Ricardo Bruno da Costa Oliveira (441A-683A-40E8)

Curriculum Vitae

Ricardo Bruno da Costa Oliveira

Ricardo Oliveira is graduated in Biochemistry from the Faculty of Sciences of the University of Porto (FCUP) and the Abel Salazar Institute of Biomedical Sciences (ICBAS) since 2015, having completed his final internship at the Science for Life Laboratory (SciLifeLab) / Stockholm University, Sweden under the Erasmus+ program. Master in Biotechnology from the University of Minho (UM) since 2017, having carried out his master's dissertation at the company Biomode SA. In 2018, he was awarded an FCT PhD scholarship (first place in the Agricultural and Food Technologies panel) for the development of aptamers for staphylococcal enterotoxins using nucleic acid mimics (NAMs) at the Faculty of Engineering of the University of Porto (FEUP) in collaboration with the National Institute for Agricultural and Veterinary Research, I. P. (INIAV). During this period, he was a visiting PhD student at the Department of Cell Biology and Molecular Genetics, University of Maryland, USA, where he strengthened his knowledge in aptamer selection approaches with NAMs. He completed his PhD in Chemical and Biological Engineering in 2023. Currently, Postdoctoral Fellow at National Institute for Agricultural and Veterinary Research, I. P. (INIAV) focusing on bacteriology, food safety and diagnostic/therapeutic solutions (special interest in the development of aptamers). Awarded the Prize Prof. Dr. Fernando Serrão by FCUP (2015) for his distinction in the area of Organic Chemistry. He was recognized as one of the 20 most talented promising researchers from across the world by the Federation of European Microbiology Societies (FEMS) and invited to the FEMS Summer School for Postdocs 2024, during which he won the best scientific project proposal. To date, R. Oliveira has authored or co-authored 21 papers in peer-reviewed international journals and 5 book chapters. He has more than 150 citations (ResearchGate. September 2024) and an H-index of 8. He was also involved on 7 oral communications (two invited) and 28 poster communications in international congresses. He participates (or participated) as researcher in several FCT-funded projects (PTDC/CVT-CVT/4620/2021, FCT_128_596771122, POCI-01-0145-FEDER-028659, PTDC/DTP-PIC/4562/2014) and in three European Cost Actions (CA22105, CA21145 and CA20103). To date, he successfully completed the supervision of 4 bachelor students and mentoredseveral other bachelor's, master's and doctoral students. R. Oliveira reviews manuscripts for several Q1 journals and in addition he is an Editorial Board Member of the Frontiers in Microbiology, Frontiers in Cellular and Infection Microbiology, Frontiers in Antibiotics, Molecular and Cellular Probes and PloS one. He was a member of the organizing committee of the 2º Simpósio INIAV para a Segurança Alimentar and several study visits to INIAV. In addition, R. Oliveira is a member of the Portuguese Microbiology Society.

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Identification

Personal identification

Full name: Ricardo Bruno da Costa Oliveira

Citation names

Oliveira, Ricardo

Author identifiers

Ciência ID: 441A-683A-40E8
ORCID iD: 0000-0001-9175-4278

Email addresses

ricardo.oliveira@iniav.pt (Professional)

Knowledge fields

Agrarian Sciences - Agrarian and Food Biotechnology - Diagnostics
Engineering and Technology - Other Engineering and Technologies - Food and Beverages
Natural sciences - Biological Sciences - Microbiology
Natural sciences - Biological Sciences - Biochemical Research Methods
Medical and Health Sciences - Medical Biotechnology - Health-Related Biotechnology

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Advanced (C1)	Advanced (C1)	Advanced (C1)	Advanced (C1)

Education

	Degree	Classification
2018/10 - 2023/10 Concluded	Chemical and Biological Engineering (Doutoramento) Universidade do Porto Faculdade de Engenharia, Portugal "Application of nucleic acid mimics (NAM) in the selection of aptamers against staphylococcal enterotoxins" (THESIS/DISSERTATION)	Approved unanimously
2023/05/08 - 2023/06/12 Concluded	Transferable skills for engineering: basic teaching skills (Pós-Graduação) Universidade do Porto Faculdade de Engenharia, Portugal	18
2016 - 2017 Concluded	Biotechnology (Mestrado) Universidade do Minho, Portugal "Design and validation of an alternative molecular method using peptide nucleic acid fluorescence in situ hybridization (PNA FISH) for the detection of Campylobacter spp. in food samples" (THESIS/DISSERTATION)	19
2012/10 - 2015/10 Concluded	Biochemistry (Licenciatura) Universidade do Porto Faculdade de Ciências, Portugal Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal "Identification of multi-drug resistant Mycobacterium tuberculosis by padlock probes and lateral flow nucleic acid biosensors" (THESIS/DISSERTATION)	17 (ECTS Grading scale: Class A - Top Student)

