) and cassette arrays (containing drfA, aadA, cmlA, estX, sat, and bla GES). In fact, the diverse integron backbones were associated with transposable elements (e.g., Tn402, Tn7, ISCR1, Tn2 (*), IS26, IS1326, and IS3) that conferred greater mobility. This is also the first appearance of In1258, In1259, and In3-13, which should be monitored to prevent their establishment as successfully dispersed mobile resistance integrons. These results underscore the growing concern about the dissemination of acquired resistance genes by mobile elements in the food chain.
- Avaliação do desempenho de uma core-facility de sequenciação genómica especializada em saúde públicaPublication . Vieira, Luís; Silva, Catarina; Duarte, Sílvia; Mendonça, Joana; Carpinteiro, Dina; Sampaio, Daniel A.; Ferrão, José; Santos, Daniela; Machado, Miguel; Isidro, Joana; Barreiro, Paula; Isidro, GlóriaA Unidade de Tecnologia e Inovação (UTI) do Departamento de Genética Humana foi criada em 2009 pelo despacho normativo n.º 15/2009. Apesar de estar integrada num departamento técnico científico, esta unidade constituiu-se desde logo como core-facility de sequenciação genómica do Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA). Este papel envolve uma gestão contínua de prioridades dos serviços a prestar aos utilizadores, no âmbito da resposta a diferentes problemas de saúde pública, aliada a uma preocupação permanente com a qualidade dos resultados e os tempos de resposta. Neste trabalho, apresentamos os resultados da avaliação do desempenho da UTI, desde a introdução da tecnologia de Next-Generation Sequencing (NGS) em 2013, em termos de: (i) métricas de produção da Unidade, (ii) impacto dos resultados publicados no âmbito de colaborações científicas com os grupos de investigação do INSA ou de entidades externas e de (iii) avaliação dos serviços através de um inquérito dirigido aos utilizadores. Até final de 2021, o número de ensaios de NGS e de citações dos trabalhos publicados cresceram, por ano, 39% e 61%, respetivamente. Os utilizadores avaliaram de forma muito positiva os serviços prestados pela UTI em 2021. Globalmente, estes resultados demonstram que o modelo de trabalho de "core- -facility" exercido pela UTI é uma mais-valia na resposta aos problemas da saúde pública em Portugal.
- Caraterização virológica dos vírus da gripe que circularam em Portugal na época 2014/2015Publication . Pechirra, Pedro; Costa, Inês; Cristóvão, Paula; Roque, Carla; Barreiro, Paula; Duarte, Sílvia; Machado, Ausenda; Rodrigues, Ana Paula; Nunes, Baltazar; Guiomar, RaquelIntrodução e objetivo: A monitorização contínua das propriedades antigénicas e genéticas dos vírus da gripe é essencial, quer para a seleção anual das estirpes virais a incluir na vacina, quer para identificar novas linhas de orientação da terapêutica antiviral. O presente estudo descreve as caraterísticas antigénicas e genéticas dos vírus da gripe identificados em Portugal no inverno de 2014/2015.
- A gripe em Portugal: análise preliminar da atividade gripal 2014/2015Publication . Pechirra, Pedro; Cristóvão, Paula; Costa, Inês; Roque, Carla; Barreiro, Paula; Duarte, Sílvia; Machado, Ausenda; Rodrigues, Ana Paula; Nunes, Baltazar; Guiomar, RaquelObjetivo: Pretende-se com a presente publicação, divulgar a análise preliminar da atividade gripal em Portugal na época de 2014/2015 (entre 15 de setembro de 2014 e 20 de março de 2015).
