Browsing by Author "Isidro, Joana"
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- Animal-to-human transmission of Mycobacterium pinnipediiPublication . Macedo, Rita; Isidro, Joana; Gomes, Maria Conceição; Botelho, Ana; Albuquerque, Teresa; Sogorb, Arlete; Bernardino, Rui; Fernandes, Teresa Lobo; Mourato, Teresa; Durval, Mário; Gomes, João PauloExtract: Mycobacterium pinnipedii, the known causative agent of tuberculosis (TB) in marine mammals, was only recognised as a member of the Mycobacterium tuberculosis complex in 2003 [1] and is believed to cause TB in several species, including nonmarine mammals [2, 3] and even humans [4]. The assumption of zoonotic transmission has been strongly reinforced by a disruptive study published in 2014 by a team of archaeologists from Tübingen, Germany [5]. Based on archaeological and genomic investigations on millennial human skeletons, the authors implicated sea mammals infected with M. pinnipedii as a source of New World human TB. Considering that this phenomenon pre-dates the human migrations to South America by several centuries, they refuted the previous scientific hypothesis of TB driven by human contact [6].
- 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.
- Bioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samplesPublication . Ribeiro, Miguel; Sousa, Margarida; Borges, Vítor; Gomes, João Paulo; Duarte, Sílvia; Isidro, Joana; Vieira, Luís; Torres, Carmen; Santos, Hugo; Capelo, José Luís; Poeta, Patrícia; Igrejas, GilbertoOne of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages. In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health.
- Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021Publication . Funk, Tjede; Pharris, Anastasia; Spiteri, Gianfranco; Bundle, Nick; Melidou, Angeliki; Carr, Michael; Gonzalez, Gabriel; Garcia-Leon, Alejandro; Crispie, Fiona; O’Connor, Lois; Murphy, Niamh; Mossong, Joël; Vergison, Anne; Wienecke-Baldacchino, Anke K.; Abdelrahman, Tamir; Riccardo, Flavia; Stefanelli, Paola; Di Martino, Angela; Bella, Antonino; Lo Presti, Alessandra; Casaca, Pedro; Moreno, Joana; Borges, Vítor; Isidro, Joana; Ferreira, Rita; Gomes, João Paulo; Dotsenko, Liidia; Suija, Heleene; Epstein, Jevgenia; Sadikova, Olga; Sepp, Hanna; Ikonen, Niina; Savolainen-Kopra, Carita; Blomqvist, Soile; Möttönen, Teemu; Helve, Otto; Gomes-Dias, Joana; Adlhoch, CorneliaWe compared 19,207 cases of SARS-CoV-2 variant B.1.1.7/S gene target failure (SGTF), 436 B.1.351 and 352 P.1 to non-variant cases reported by seven European countries. COVID-19 cases with these variants had significantly higher adjusted odds ratios for hospitalisation (B.1.1.7/SGTF: 1.7, 95% confidence interval (CI): 1.0-2.9; B.1.351: 3.6, 95% CI: 2.1-6.2; P.1: 2.6, 95% CI: 1.4-4.8) and B.1.1.7/SGTF and P.1 cases also for intensive care admission (B.1.1.7/SGTF: 2.3, 95% CI: 1.4-3.5; P.1: 2.2, 95% CI: 1.7-2.8).
- Characterization of Multidrug-Resistant Isolates of Salmonella enterica Serovars Heidelberg and Minnesota from Fresh Poultry Meat Imported to PortugalPublication . Silveira, Leonor; Nunes, Alexandra; Pista, Ângela; Isidro, Joana; Belo Correia, Cristina; Saraiva, Margarida; Batista, Rita; Castanheira, Isabel; Machado, Jorge; Gomes, João PauloSalmonella enterica serovars Heidelberg and Minnesota frequently display several genetic mobile elements making them potential spreaders of resistance genes. Here, we phenotypically determined the antibiotic resistance profile and subsequently performed whole-genome sequencing on 36 isolates recovered from samples of fresh poultry meat, within the Portuguese Official Inspection Plan for Imported Foodstuffs. Several isolates of both serovars showed high genetic relatedness either with isolates from raw poultry meat imported to the Netherlands from Brazil or with isolates from samples from the broiler production chain in Brazil. The multidrug-resistant (MDR) character was common to the vast majority (94.4%) of isolates from both serovars, and several isolates carried the plasmid IncA/C2 containing the β-lactamase gene blaCMY-2 and IncX1 containing a type IV secretion system. These results somehow mirror the scenario observed in the Netherlands, showing the introduction, through fresh imported poultry meat in compliance with European legislation, of MDR Salmonella enterica serovars Heidelberg and Minnesota in Europe, with the potential spread of resistance markers. These data suggest the need to revise the hygiene criteria for foodstuffs monitoring before its placement on the market, with the determination of the resistome being an invaluable contribute to limit the dissemination of resistance markers.
- Chlamydia trachomatis outbreak: when the virulence-associated genome backbone imports a prevalence-associated major antigen signaturePublication . Borges, Vitor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; Rodrigues, Ana; Azevedo, Jacinta; Alves, João; Rôxo, João; Rocha, Miguel; Corte-Real, Rita; Vieira, Luís; Borrego, Maria José; Gomes, João PauloChlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM).