Affiliation

Science

	Category Host institution	Employer
2023/12 - Current	Postdoc (Research)	Instituto Nacional de Investigação Agrária e Veterinária, I. P. , Portugal
	Instituto Nacional de Investigação Agrária e Veterinária, I. P. , Portugal
2018/10 - 2023/10	Research Trainee (Research)	Instituto Nacional de Investigação Agrária e Veterinária, I. P. , Portugal
	Instituto Nacional de Investigação Agrária e Veterinária, I. P. , Portugal (...)
2023/02 - 2023/05	Contracted Researcher (Research)	Universidade do Porto Faculdade de Engenharia, Portugal
	Universidade do Porto Faculdade de Engenharia, Portugal
2018/10 - 2023/02	Research Trainee (Research)	Universidade do Porto Faculdade de Engenharia, Portugal
	Universidade do Porto Faculdade de Engenharia, Portugal
2019/05 - 2019/07	Visiting Researcher (Research)	Fundação para a Ciência e a Tecnologia, Portugal
	University of Maryland at College Park Cell Biology and Molecular Genetics, United States
2018/02 - 2018/09	Contracted Researcher (Research)	Universidade do Minho Centro de Engenharia Biológica, Portugal
	Universidade do Minho Centro de Engenharia Biológica, Portugal
2016/09 - 2017/11	Research Trainee (Research)	Biomode SA, Portugal
	International Iberian Nanotechnology Laboratory, Portugal
2015/02 - 2015/07	Research Trainee (Research)	Stockholms Universitet, Sweden
	Science for Life Laboratory (SciLifeLab), Sweden
2013/11 - 2014/06	Research Trainee (Research)	REQUIMTE LAQV Porto, Portugal
	Universidade do Porto Faculdade de Ciências, Portugal

Projects

Contract

	Designation	Funders
2022/01/01 - Current	APTAcoli: NAM-aptamers for blocking enterotoxins in pig colibacillosis PTDC/CVT-CVT/4620/2021 Post-doc Fellow International Iberian Nanotechnology Laboratory, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal Universidade de Trás-os-Montes e Alto Douro, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2018/10 - 2023/07	NAM4toxins - De novo selection of toxin-specific aptamers using nucleic acid mimics POCI-01-0145-FEDER- 028659 PhD Student Fellow Instituto Nacional de Investigação Agrária e Veterinária, Portugal Universidade do Porto Faculdade de Engenharia, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2023/02/01 - 2023/05/31	FLUDS - Desenvolvimento de sistemas baseados em espectroscopia de fluorescência para deteção microbiana NORTE-01-0247-FEDER-046970 Research Fellow Universidade do Porto Faculdade de Engenharia, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2018/10 - 2022/10	Locked nucleic acid (LNA) aptamers for the detection of Staphylococcal Enterotoxins SFRH/BD/138883/2018	Fundação para a Ciência e a Tecnologia Concluded
2018/02 - 2018/09	Coded-FISH: Development of a novel colour-coded RING FISH method: an innovative tool for the detection of antibiotic resistant clinical pathogens PTDC/DTP-PIC/4562/2014 Master Student Fellow Universidade do Minho Centro de Engenharia Biológica, Portugal Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Other

	Designation	Funders
2023/09 - Current	BeSafeBeeHoney - BEekeeping products valorization and biomonitoring for the SAFEty of BEEs and HONEY CA22105 Researcher Instituto Nacional de Investigação Agrária e Veterinária, Portugal	European Cooperation in Science and Technology Ongoing
2022/09 - Current	EURESTOP - European Network for diagnosis and treatment of antibiotic-resistant bacterial infections CA21145 Researcher Instituto Nacional de Investigação Agrária e Veterinária, Portugal	European Cooperation in Science and Technology Ongoing
2022/05 - Current	BETTER - Biosecurity Enhanced Through Training Evaluation and Raising Awareness CA20103 Researcher Instituto Nacional de Investigação Agrária e Veterinária, Portugal	European Cooperation in Science and Technology Ongoing
2022/01 - 2023/06	NAMShield - Controlo de Salmonella spp, na indústria pecuária, através de aptâmeros nanoensapsulados POCI-01-0247-FEDER-069756 Researcher Instituto Nacional de Investigação Agrária e Veterinária, Portugal	Fundação para a Ciência e a Tecnologia Concluded
2020/05 - 2020/12	NAM4Covid19 - Nucleic acid mimic lateral flow assay (NAM-LFA) for the detection of Covid19 19128_596771122 Researcher Instituto Nacional de Investigação Agrária e Veterinária, Portugal Universidade do Porto Faculdade de Engenharia, Portugal Instituto Nacional de Saúde Doutor Ricardo Jorge, Portugal	Fundação para a Ciência e a Tecnologia Concluded

