Percorrer por autor "Sampaio, Daniel A."
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- 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.
- Burkholderia pseudomallei: first case of melioidosis in PortugalPublication . Pelerito, Ana; Nunes, Alexandra; Coelho, Susana; Piedade, Cátia; Paixão, Paulo; Cordeiro, Rita; Sampaio, Daniel A.; Vieira, Luís; Gomes, João Paulo; Núncio, M. SofiaBurkholderia pseudomallei is a Gram-negative bacillus and the causative agent of melioidosis, a serious infection associated with high mortality rate in humans. It can be naturally found as an environmental saprophyte in soil or stagnant water, and rice paddies that predominate in regions of endemicity such as Northeast Thailand. B. pseudomallei is a Biosafety Level 3 organism due to risks of aerosolization and severe disease and is now included in formal emergency preparedness plans and guidelines issued by various authorities in the United States and Europe. Here, we report the first case of imported melioidosis in Portugal. B. pseudomallei was isolated from the patient’s blood as well as from a left gluteal abscess pus. The isolate strain showed the unusual resistance profile to first-line eradication therapy trimethroprim/sulfamethoxazole. Whole genome sequencing revealed its similarity with isolates from Southeast Asia, suggesting the Thai origin of this Portuguese isolate, which is in agreement with a recent patient’s travel to Thailand.
- Burkholderia pseudomallei: primeiro caso de melioidose em PortugalPublication . Pelerito, Ana; Nunes, Alexandra; Coelho, Susana; Piedade, Cátia; Paixão, Paulo; Cordeiro, Rita; Sampaio, Daniel A.; Vieira, Luís; Gomes, João Paulo; Núncio, SofiaObjetivo: Este estudo apresenta o primeiro caso de melioidose em Portugal, revelando o importante papel da metodologia de Sequenciação Total do Genoma para a correta identificação e caracterização da estirpe isolada.
- Chlamydia trachomatis In Vivo to In Vitro Transition Reveals Mechanisms of Phase Variation and Down-Regulation of Virulence FactorsPublication . Borges, Vítor; Pinheiro, Miguel; Antelo, Minia; Sampaio, Daniel A.; Vieira, Luís; Ferreira, Rita; Nunes, Alexandra; Almeida, Filipe; Mota, Luís J.; Borrego, Maria José; Gomes, João PauloResearch on the obligate intracellular bacterium Chlamydia trachomatis demands culture in cell-lines, but the adaptive process behind the in vivo to in vitro transition is not understood. We assessed the genomic and transcriptomic dynamics underlying C. trachomatis in vitro adaptation of strains representing the three disease groups (ocular, epithelial-genital and lymphogranuloma venereum) propagated in epithelial cells over multiple passages. We found genetic features potentially underlying phase variation mechanisms mediating the regulation of a lipid A biosynthesis enzyme (CT533/LpxC), and the functionality of the cytotoxin (CT166) through an ON/OFF mechanism. We detected inactivating mutations in CT713/porB, a scenario suggesting metabolic adaptation to the available carbon source. CT135 was inactivated in a tropism-specific manner, with CT135-negative clones emerging for all epithelial-genital populations (but not for LGV and ocular populations) and rapidly increasing in frequency (~23% mutants per 10 passages). RNA-sequencing analyses revealed that a deletion event involving CT135 impacted the expression of multiple virulence factors, namely effectors known to play a role in the C. trachomatis host-cell invasion or subversion (e.g., CT456/Tarp, CT694, CT875/TepP and CT868/ChlaDub1). This reflects a scenario of attenuation of C. trachomatis virulence in vitro, which may take place independently or in a cumulative fashion with the also observed down-regulation of plasmid-related virulence factors. This issue may be relevant on behalf of the recent advances in Chlamydia mutagenesis and transformation where culture propagation for selecting mutants/transformants is mandatory. Finally, there was an increase in the growth rate for all strains, reflecting gradual fitness enhancement over time. In general, these data shed light on the adaptive process underlying the C. trachomatis in vivo to in vitro transition, and indicates that it would be prudent to restrict culture propagation to minimal passages and check the status of the CT135 genotype in order to avoid the selection of CT135-negative mutants, likely originating less virulent strains.
- Complete Genome Sequence of Chlamydia trachomatis Ocular Serovar C Strain TW-3Publication . Borges, V.; Pinheiro, M.; Vieira, Luís; Sampaio, Daniel A.; Nunes, A.; Borrego, M.J.; Gomes, João PauloChlamydia trachomatis is the etiological agent of trachoma, the leading infectious cause of blindness worldwide. We report here the first complete and annotated genome of a C. trachomatis trachoma-causing serovar C strain (strain TW-3). The chromosome and plasmid are 1,043,554 bp and 7,501 bp in length, respectively.
- Draft Genome Sequence of a Pathogenic O86:H25 Sequence Type 57 Escherichia coli Strain Isolated from Poultry and Carrying 12 Acquired Antibiotic Resistance GenesPublication . Jones-Dias, Daniela; Manageiro, Vera; Sampaio, Daniel A.; Vieira, Luís; Caniça, ManuelaEscherichia coli is a commensal bacterium that is frequently associated with multidrug-resistant zoonotic and foodborne infections. Here, we report the 5.6-Mbp draft genome sequence of an E. coli recovered from poultry, which encodes multiple acquired antibiotic resistance determinants, virulence factors, pathogenicity determinants, and mobile genetic elements.
