10 documents found, page 1 of 1
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...
Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in...
Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel LopesPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the hi...
ReporTree: a surveillance-oriented tool to strengthen the linkage between patho...
Mixão, Verónica; Pinto, Miguel; Sobral, Daniel; Di Pasquale, Adriano; Gomes, João Paulo; Borges, VítorBackground: Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases' prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual explorati...
Candida auris in Intensive Care Setting: The First Case Reported in Portugal
Henriques, João; Mixão, Verónica; Cabrita, Joana; Duarte, Tiago Isidoro; Sequeira, Tânia; Cardoso, Sofia; Germano, Nuno; Dias, Liliana; Bento, LuísCandida auris is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of C. auris in Portugal, which was associated with a patient transferred from Angola to an ICU in Portugal for liver transplantation after a SARS-CoV-2 infection. C. auris was isolated during the course ...
Viral genetic clustering and transmission dynamics of the 2022 mpox outbreak in...
Borges, Vítor; Duque, Mariana Perez; Martins, João Vieira; Vasconcelos, Paula; Ferreira, Rita; Sobral, Daniel; Pelerito, Ana; de Carvalho, Isabel LopesPathogen genome sequencing during epidemics enhances our ability to identify and understand suspected clusters and investigate their relationships. Here, we combine genomic and epidemiological data of the 2022 mpox outbreak to better understand early viral spread, diversification and transmission dynamics. By sequencing 52% of the confirmed cases in Portugal, we identified the mpox virus sublineages with the hi...
Escherichia coli patogénica, Salmonella spp. e Campylobacter spp. em dois Centr...
Pista, Ângela; Silveira, Leonor; Ribeiro, Sofia; Fontes, Mariana; Castro, Rita; Coelho, Anabela; Furtado, Rosália; Lopes, Teresa; Maia, CarlaA coexistência entre humanos e animais selvagens pode aumentar o risco de transmissão direta de agentes patogénicos zoonóticos emergentes ou reemergentes para humanos. Este trabalho teve como objetivo avaliar a ocorrência de três importantes agentes patogénicos de origem alimentar em animais selvagens de dois centros de conservação da vida selvagem, em Portugal. Para tal, foram testadas 132 amostras fecais para...
Candida auris in intensive care setting: the first case reported in Portugal
Henriques, João; Mixão, Verónica; Cabrita, Joana; Duarte, Tiago Isidoro; Sequeira, Tânia; Cardoso, Sofia; Germano, Nuno; Dias, Liliana; Bento, LuísCandida auris is an opportunistic human pathogen that has rapidly spread to multiple countries and continents and has been associated with a high number of nosocomial outbreaks. Herein, we report the first case of C. auris in Portugal, which was associated with a patient transferred from Angola to an ICU in Portugal for liver transplantation after a SARS-CoV-2 infection. C. auris was isolated during the course ...
Phylogenomic characterization and signs of microevolution in the 2022 multi-cou...
Isidro, Joana; Borges, Vítor; Pinto, Miguel; Sobral, Daniel; Santos, João Dourado; Nunes, Alexandra; Mixão, Verónica; Ferreira, Rita; Santos, DanielaThe largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. 1-6). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered ...
Pathogenic Escherichia coli, Salmonella spp. and Campylobacter spp. in Two Natu...
Pista, Angela; Silveira, Leonor; Ribeiro, Sofia; Fontes, Mariana; Castro, Rita; Coelho, Anabela; Furtado, Rosália; Lopes, Teresa; Maia, CarlaHuman–wildlife coexistence may increase the potential risk of direct transmission of emergent or re-emergent zoonotic pathogens to humans. Intending to assess the occurrence of three important foodborne pathogens in wild animals of two wildlife conservation centers in Portugal, we investigated 132 fecal samples for the presence of Escherichia coli (Shiga toxin-producing E. coli (STEC) and non-STEC), Salmonella ...