Outputs

Publications

Book chapter	Araújo, Daniela; Ana Rita Silva; Oliveira, Ricardo; Campos, Ana Maria; Barros, Maria Margarida; Rosca, Aliona S.; Mira, Nuno Pereira; et al. "Probiotics, Prebiotics, and Synbiotics as Antimicrobials: One-Health Perspective". In Advances in Health and Disease, edited by Lowel T.Duncan. United States: Nova Science Publishers, 2024. Published Araújo, Daniela; Oliveira, Ricardo; Ana Maria Campos; Maria Margarida Barros; Andreia S. Azevedo; Ana Barbosa; Laura Cerqueira; et al. "Exploring the Spectrum of Biofilm Complexity". In Microbial Biofilm Dynamics.. Taylor & Francis Group, LLC, 2024. Accepted Castro, Joana; Oliveira, Ricardo; Campos, Ana Maria; Barros, Maria Margarida; Andreia Azevedo; Barbosa, Ana; Cerqueira, Laura; et al. "Laboratory Models for Biofilm Studies". In Microbial Biofilm Dynamics. United Kingdom: Taylor and Francis, 2024. Accepted Oliveira, Ricardo; Azevedo, Andreia S.; Mendes, Luzia. "Application of Nucleic Acid Mimics in Fluorescence In Situ Hybridization". In Fluorescence In-Situ Hybridization (FISH) for Microbial Cells, 69-86. Springer US, 2021. Published • 10.1007/978-1-0716-1115-9_5 Oliveira, Ricardo; Almeida, Carina; Azevedo, Nuno Filipe. "Detection of Microorganisms by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid". In Methods in Molecular Biology, 217-230. Springer US, 2020. Published • 10.1007/978-1-0716-0243-0_13
Conference abstract	Margarida Barros; Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Selection of DNA aptamers for the detection of foodborne toxins". Paper presented in 36th EFFoST International Conference 2022, Dublin, 2022. Oliveira, Ricardo; Pinho, Eva. "Prevalência e diversidade de Staphylococcus aureus e enterotoxinas estafilocócicas em leite cru na região norte de Portugal". Paper presented in Microbiologia 2022, 2022. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "In silico prediction of three-dimensional structure and docking of aptamers containing nucleic acid mimics (NAMs)". Paper presented in 4th Doctoral Congress in Engineering, Porto, 2021. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina; Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Easy-to-use pipeline to predict NAM-aptamers 3D structure and docking". Paper presented in World Microbe Forum, 2021. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Surveillance study of Staphylococcus aureus in raw milk from Northern Portugal: enterotoxins and resistance genetic profiles". Paper presented in Microbiotec'21, 2021. Oliveira, Ricardo; Ana Sousa; Pinho, Eva; Azevedo, Nuno Filipe; Jeffrey Destefano; Almeida, Carina. "De novo selection of toxin-specific aptamers using nucleic acid mimic". Paper presented in Microbiotec 19, 2019.
Conference paper	Oliveira, Hugo Alexandre Mendes; Duarte, José; Domingues, Rita; Vieira, Maria; Silva, Sónia Carina; Santos, Sílvio Roberto Branco; Oliveira, Ricardo; et al. "Understanding the complete reservoir of bacteriophage depolymerases against A. baumannii capsules". 2022.
Conference poster	Oliveira, Ricardo; Azevedo, Nuno Filipe; Almeida, Carina. "Development of an aptasensor for the detection of staphylococcal enterotoxin A". Paper presented in Encontro Ciência 2024, 2024. Campos, Ana Maria; Barros, Maria Margarida; Oliveira, Ricardo; Castro, Joana; Araújo, Daniela; Outor-Monteiro, Divanildo; Carina Almeida. "Aptamers as Novel Therapeutics Against Enterotoxigenic Escherichia coli: Targeting Fimbrial Adhesion". Paper presented in Ciência 2024, 2024. Oliveira, Ricardo; Araújo, Daniela; Beatriz Loureiro; Castro, Joana; Silva, Sónia; Almeida, Carina. "ST8475: a new sequence type identified in methicillin-resistant staphylococci (MRS) in Portugal". Paper presented in Congress of Microbiology and Biotechnology 2023, 2023. Barros, Maria Margarida; Oliveira, Ricardo; Castro, Joana; Campos, Ana Maria; Almeida, Gonçalo; Araújo, Daniela; Silva, Sónia; Outor-Monteiro, Divanildo; Almeida, Carina. "Detecting Enterotoxigenic Escherichia coli in animal production: method development and validation". Paper presented in Congress of Microbiology and Biotechnology 2023, 2023. Araújo, Daniela; Castro, Joana; Oliveira, Ricardo; Oliveira, Hugo; Fernandes, Liliana; Carvalho, Isabel; Cho, GS; et al. "Characterization of molecular features and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolates from companion animals in Portugal.". Paper presented in Congress of Microbiology and Biotecnology, 2023. Castro, Joana; Araújo, Daniela; Oliveira, Hugo; Fernandes, Liliana; Oliveira, Ricardo; Cho, GS; Franz, C; et al. "Genomic and phenotypic profiling of multidrug- resistant Klebsiella pneumoniae and Klebsiella variicola isolated from northern Portuguese hospitals". Paper presented in Congress of Microbiology and Biotecnology, 2023. