Browsing by Author "Gomes, J.P."
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- Congenital SARS-CoV-2 Infection in a Neonate With Severe Acute Respiratory SyndromePublication . Correia, C.R.; Marçal, M.; Vieira, F.; Santos, E.; Novais, C.; Maria, A.T.; Malveiro, D.; Prior, A.R.; Aguiar, M.; Salazar, A.; Pinto, C.G.; Rodrigues, L.C.; Pessanha, M.A.; Borges, V.; Isidro, J.; Gomes, J.P.; Duarte, S.; Vieira, L.; Costa, I.; Alves, M.J.; Calhau, C.; Guiomar, R.; Tuna, M.L.Coronavirus disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is mainly transmitted through droplets, but other ways of transmission have been hypothesized. We report a case of vertical transmission of SARS-CoV-2 in a preterm born to an infected mother, confirmed by the presence of the virus in the neonatal blood, nasopharyngeal and oropharyngeal swabs collected in the first half an hour of life. The neonate presented with acute respiratory distress, similar to the findings in severely affected adults. This case highlights the importance of pregnancy, labor and neonatal period surveillance of affected mothers and their newborns.
- Genomes of Helicobacter pylori prophagesPublication . Vale, F.F.; Nunes, A.; Oleastro, M.; Gomes, J.P.; Sampaio, D.; Rocha, R.; Vítor, J.; Engstrand, L.; Pascoe, B.; Berthenet, E.; Sheppard, S.; Hitchings, M.D.; Mégraud, F.; Vadivedu, J.; Lehours, P.Nearly 20% of the Helicobacter pylori genomes carry prophages genes. Recently we were able to clearly differentiate four populations of prophages according to geographical origin of host strain. Interestingly we were able to discriminate between Northern Europe and Southern Europe using a phage sequence typing based on 2 prophage genes of H. pylori (integrase and holin) but present in only a minority of strains.
- 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.
- Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosisPublication . Oliveira, M.; Pinto, M.; Simões, H.; Gomes, J.P.; Veríssimo, C.; Sabino, R.Objective: Aspergillosis diagnosis depends on the detection of Aspergillus in biological samples ─ usually using cultural and immunoenzyme techniques ─ but their sensitivity and specificity varies. We aimed to study the prevalence of Aspergillus in patients at higher risk of chronic pulmonary aspergillosis (i.e., HIV-infected patients and individuals with active or previous tuberculosis), and to determine the potential role of molecular approaches to increase detection of Aspergillus in respiratory samples. Methods: The DNA extracted from 43 respiratory samples that had been previously analyzed by immunoenzyme and/or cultural techniques was amplified by real-time multiplex PCR, and the results of these methods were compared. We also sequenced the ITS1 region and the calmodulin gene in 10 respiratory samples to perform a pilot metagenomic study to understand the ability of this methodology to detect potential pathogenic fungi in the lung mycobiome. Results: Real-time Aspergillus PCR test exhibited a higher positivity rate than the conventional techniques used for aspergillosis diagnosis, particularly in individuals at risk for chronic pulmonary aspergillosis. The metagenomic analysis allowed for the detection of various potentially pathogenic fungi. Conclusions: Molecular techniques, including metagenomics, have great ability to detect potentially pathogenic fungi rapidly and efficiently in human biological samples.
- SARS-CoV-2 introductions and early dynamics of the epidemic in PortugalPublication . Borges, V.; Isidro, J.; Trovão, N.S.; Duarte, S.; Cortes-Martins, H.; Martiniano, H.; Gordo, I.; Leite, R.; Vieira, L.; Portuguese network for SARS-CoV-2 genomics (Consortium); Guiomar, R.; Gomes, J.P.Background: Genomic surveillance of SARS-CoV-2 in Portugal was rapidly implemented by the National Institute of Health in the early stages of the COVID-19 epidemic, in collaboration with more than 50 laboratories distributed nationwide. Methods: By applying recent phylodynamic models that allow integration of individual-based travel history, we reconstructed and characterized the spatio-temporal dynamics of SARS-CoV-2 introductions and early dissemination in Portugal. Results: We detected at least 277 independent SARS-CoV-2 introductions, mostly from European countries (namely the United Kingdom, Spain, France, Italy, and Switzerland), which were consistent with the countries with the highest connectivity with Portugal. Although most introductions were estimated to have occurred during early March 2020, it is likely that SARS-CoV-2 was silently circulating in Portugal throughout February, before the first cases were confirmed. Conclusions: Here we conclude that the earlier implementation of measures could have minimized the number of introductions and subsequent virus expansion in Portugal. This study lays the foundation for genomic epidemiology of SARS-CoV-2 in Portugal, and highlights the need for systematic and geographically-representative genomic surveillance.