Browsing by Author "Duarte, S."
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- Assessment of multiple mycotoxins in maize flour samples from Portugal under SafeGrains projectPublication . Duarte, S.; Magro, A.; Oliveira, C.; Rosim, R.; Alvito, Paula; Carvalho, M.O.One of the most relevant problems in stored grains is the contamination by insects and mycotoxin-producing fungi. Tribolium castaneum is one of the most common insect pests of stored products. Its presence makes cereals more susceptible to the spread of the fungi Aspergillus flavus, which may produce mycotoxins. The aim of this work was to evaluate the mycotoxin profile of maize flour infested by T. castaneum adults, alone or in combination with mycotoxigenic A. flavus strain (MUM-UMinho). Maize collected directly from fields was stored at 4 ºC and then ground and sieved to obtain maize fl our. Multiple mycotoxin profile of maize flour was determined in three different assays: i) controls (n=8), ii) inoculated with T. castaneum adults (insect assay, n = 24), iii) inoculated with A. flavus conidia (fungus assay, n = 8) and iv) inoculated with both organisms (mixed assay, n = 24). Samples were analyzed by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) according to Franco et al. (2019) for determination of aflatoxins (AFs) B1, B2, G1 and G2, deoxynivalenol (DON), zearalenone(ZEN) and fumonisins (FBs) B1 and B2. The limits of detection (LOD) and quantification (LOQ) of the analytical method were 6.1 and 18.0 μg/ kg for DON, respectively. For AFs, ZEN and FBs, LOD and LOQ varied between 0.2 – 0.9 and 0.6 – 2.5 μg/kg, respectively. DON, ZEA, FB1 and FB2 were detected in control assays at mean levels ranging from 33-50, 2-6, 112-144 and 49-75 μg/kg, respectively. AFs were not detected in controls. Insect, fungi and mixed assays presented the same mycotoxin profile (with contents in the same order of magnitude), except for AFB1, which was detected only in mixed assays. Although the levels of mycotoxins are below the legislated ones (Commission Regulation (EU) 2023/915), they point out to the presence of multiple mycotoxins in raw maize flour and to a potential impact between insects and mycotoxigenic strains in which concerns AFB1. Data presented here agree with previous assays from this team describing significantly higher concentration in the maize flour inoculated with both organisms (Duarte et al, 2021).
- 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.
- 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.
- Mutation rate of SARS-CoV-2 and emergence of mutators during experimental evolutionPublication . Amicone, M.; Borges, V.; Alves, M.J.; Isidro, J.; Zé-Zé, L.; Duarte, S.; Gomes, J. P.; Gordo, I.Background and objectives: To understand how organisms evolve, it is fundamental to study how mutations emerge and establish. Here, we estimated the rate of mutation accumulation of SARS-CoV- 2 in vitro and investigated the repeatability of its evolution when facing a new cell type but no immune or drug pressures. Methodology: We performed experimental evolution with two strains of SARS-CoV-2, one carrying the originally described spike protein (CoV-2-D) and another carrying the D614G mutation that has spread worldwide (CoV-2-G). After 15 passages in Vero cells and whole genome sequencing, we characterized the spectrum and rate of the emerging mutations and looked for evidences of selection across the genomes of both strains. Results: From the frequencies of the mutations accumulated, and excluding the genes with signals of selection, we estimate a spontaneous mutation rate of 1.3 10 6 6 0.2 10 6 per-base per-infection cycle (mean across both lineages of SARS-CoV-262SEM). We further show that mutation accumulation is larger in the CoV-2-D lineage and heterogeneous along the genome, consistent with the action of positive selection on the spike protein, which accumulated five times more mutations than the corresponding genomic average. We also observe the emergence of mutators in the CoV-2-G background, likely linked to mutations in the RNA-dependent RNA polymerase and/or in the error-correcting exonuclease protein. Conclusions and implications: These results provide valuable information on how spontaneous mutations emerge in SARS-CoV-2 and on how selection can shape its genome toward adaptation to new environments. Lay Summary: Each time a virus replicates inside a cell, errors (mutations) occur. Here, via laboratory propagation in cells originally isolated from the kidney epithelium of African green monkeys, we estimated the rate at which the SARS-CoV-2 virus mutates—an important parameter for understanding how it can evolve within and across humans. We also confirm the potential of its Spike protein to adapt to a new environment and report the emergence of mutators—viral populations where mutations occur at a significantly faster rate.
- SafeGrains - Contamination of stored grain and derivatives by insect pests and fungiPublication . Carvalho, M.O.; Mourato, M.; Louro, L.; Sousa, I.; Raymundo, A.; Alvito, P.; Magro, A.; Barros, G.; Ferreira, R.; Duarte, S.About contamination of stored grain and derivatives by insect pests and fungi.
- 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.