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Selection of nucleic acid mimic (NAM) aptamers: from de novo SELEX to post-SELEX enhancement". Paper presented in 5th Doctoral Congress Engineering (DCE23), 2023. Barros, Maria Margarida ; Oliveira, Ricardo; Campos, Ana Maria; Castro, Joana; Araújo, Daniela ; Silva, Sónia; Outor-Monteiro, Divanildo; Almeida, Carina. "Aptamers for blocking Enterotoxigenic Escherichia coli". Paper presented in Dare2Change: Inovattion-Driven Agrifood Business, 2023. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. Corresponding author: Oliveira, Ricardo. "Development of an aptamer based-biosensor for the detection of food toxins". Paper presented in Dare2Change, 2023. Nunes, Bárbara; Barata, Ana; Oliveira, Ricardo; Guedes, Hugo; Almeida, Carina; Silva, Gabriela; M. J. Saavedra; Almeida, Gonçalo. "Fecal carriage of Listeria monocytogenes in dairy cows". Paper presented in Under One Health Concept, 2022. Bárbara Nunes; Ana Rita Barata; Oliveira, Ricardo; Guedes, Hugo; Carina Manuela Fernandes Almeida; da Silva, Gabriela Jorge; Saavedra, Maria José ; Almeida, Gonçalo. Corresponding author: Almeida, Gonçalo. "Fecal carriage of Listeria monocytogenes in dairy". Paper presented in I International Congress on Animal and Veterinary Sciences ¿Under One Health Concept¿, 2022. Campos, Ana Maria; Oliveira, Ricardo; Vieira, Filipa ; Silva, Regina A.; Silva, Regina ; Almeida, Carina. ""Optimisation of a molecular methodology for the detection of virulence factors of enterotoxigenic Escherichia coli in the diagnosis of swine colibacillosis"". 2022. Oliveira, Ricardo; Pinho, Eva; Almeida, Gonçalo; Nuno Azevedo; Carina Manuela Fernandes Almeida. Corresponding author: Carina Manuela Fernandes Almeida. "Prevalence and diversity of Staphylococcus aureus and staphylococal enterotoxins in raw milk from the North of Portugal". Paper presented in Microbiology 2022, 2022. Oliveira, Ricardo; Pinho, Eva; Almeida, Gonçalo; Azevedo, Nuno Filipe; Almeida, Carina. "Characterization of Staphylococcus aureus and staphylococcal enterotoxins in raw milk from northern Portugal". Paper presented in FEMS Conference on Microbiology, 2022. Bárbara Nunes; Ana Rita Barata; Oliveira, Ricardo; Guedes, Hugo; Carina Manuela Fernandes Almeida; Gabriela Silva; Saavedra, Maria José ; Almeida, Gonçalo. Corresponding author: Almeida, Gonçalo. "Raw milk as a source of Listeria monocytogenes". Paper presented in workshop of the National Reference Laboratories for Listeria monocytogenes, 2022. Oliveira, Ricardo; Pinho, Eva; DeStefano, Jeffrey; Azevedo, Nuno Filipe; Almeida, Carina. "Aptamers For Detection of Staphylococcal Enterotoxins in Food Samples". Paper presented in Dare2Change, 2021. Oliveira, Ricardo; Pinho, Eva; Almeida, Gonçalo; Azevedo, Nuno Filipe; Almeida, Carina. "Prevalence of Staphylococcus aureus and staphylococcal enterotoxins in raw milk from Northern Portugal". Paper presented in Dare2Change, 2021. Ana Rita Barata; Oliveira, Ricardo; Bárbara Nunes; Guedes, Hugo; Almeida, Carina; Saavedra, Maria José ; Silva, Gabriela; Almeida, Gonçalo. "Raw milk as a source of food zoonotic pathogens". Paper presented in Dare2Change, 2021. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "In silico prediction of the functional 3D conformation of NAM aptamers". Paper presented in 1st Symposium on Oligonucleotide Technologies and Therapeutics, 2021. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Prediction of single-stranded nucleic acids structure: from the sequence to the three-dimensional docking of aptamers". Paper presented in World Microbe Forum 2021, 2021. Vindeirinho, Joao; Pinho, Eva; Oliveira, Ricardo; Azevedo, Nuno Filipe; Almeida, Carina. "SARS-CoV-2 detection: a simple solution for end-point sensing of RT-PCR products". Paper presented in 1st Symposium on Oligonucleotide Technologies and Therapeutics, 2021. Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "De novo SELEX of toxin specific aptamers using nucleic acid mimics (NAMs)". Paper presented in Encontro Ciência 2020, 2020. Oliveira, Ricardo; Sousa, Ana Luísa; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Prediction and design of aptamer structures and their interaction with a target molecule". Paper presented in Microbiotec 19 - Congress of Microbiology and Biotechnology 19, Coimbra, Portugal, 2019. Oliveira, Ricardo; Ferreira-Bravo, Irani A; Sousa, Ana Luísa; Pinho, Eva; Azevedo, Nuno Filipe; DeStefano, Jeffrey; Almeida, Carina. "Application of nucleic acid mimics (NAMs) in the selection of aptamers against staphylococcal enterotoxins". Paper presented in 1º Simpósio INIAV para a Segurança Alimentar - Rumo à Alimentação do Futuro, Vila do Conde, Portugal, 2019. Ana Sousa; Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Prediction of aptamers´ structures and their