- Influenza in Portugal, 2014/2015 seasonPublication . Pechirra, Pedro; Cristóvão, Paula; Costa, Inês; Roque, Carla; Barreiro, Paula; Duarte, Sílvia; Machado, Ausenda; Rodrigues, Ana Paula; Nunes, Baltazar; Guiomar, RaquelDuring 2014/2015 season the influenza activity was high, the epidemic period was observed between week 1/2015 and 8/2015 with a maximum of 148 ILI cases per 105 inhabitants in week 4/2015. The influenza B virus, A(H3) and A(H1)pdm09 co-circulated during the season, although influenza B were dominant throughout the winter, except for weeks 4, 6 and 7/2015 where it was detected in co-dominance with influenza A virus, situation that contrasts with European influenza picture. The antigenic and genetic analysis of circulating influenza A(H3) and B virus showed differences regarding 2014/2015 influenza vaccine strains. 70% of A(H3) viruses belonged to subgroup 3C.2a, antigenically different from vaccine strain. A (H3) positive were recorded in higher percentage in children (0 to 4 years: 40.0% and 5 to 14 years: 39.7%) and in adults over 65 years (36, 8%). A(H1)pdm09 virus were sporadically detected and were similar to the vaccine A/California/7/2009 strain. In general, the detected influenza viruses were similar to those recommended strains for next winter`s vaccine 2015/2016.
- 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.
- The Technology and Innovation Unit of the National Institute of Health: A sequencing and bioinformatics core facility specializing in public health genomicsPublication . Silva, Catarina; Ataíde Sampaio, Daniel; Mendonça, Joana; Carpinteiro, Dina; Duarte, Sílvia; Barreiro, Paula; Isidro, Joana; Machado, Miguel; Vieira, LuísThe National Institute of Health (INSA) has a long tradition in investigating the molecular etiology of genetic and complex diseases. These activities greatly benefit from centralized sequencing services provided by the Technology and Innovation Unit (UTI). Its mission is to perform sequencing and genotyping assays in the framework of research, diagnosis and epidemiological surveillance, as well as to implement data analysis pipelines for the study of human gene variants. The equipment portfolio includes a NextSeq 550, a MiSeq, two 3500 AB Genetic Analyzers, a Fragment Analyzer and a 7500 Real-time PCR system. UTI provides results for average of 36.000 sequencing/fragment samples per year. The team has already performed >300 small genome, amplicon, gene panel (including clinical exome), 16S rRNA gene and RNA/microRNA next-generation sequencing assays for INSA and for several Universities in the scope of scientific collaborations. Technical procedures are conducted under a quality control system that includes external quality assessment for next-generation sequencing/Sanger sequencing and ISO 15189 accreditation for Sanger sequencing. UTI plays a key role in public health genomics, providing state-of-the-art equipment, centralized resources, technical expertise and short response times.
- The Technology and Innovation Unit of the National Institute of Health: a sequencing and bioinformatics core facility specializing in public health genomicsPublication . Silva, Catarina; Ataíde Sampaio, Daniel; Mendonça, Joana; Carpinteiro, Dina; Duarte, Sílvia; Barreiro, Paula; Isidro, Joana; Machado, Miguel; Vieira, LuísThe National Institute of Health (INSA) is the state laboratory in the health sector. INSA has a long tradition in investigating the molecular etiology of genetic and complex diseases and in the identification of pathogenic organisms responsible for disease outbreaks and environmental imbalances. These activities benefit greatly from the existing centralized sequencing services provided by the Technology and Innovation Unit (UTI). Its mission includes performing sequencing and genotyping assays in the framework of research, diagnosis and epidemiological surveillance, as well as implementing data analysis pipelines for the study of variation in human genes. The equipment portfolio includes two next-generation sequencers and two capillary electrophoresis instruments for Sanger sequencing/fragment analysis, that altogether process an average of 36.000 samples/year. The team performed over 300 next-generation sequencing workflows for small genomes, amplicons, gene panels, clinical exome, 16S rRNA gene and RNA/microRNAs. Standard of operation procedures are conducted by trained technicians under a quality control system that includes external quality assessment and ISO 15189 accreditation. UTI plays a key role in public health genomics, providing state-of-the-art equipment, centralized resources, technical expertise and short response times for public health problems.