- Draft Genome Sequence of the First NDM-1-ProducingProvidencia stuartiiStrain Isolated in PortugalPublication . Manageiro, Vera; Sampaio, Daniel A.; Pereira, Patrícia; Rodrigues, Paulo; Vieira, Luís; Palos, Carlos; Caniça, ManuelaWe report here the draft genome sequence of the first NDM-1-producing Providencia stuartii strain isolated in Portugal. Sequence analyses revealed the presence of an incompatibility group A/C2 (IncA/C2) plasmid and of diverse acquired genes conferring resistance to β-lactams, aminoglycosides, tetracycline, macrolides, chloramphenicol, and sulfonamides. This sequence contributes to the evaluation of the spread of NDM-1 producers.
- Genome Sequencing of 10 Helicobacter pylori Pediatric Strains from Patients with Nonulcer Dyspepsia and Peptic Ulcer DiseasePublication . Nunes, Alexandra; Rocha, Raquel; Vale, Filipa F.; Vieira, Luís; Sampaio, Daniel A.; Dias, Ricardo; Gomes, João Paulo; Oleastro, MónicaWe present draft genome sequences of 10 Helicobacter pylori clinical strains isolated from children. This will be important for future studies of comparative genomics in order to better understand the virulence determinants underlying peptic ulcer disease.
- Genomic analysis of multidrug resistant qnrD-harbouring Morganella morganii with zoonotic transmission potentialPublication . Jones-Dias, Daniela; Moura, Inês Barata; Clemente, Lurdes; Vieira, Luís; Sampaio, Daniel A.; Manageiro, Vera; Caniça, ManuelaStudy Purpose: Morganella morganii is a Gram-negative bacteria from the Enterobacteriaceae family, usually prevalent as a human commensal organism. In this study, we aimed to investigate the molecular background sustaining multidrug resistance and pathogenicity in an avian M. morganii isolate. Methods: M. morganii INSLV892 was recovered from 13-day old broilers belonging to a poultry industrial unit during post-mortem examination. The isolate was tested for its antimicrobial resistance and found to be non wild-type to ampicillin, ciprofloxacin, tetracycline, chloramphenicol and trimethoprim, which is consistent with multidrug resistance. Whole genome sequencing was performed on a MiSeq (Illumina) using 150 bp paired-end reads. Sequence reads were trimmed and filtered according to quality criteria, and assembled de novo using CLC genomics workbench version 8.0. A set of bioinformatic web tools were used to estimate the presence of pathogenicity determinants, antibiotic resistance genes, and clinically relevant mobile genetic elements within the M. morganii genome. Results: The assembly yielded 74 contigs, which together comprised 4,267,817bp. The genome sequence comprised 4,116 putative genes, among which 3,950 consisted of protein encoding sequences. In silico analysis of the antibiotic resistance genes revealed the presence of acquired resistance to aminoglycosides (aadA1y, aph(3')-Ic, and strA-strB), β-lactam (blaOXA-1), fluoroquinolones (qnrD, aac(6’)-Ib-cr), phenicols (catA2 and catB3), rifampicin (arr-2) sulphonamides (sul2), trimethoprim (dfrA1), tetracycline (tetY), and streptothricin (sat2). The qnrD antibiotic resistant gene was enclosed in an 8449bp length contig, displaying a mean coverage of 183.9-fold and a total read count of 13382. PHAST analyses identified 12 prophage regions and PathogenFinder estimated a 68.9% certainty of the isolate being a human pathogen. Conclusion: The detection of an avian M. morganii isolate harbouring multiple clinically important antibiotic resistance genes and pathogenicity factors raises concerns regarding the dissemination of infection in the food-chain and potential risk of zoonotic transmission.
- Genomic structure and insertion sites of Helicobacter pylori prophages from various geographical originsPublication . Vale, Filipa F.; Nunes, Alexandra; Oleastro, Mónica; Gomes, João P.; Sampaio, Daniel A.; Rocha, Raquel; Vítor, Jorge M. B.; Engstrand, Lars; Pascoe, Ben; Berthenet, Elvire; Sheppard, Samuel K.; Hitchings, Matthew D.; Mégraud, Francis; Vadivelu, Jamuna; Lehours, PhilippeHelicobacter pylori genetic diversity is known to be influenced by mobile genomic elements. Here we focused on prophages, the least characterized mobile elements of H. pylori. We present the full genomic sequences, insertion sites and phylogenetic analysis of 28 prophages found in H. pylori isolates from patients of distinct disease types, ranging from gastritis to gastric cancer, and geographic origins, covering most continents. The genome sizes of these prophages range from 22.6-33.0 Kbp, consisting of 27-39 open reading frames. A 36.6% GC was found in prophages in contrast to 39% in H. pylori genome. Remarkably a conserved integration site was found in over 50% of the cases. Nearly 40% of the prophages harbored insertion sequences (IS) previously described in H. pylori. Tandem repeats were frequently found in the intergenic region between the prophage at the 3' end and the bacterial gene. Furthermore, prophage genomes present a robust phylogeographic pattern, revealing four distinct clusters: one African, one Asian and two European prophage populations. Evidence of recombination was detected within the genome of some prophages, resulting in genome mosaics composed by different populations, which may yield additional H. pylori phenotypes.