interaction with staphylococcal enterotoxin A". Paper presented in 1º Simpósio INIAV para a Segurança Alimentar, 2019. Oliveira, Ricardo; Azevedo, Andreia S; Fernandes, Ricardo; Azevedo, Nuno Filipe; Almeida, Carina. "Identification of genes associated with beta lactam resistance in clinical isolates of Gram negative bacteria". Paper presented in FEMS 2019 - 8th Congress of European Microbiologists, Glasgow, Scotland, 2019. Oliveira, Ricardo; Sousa, Ana Luísa; Pinho, Eva; Almeida, Gonçalo; Azevedo, Nuno Filipe; Almeida, Carina. "De novo selection of toxin-specific aptamers using nucleic acid mimics". Paper presented in Doctoral Congress in Engineering 2019 - FEUP, Porto, Portugal, 2019. Oliveira, Ricardo; Rocha, Rui; Sousa, Mário; Cerqueira, Laura; Azevedo, Nuno Filipe (BE1B-918B-A853); Almeida, Carina. "Rapid identification of Campylobacter spp. using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) in food samples". Paper presented in V AEICBAS Biomedical Congress - Abel Salazar Biomedical Sciences Institute (ICBAS), Porto, Portugal, 2017.
Journal article	Castro, Joana; Araújo, Daniela; Oliveira, Hugo Alexandre Mendes; Fernandes, Liliana; Oliveira, Ricardo; Brinks, Erick; Cho, Gyu-Sung; et al. "Multidrug-resistant Klebsiella pneumoniae and Klebsiella variicola isolated from patients in Portuguese hospitals: Genomic and phenotypic characterization". The Microbe 5 (2024): 100172. http://dx.doi.org/10.1016/j.microb.2024.100172. Published • 10.1016/j.microb.2024.100172 Domingues, Rita; Oliveira, Ricardo; Silva, Sónia; Araújo, Daniela; Almeida, Carina; Cho, Gyu-Sung; Franz, Charles M.A.P.; et al. "Molecular Detection of Carbapenemases in Acinetobacter baumannii Strains of Portugal and Association With Sequence Types, Capsular Types, and Virulence". Clinical Therapeutics (2024): http://dx.doi.org/10.1016/j.clinthera.2024.09.005. Published • 10.1016/j.clinthera.2024.09.005 Oliveira, Ricardo. "Emergence of New Sequence Types of Methicillin-Resistant Staphylococcus aureus (MRSA) on Dairy Farms from Northern Portugal". Gene (2024): Under revision Barros, Maria Margarida; Castro, Joana; Araújo, Daniela; Oliveira, Ricardo; Campos, Ana Maria; Silva, Sónia; Outor-Monteiro, Divanildo; Almeida, Carina. "Application of DNA aptamers to block enterotoxigenic Escherichia coli toxicity in a Galleria mellonella larval model". Frontiers in Chemistry 12 (2024): http://dx.doi.org/10.3389/fchem.2024.1425903. Published • 10.3389/fchem.2024.1425903 Oliveira, Ricardo; Pinho, Eva; Barros, Maria Margarida; Azevedo, Nuno Filipe; Almeida, Carina. "In vitro selection of DNA aptamers against staphylococcal enterotoxin A". Scientific Reports 14 1 (2024): http://dx.doi.org/10.1038/s41598-024-61094-3. Published • 10.1038/s41598-024-61094-3 Vindeirinho, João M.; Oliveira, Ricardo; Pinho, Eva; Guiomar, Raquel; Azevedo, Nuno F.; Almeida, Carina. "The potential of tailed amplicons for SARS-CoV-2 detection in Nucleic Acid Lateral Flow Assays". PLOS ONE 19 5 (2024): e0301234. http://dx.doi.org/10.1371/journal.pone.0301234. Published • 10.1371/journal.pone.0301234 Araújo, Daniela; Silva, Ana Rita; Fernandes, Rúben; Serra, Patrícia; Barros, Maria Margarida; Campos, Ana Maria; Oliveira, Ricardo; et al. "Emerging Approaches for Mitigating Biofilm-Formation-Associated Infections in Farm, Wild, and Companion Animals". Pathogens 13 4 (2024): 320. http://dx.doi.org/10.3390/pathogens13040320. Published • 10.3390/pathogens13040320 Oliveira, Ricardo; Barbosa, Ana; Sousa, Mário; Azevedo, Nuno Filipe (BE1B-918B-A853); Cerqueira, Laura; Almeida, Carina. "Using peptide nucleic acid fluorescence in situ hybridization (PNA-FISH) to detect Campylobacter spp. in food samples". LWT (2024): 115922. http://dx.doi.org/10.1016/j.lwt.2024.115922. Published • 10.1016/j.lwt.2024.115922 Castro, J; Oliveira, Ricardo; Fernandes, L; Carvalho; Oliveira, H; Brinks, E; Cyu-Sung, Cho; et al. "Molecular characterization and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill cats and dogs in Portugal". Veterinary Microbiology (2024): 110056. http://dx.doi.org/10.1016/j.vetmic.2024.110056. Published • 10.1016/j.vetmic.2024.110056 Nunes, Bárbara; Barata, Ana Rita; Oliveira, Ricardo; Guedes, Hugo; Almeida, Carina; da Silva, Gabriela Jorge; Nogueira, Teresa; Saavedra, Maria José; Almeida, Gonçalo. "Occurrence and diversity of Listeria monocytogenes in Portuguese dairy farms". The Microbe (2024): 100063. http://dx.doi.org/10.1016/j.microb.2024.100063. Published • 10.1016/j.microb.2024.100063 Oliveira, Ricardo; Pinho, Eva; Azevedo, Nuno Filipe; Almeida, Carina. "Post-SELEX modifications with locked nucleic acids (LNA) of a SEA-specific DNA aptamer assisted by in silico modelling". Molecular Systems Design and Engineering (2024): http://dx.doi.org/10.1039/d4me00043a. Published • 10.1039/d4me00043a Araujo, D.; Oliveira, Ricardo; Silva, B. L.; Castro, J.; Ramos, C.; Matos, F.; Almeida, C.; Silva, S.. "Antimicrobial resistance patterns of Staphylococcus spp. isolated from clinical specimens of companion animals in Northern Portugal, 2021-2023". The Veterinary Journal (2024): https://publons.com/wos-op/publon/68247629/. Published • 10.1016/J.TVJL.2024.106153 Araújo, D.; Castro, J.; Matos, F.; Oliveira, R.; Ramos, C.; Almeida, C.; Silva, S.. "Exploring the prevalence and antibiotic resistance profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from clinically ill companion animals from North of Portugal". Research in Veterinary Science 159 (2023): 183-188. http://dx.doi.org/10.1016/j.rvsc.2023.04.009. 