102 documents found, page 1 of 11
Assessment of the Genotoxic Hazard of Estuarine Sediments Using an Integrative ...
Pinto, Miguel; Sacadura, Joana; Costa, Pedro M.; Caeiro, Sandra; Louro, Henriqueta; Silva, Maria J.Under the influence of multiple anthropogenic pressures, from industrial to agricultural activities, estuaries have long been regarded as particularly sensitive ecosystems to contamination. The present study aimed at investigating the genotoxic potential of a contaminated sediment sample from an urban and industrial area of the Sado Estuary, by combining the analysis of multiple endpoints in the <jats:italic>La...
Whole-genome sequencing-based surveillance system for Mycobacterium tuberculosi...
Pinto, Miguel; Macedo, RitaTo improve TB surveillance and diagnosis, the Portuguese National Reference Laboratory (NRL) began implementing whole-genome sequencing (WGS) for all RR/MDR-TB cases in 2019. Since 2020, this approach has been expanded to indiscriminately include all received isolates. We describe the current WGS-based surveillance system in Portugal, framed in prospective and retrospective data (n = 1171), upgraded for antimic...
Source attribution of human infection: a multi-country model in the European Union
Thystrup, Cecilie; Brinch, Maja Lykke; Henri, Clementine; Mughini-Gras, Lapo; Franz, Eelco; Wieczorek, Kinga; Gutierrez, MontserratIntroduction: Infections caused by spp. represent a severe threat to public health worldwide. National action plans have included source attribution studies as a way to quantify the contribution of specific sources and understand the dynamic of transmission of foodborne pathogens like and . Such information is crucial for implementing targeted intervention. The aim of this study was to predict the sources of hu...
Multi-country and intersectoral assessment of cluster congruence between pipeli...
Mixão, Verónica; Pinto, Miguel; Brendebach, Holger; Sobral, Daniel; Santos, João Dourado; Radomski, Nicolas; Uldall, Anne Sophie MajgaardDifferent laboratories employ different Whole-Genome Sequencing (WGS) pipelines for Food and Waterborne disease (FWD) surveillance, casting doubt on the comparability of their results and hindering optimal communication at intersectoral and international levels. Through a collaborative effort involving eleven European institutes spanning the food, animal, and human health sectors, we aimed to assess the inter-p...
Probe-based metagenomic pathogen detection: advancing laboratory capacity for c...
Ferreira, Rita; Coelho, Luís; Santos, João Dourado; Sobral, Daniel; Isidro, Joana; Mixão, Verónica; Pinto, Miguel; Nunes, Alexandra; Borrego, Maria JoséProbe-based pathogen enrichment, followed by NGS, is a promising tool for complex diagnosis, overcoming traditional challenges of shotgun metagenomics, namely small microbial/human genetic material ratio and demanding computational resources. Here, we assessed the combined detection performance of two Illumina probe-based panels, the Respiratory and the Urinary Pathogen ID panels (RPIP and UPIP), using 99 clini...
Genome-scale analysis of Mycobacterium avium complex isolates from Portugal rev...
Carneiro, Sofia; Pinto, Miguel; Rodrigues, Joana; Gomes, João Paulo; Macedo, RitaOpportunist infections caused by nontuberculous mycobacteria (NTM) have emerged as a significant public health problem. Among these, species of the Mycobacterium avium complex (MAC) are the main responsible for the increase in the number of human disease cases. In order to address the current needs in the detection and surveillance of MAC disease cases, we evaluated different species classification methodologie...
Epidemiological Data and Antimicrobial Resistance of Campylobacter spp. in Port...
Duarte, Andreia; Pereira, Luísa; Lemos, Maria-Leonor; Pinto, Miguel; Rodrigues, João Carlos; Matias, Rui; Santos, Andrea; PTCampyNet; Oleastro, MónicaThis study extensively analyzed campylobacteriosis surveillance in Portugal from 2009 to 2021, aiming to investigate demographic shifts, seasonal variations, and antimicrobial resistance (AMR) within Campylobacter isolates. Surveillance network and sentinel laboratory-based system data revealed a substantial under-notification of campylobacteriosis cases, suggesting an underestimated disease burden. Notificatio...
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic d...
Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; Santos, André; Mamede, RafaelBackground: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and deve...
Strengthening the genomic surveillance of Francisella tularensis by using cultu...
Isidro, Joana; Escudero, Raquel; Luque-Larena, Juan José; Pinto, Miguel; Borges, Vítor; González-Martín-Niño, Rosa; Duarte, Sílvia; Vieira, LuísIntroduction: Francisella tularensis is a highly infectious bacterium that causes the zoonotic disease tularemia. The development of genotyping methods, especially those based on whole-genome sequencing (WGS), has recently increased the knowledge on the epidemiology of this disease. However, due to the difficulties associated with the growth and isolation of this fastidious pathogen in culture, the availability...
INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic d...
Santos, João Dourado; Sobral, Daniel; Pinheiro, Miguel; Isidro, Joana; Bogaardt, Carlijn; Pinto, Miguel; Eusébio, Rodrigo; Santos, André; Mamede, RafaelBackground: Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and deve...