- Chlamydia trachomatis: when the virulence-associated genome backbone imports a prevalence-associated major antigen signaturePublication . Borges, Vítor; Cordeiro, Dora; Salas, Ana Isabel; Lodhia, Zohra; Correia, Cristina; Isidro, Joana; Fernandes, Cândida; Rodrigues, Ana Maria; Azevedo, Jacinta; Alves, João; Roxo, João; Rocha, Miguel; Côrte-Real, Rita; Vieira, Luís; Borrego, Maria José; Gomes, João PauloChlamydia trachomatis is the most prevalent sexually transmitted bacterium worldwide and the causative agent of trachoma. Its strains are classified according to their ompA genotypes, which are strongly linked to differential tissue tropism and disease outcomes [ocular disease, urogenital disease and lymphogranuloma venereum (LGV)]. While the genome-based species phylogenetic tree presents four main clades correlating with tropism/prevalence, namely ocular, LGV, urogenital T1 (more prevalent genotypes) and urogenital T2 (less prevalent genotypes), inter-clade exchange of ompA is considered a rare phenomenon probably mediating marked tropism alterations. An LGV epidemic, associated with the clonal expansion of the L2b genotype, has emerged in the last few decades, raising concerns particularly due to its atypical clinical presentation (ulcerative proctitis) and circulation among men who have sex with men (MSM). Here, we report an LGV outbreak, mostly affecting human immunodeficiency virus-positive MSM engaging in high-risk sexual practices, caused by an L2b strain with a rather unique non-LGV ompA signature that precluded the laboratory notification of this outbreak as LGV. C. trachomatis whole-genome capture and sequencing directly from clinical samples was applied to deeply characterize the genomic backbone of this novel LGV outbreak-causing clone. It revealed a chimeric genome structure due to the genetic transfer of ompA and four neighbouring genes from a serovar D/Da strain, likely possessing the genomic backbone associated with the more prevalent urogenital genotypes (T1 clade), to an LGV (L2b) strain. The hybrid L2b/D-Da strain presents the adhesin and immunodominant antigen MOMP (major outer membrane protein) (encoded by ompA) with an epitope repertoire typical of non-invasive genital strains, while keeping the genome-dispersed virulence fingerprint of a classical LGV strain. As previously reported for inter-clade ompA exchange among non-LGV clades, this novel C. trachomatis genomic mosaic involving a contemporary epidemiologically and clinically relevant LGV strain may have implications on its transmission, tissue tropism and pathogenic capabilities. The emergence of variants with epidemic and pathogenic potential highlights the need for more focused surveillance strategies to capture C. trachomatis evolution in action.
- Clostridium difficile: diversidade genética e perfis de suscetibilidade aos antimicrobianosPublication . Santos, Andrea; Isidro, Joana; Júlio, Cláudia; Oleastro, MónicaEste trabalho teve como objetivo estudar a variabilidade genética e o perfil de suscetibilidade aos antimicrobianos de estirpes de C. difficile recebidas no Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) entre julho de 2012 e dezembro de 2014.
- Comparative Effectiveness of COVID-19 Vaccines in Preventing Infections and Disease Progression from SARS-CoV-2 Omicron BA.5 and BA.2, PortugalPublication . Kislaya, Irina; Casaca, Pedro; Borges, Vítor; Sousa, Carlos; Ferreira, Bibiana I.; Fonte, Ana; Fernandes, Eugénia; Dias, Carlos Matias; Duarte, Sílvia; Almeida, José Pedro; Grenho, Inês; Coelho, Luís; Ferreira, Rita; Ferreira, Patrícia Pita; Borges, Cláudia Medeiros; Isidro, Joana; Pinto, Miguel; Menezes, Luís; Sobral, Daniel; Nunes, Alexandra; Santos, Daniela; Gonçalves, António Maia; Vieira, Luís; Gomes, João Paulo; Leite, Pedro Pinto; Nunes, Baltazar; Machado, Ausenda; Peralta-Santos, AndréWe estimated comparative primary and booster vaccine effectiveness (VE) of SARS-CoV-2 Omicron BA.5 and BA.2 lineages against infection and disease progression. During April-June 2022, we implemented a case-case and cohort study and classified lineages using whole-genome sequencing or spike gene target failure. For the case-case study, we estimated the adjusted odds ratios (aORs) of vaccination using a logistic regression. For the cohort study, we estimated VE against disease progression using a penalized logistic regression. We observed no reduced VE for primary (aOR 1.07 [95% CI 0.93-1.23]) or booster (aOR 0.96 [95% CI 0.84-1.09]) vaccination against BA.5 infection. Among BA.5 case-patients, booster VE against progression to hospitalization was lower than that among BA.2 case-patients (VE 77% [95% CI 49%-90%] vs. VE 93% [95% CI 86%-97%]). Although booster vaccination is less effective against BA.5 than against BA.2, it offers substantial protection against progression from BA.5 infection to severe disease.
- Estudo da diversidade genética do SARS-CoV-2 (COVID-19) em PortugalPublication . Borges, Vítor; Isidro, Joana; Cortes-Martins, Helena; Duarte, Sílvia; Vieira, Luís; Guiomar, Raquel; Gomes, João PauloOs primeiros casos de COVID-19 em Portugal foram reportados no início de março, verificando-se rapidamente uma subida exponencial dos mesmos até ao início de abril. Neste âmbito, o Instituto Nacional de Saúde Doutor Ricardo Jorge (INSA) iniciou o estudo da variabilidade genética do SARS-CoV-2 no país, criando um consórcio constituído por mais de 60 laboratórios, os quais possibilitaram a recolha de cerca de 3000 amostras positivas, de 159 concelhos. Nesta fase sequenciaram-se cerca de 1800 genomas de SARS-CoV-2, colocando Portugal como um dos países a nível mundial com maior empenho na caracterização das variantes genéticas do novo coronavírus em circulação. Os resultados obtidos possibilitaram a caracterização do início da epidemia em Portugal, permitindo, de alguma forma, avaliar a adequação de medidas de saúde pública que foram tomadas. O presente artigo debruça-se sobre os principais resultados obtidos neste âmbito, enumerando também uma série de estudos genéticos mais específicos que foram sendo realizados pelo INSA e com relevância em saúde pública.