10.1016/j.rvsc.2023.04.009 Barros, Maria Margarida; Castro, Joana; Araújo, Daniela; Campos, Ana Maria; Oliveira, Ricardo; Silva, Sónia; Outor-Monteiro, Divanildo; Almeida, Carina. "Swine Colibacillosis: Global Epidemiologic and Antimicrobial Scenario". Antibiotics 12 4 (2023): 682. http://dx.doi.org/10.3390/antibiotics12040682. 10.3390/antibiotics12040682 Oliveira, Ana; Dias, Carla; Oliveira, Ricardo; Almeida, Carina; Fuciños, Pablo; Sillankorva, Sanna; Oliveira, Hugo. "Paving the way forward: Escherichia coli bacteriophages in a One Health approach". Critical Reviews in Microbiology (2023): 1-18. http://dx.doi.org/10.1080/1040841x.2022.2161869. 10.1080/1040841x.2022.2161869 Barata, Ana Rita; Nunes, Bárbara; Oliveira, Ricardo; Guedes, Hugo; Almeida, Carina; Saavedra, Maria José; da Silva, Gabriela Jorge; Almeida, Gonçalo. "Occurrence and seasonality of Campylobacter spp. in Portuguese dairy farms". International Journal of Food Microbiology 383 (2022): 109961. http://dx.doi.org/10.1016/j.ijfoodmicro.2022.109961. 10.1016/j.ijfoodmicro.2022.109961 Oliveira, Ricardo; Castro, Joana; Silva, Sónia; Oliveira, Hugo; Saavedra, Maria José; Azevedo, Nuno Filipe; Almeida, Carina. "Exploring the Antibiotic Resistance Profile of Clinical Klebsiella pneumoniae Isolates in Portugal". Antibiotics 11 11 (2022): 1613. http://dx.doi.org/10.3390/antibiotics11111613. Published • 10.3390/antibiotics11111613 Castro, Joana; Barros, Maria Margarida; Araújo, Daniela; Campos, Ana Maria; Oliveira, Ricardo; Silva, Sónia; Almeida, Carina. "Swine enteric colibacillosis: Current treatment avenues and future directions". Frontiers in Veterinary Science 9 (2022): http://dx.doi.org/10.3389/fvets.2022.981207. Published • 10.3389/fvets.2022.981207 Oliveira, Ricardo; Pinho, Eva; Sousa, Ana Luísa; Dias, Óscar; Azevedo, Nuno Filipe; Almeida, Carina. "Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking". PLOS ONE 17 3 (2022): e0264701. http://dx.doi.org/10.1371/journal.pone.0264701. Open access • 10.1371/journal.pone.0264701 Oliveira, Ricardo; Pinho, Eva; Almeida, Gonçalo; Azevedo, Nuno Filipe; Almeida, Carina. "Prevalence and diversity of Staphylococcus aureus and staphylococcal enterotoxins in raw milk from northern Portugal". Frontiers in Microbiology (2022): https://www.frontiersin.org/articles/10.3389/fmicb.2022.846653/abstract. Open access • In press • 10.3389/fmicb.2022.846653 Oliveira, Ricardo; Pinho, Eva; Sousa, Ana Luísa; DeStefano, Jeffrey J.; Azevedo, Nuno Filipe; Almeida, Carina. "Improving aptamer performance with nucleic acid mimics: de novo and post-SELEX approaches". Trends in Biotechnology (2021): http://dx.doi.org/10.1016/j.tibtech.2021.09.011. 10.1016/j.tibtech.2021.09.011 Fernandes, Ricardo M; Silva, Hélder; Oliveira, Ricardo; Almeida, Carina; Azevedo, Nuno Filipe; Vieira, Maria J. "Morphological transition of Helicobacter pyloriadapted to water". Future Microbiology 12 13 (2017): 1167-1179. http://dx.doi.org/10.2217/fmb-2016-0174. 10.2217/fmb-2016-0174
Magazine article	Castro, Joana; Barros, Maria Margarida; Oliveira, Ricardo; Araújo, Daniela; Campos, Ana Maria; Ana Margarida Duarte; FAGULHA, TERESA; et al. "Coinfecção pelo Vírus da Síndrome Respiratória e Reprodutiva dos Suínos (PRRS), Actinobacillus pleuropneumoniae, Pasteurella multocida e Streptococcus suis 2 - Relato de um caso numa exploração familiar de suínos em Portugal", Revista Portuguesa de Ciências Veterinárias 119, 625, 2024
Thesis / Dissertation	"Application of nucleic acid mimics (NAM) in the selection of aptamers against staphylococcal enterotoxins". PhD, Universidade do Porto Faculdade de Engenharia, 2023. Oliveira, Ricardo. "Design and validation of an alternative molecular method using peptide nucleic acid fluorescence in situ hybridization (PNA FISH) for the detection of Campylobacter spp. in food samples". Master, Universidade do Minho Departamento de Engenharia Biológica, 2017. Oliveira, Ricardo. "Identification of multi-drug resistant Mycobacterium tuberculosis by padlock probes and lateral flow nucleic acid biosensors". Degree, Universidade do Porto, 2015.

Artistic / Performance

Visual artwork

Barros, Maria Margarida; Castro, Joana; Araújo, Daniela; Oliveira, Ricardo; Silva, Sónia; Almeida, Carina. Impacto da Colibacilose Suína: da Quinta ao Homem.
Rúben Fernandes; Vindeirinho, João M. ; Castro, Joana; Araújo, Daniela; Barros, Maria Margarida; Oliveira, Ricardo; Campos, Ana Maria; Silva, Sónia; Almeida, Carina. Os Vilões Invisíveis.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2024/10/23	Action Tank "Food Security"	BIN@PORTO 2024 ‘Innovation for Resilience" Faculty of Engineering, University of Porto (Porto, Portugal)
2022/11/08	Selection of DNA aptamers for the detection of foodborne toxins	36th EFFoST International Conference 2022 European Federation of Food Science and Technology (Dublin, Ireland)
2022/10/18	Prevalência e diversidade de Staphylococcus aureus e enterotoxinas estafilocócicas em leite cru na região norte de Portugal	Microbiologia 2022 Sociedade Portuguesa de Microbiologia (Portugal)
2022/01/20	Staphylococcal enterotoxins and mycotoxins in raw milk: a combined risk?	SciMonday National Institute for Agricultural and Veterinary Research (INIAV) (Vairão, Portugal)
2021/11/25	Surveillance study of Staphylococcus aureus in raw milk from Northern Portugal: Enterotoxins and resistance genetic profiles.	Microbiotec'21 NOVA University of Lisbon (Lisboa, Portugal)
2021/06/28	In silico prediction of three-dimensional structure and docking of aptamers containing nucleic acid mimics (NAMs)	4th Doctoral Congress in Engineering Faculty of Engineering, University of Porto (Porto, Portugal)
2020/06/26	NAM4Covid19 – What if you could know the test results in less than 1 hour?	LEPABE talks Faculty of Engineering, University of Porto (Porto, Portugal)
2019/12	Application of nucleic acid mimics in the selection of aptamers against staphylococcal enterotoxins	Microbiotec'19 - Congress of Microbiology and Biotechnology 2019 Faculdade de Ciências da Universidade de Coimbra (Coimbra, Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2024/09/09 - 2024/09/27	Characterisation of Staphylococcus sp. isolates from animals in the INIAV collection using culturomics methods. Supervisor	Ciências Biomédicas Laboratoriais (Scientific initiation) Instituto Politécnico do Porto Escola Superior de Saúde, Portugal
2024/04/29 - 2024/06/17	Própolis português e infeções bacterianas de animais domésticos: que potencial? Co-supervisor of Rui Francisco Sousa Almeida	Licenciatura em Bioquímica (Degree) Universidade do Minho Departamento de Biologia, Portugal
2024/01/08 - 2024/01/27	Selection and characterization of aptamers against enterotoxigenic E. coli Supervisor of Denise Marques	Ciências Biomédicas Laboratoriais (Degree) Instituto Politécnico do Porto Escola Superior de Saúde, Portugal
2021/01 - 2021/07	Aptamers for Staphylococcal enterotoxin A: effects on incorporating nucleic acid mimics Co-supervisor of Roberto Pinto	Biotecnologia Medicinal (Degree) Instituto Politécnico do Porto Escola Superior de Saúde, Portugal

Event organisation

	Event name Type of event (Role)	Institution / Organization
2024/11/27 - Current	2º Simpósio INIAV para a Segurança Alimentar- “Sistemas Alimentares Sustentáveis e Seguros (2024/11/27) Symposium (Member of the Organising Committee)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2023/03/17 - Current	Co-organização da visita de estudo ao INIAV dedicada a alunos do secundário (escolas secundárias de Viana do Castelo e da Galícia), no tema “Papel da PAC na promoção da inovação”, 17 de Março de 2023. Total de 40 alunos. Breve seminário seguido de atividades laboratoriais: identificação de agentes patogénicos em amostras alimentares; pesquisa de antibióticos em alimentos; modelo larvar para estudo de citotoxicidade. (2023/03/17) Other (Co-organisor)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2024/04/03 - 2024/04/03	Co-organização da visita de estudo ao INIAV, alunos da Licenciatura de Ciências Biomédicas (Escola Universitária Vasco da Gama, Coimbra), 3 de Abril de 2024. Total de 15 alunos. Atividades: visita aos laboratórios de Segurança Alimentar e Saúde Animal; avaliação de toxicidade em modelo animal. (2024/04/03) Other (Co-organisor)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2023/07/13 - 2023/07/13	Co-organização da visita de estudo ao INIAV de alunos da escola primária e pré-escolar da escola de Vairão e Fornelo, 13 de Julho de 2023, com organização de 4 atividades de ciência dedicadas as crianças dos 4 aos 11 anos. Total de 51 alunos. Atividades de ciência organizadas: (1) O ciclo de vida das larvas; (2) Morfologia de bactérias e os fungos; (3) O vulcão: conceito de reação química; (4) A família dos coronavírus. (2023/07/13) Other (Co-organisor)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2023/04/04 - 2023/04/04	Co-organização da visita de estudo ao INIAV dedicada a alunos do ensino primário (1º ao 4º ano), das freguesias de Vairão e Fornelo (Vila do Conde), 4 de Abril de 2023. Total de 20 alunos. Vista ao polo com atividades de ciência dedicadas às crianças: formação de arco-íris com soluções salinas, crescimento de larvas, morfologia das bactérias no microscópio, moldagem da morfologia de bactérias com plasticina. (2024/04/04) Other (Co-organisor)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2023/02/01 - 2023/02/01	Co-organização da visita de estudo ao INIAV, alunos do secundário (Curso Profissional de Análises Laboratoriais), da escola Oliveira Júnior, de S. João da Madeira, 1 de fevereiro de 2023. Total de 13 alunos. Atividades: analise de contaminantes por cromatografia fina; deteção de patogénicos por PCR em tempo real, avaliação de toxicidade em modelo animal. (2023/02/01) Other (Co-organisor)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal

Event participation

	Activity description Type of event	Event name Institution / Organization
2024/09/02 - 2024/09/10	Climate Change: Challenges and Influence on Microbial Safety of Water and Food Meeting	FEMS Summer School for Postdocs 2024 Mediterranean Institute for Life Sciences, Croatia
2024/05/28 - 2024/05/29	BEekeeping products valorization and biomonitoring for the SAFEty of BEEs and HONEY Conference	1st International Conference - BeSafeBeeHoney Panepistemio Thessalias - Larisa, Greece
2024/04/09 - 2024/04/24	e.Biofilm Training School - Fundamentals of Biofilm Engineering Workshop	e.Biofilm Training School - Fundamentals of Biofilm Engineering Universidade do Porto Faculdade de Engenharia, Portugal
2023/09/06 - 2023/09/07	COST Academy Leadership Workshop Workshop	European Cooperation in Science and Technology, Belgium
2020/08/27 - 2020/08/28	Antimicrobial drugs, drug delivery vectors, bio-barriers and characterization assays. Workshop	DelNAM’s Workshop 3 - “Drug Delivery meets Bacteria" Universidade do Porto Faculdade de Engenharia, Portugal
2019/05 - 2019/06	Radiation Protection Training for Use of Radiation-Producing Materials Workshop	University of Maryland at College Park, United States
2019/03/21 - 2019/03/22	Design and Synthesis of Nucleic Acids Mimics Workshop	Syddansk Universitet, Denmark
2018/11/21 - 2018/11/23	XXIV Encontro Luso-Galego de Química Meeting	XXIV Encontro Luso-Galego de Química Universidade do Porto Faculdade de Ciências, Portugal

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2024/12/09	Evaluating Essential Oils for Treating Skin Infections Caused by Staphylococcus pseudintermedius (Thesis) Main arguer	Taísa Cebotari (Other) Instituto Politécnico de Coimbra Escola Superior Agrária de Coimbra, Portugal
2024/07/12	Characterization of pathogenicity and virulence factors of Staphylococcus spp. recovered from company animals (Thesis) Main arguer	Rodrigo Miranda Magalhães (Other) Instituto Politécnico do Porto Escola Superior de Saúde, Portugal
2022	Development and optimization of a PCR methodology for the detection of the main virulence factors (i.e., toxins and fimbriae) of enterotoxigenic E. coli (ETEC) Supervisor	Ana Campos (Other) Instituto Politécnico do Porto Escola Superior de Saúde, Portugal

Association member

	Society Organization name	Role
2024/01/19 - Current	Gonditrilhos - Associação de Ciclismo de Gondifelos	President
2019 - Current	Portuguese Society of Microbiology	Member

Committee member

	Activity description Role	Institution / Organization
2024/09 - Current	Topic Coordinator for the Research Topic ‘Perspectives in Clinical Infectious Diseases: 2024’ in Frontiers in Cellular and Infection Microbiology Coordinator

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2024/12 - Current	Engenharia Metabólica e Biomolecular	Mestrado em Bioengenharia (Mestrado)	Universidade do Porto Faculdade de Engenharia, Portugal
2024/07/22 - Current	Aplicação de métodos de deteção de fatores de patogenicidade de Escherichia coli, e a sua importância num contexto de Saúde Pública	(Outros)	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal
2018/11 - 2018/12	Engenharia Metabólica e Celular	Bioengenharia (Mestrado integrado)	Universidade do Porto Faculdade de Engenharia, Portugal

Evaluation committee

	Activity description Role	Institution / Organization	Funding entity
2024/11/27 - Current	Evaluation/selection of the best poster presentations at the 2º Simpósio INIAV para a Segurança Alimentar Evaluator	Instituto Nacional de Investigação Agrária e Veterinária - Polo de Vairão, Portugal

Journal scientific committee

	Journal title (ISSN)	Publisher
2024/07 - Current	Frontiers in Microbiology (1664-302X)	Frontiers Media
2024/06 - Current	Molecular and cellular probes (0890-8508)	Elsevier Editorial
2024/06 - Current	PloS one (1932-6203)	PLOS
2024/02 - Current	Frontiers in Cellular and Infection Microbiology (2235-2988)	Frontiers Media
2023/08 - Current	Frontiers in Antibiotics (2813-2467)	Frontiers Media

Mentoring / Tutoring

	Topic	Student name
2024/01 - Current	Aptamers for blocking Escherichia coli Shiga-toxins	Ana Campos
2022/07 - Current	Aptamers to control colibacillosis in piglets	Maria Margarida Barros
2022/09 - 2024/11	Aptamers for blocking enterotoxigenic Escherichia coli	Ana Campos
2023/07/03 - 2023/07/23	Previsão da afinidade de aptâmeros para a enterotoxina A de Staphylococcus aureus	Catarina Machado Rebelo
2022/04/26 - 2022/07/14	Desenvolvimento de uma metodologia molecular para deteção de fatores de virulência de Escherichia coli enterotoxigénica em suínos de explorações portuguesas.	Ana Maria da Silva Campos
2022/04 - 2022/05	Development and optimization of a PCR methodology for the detection of the main virulence factors (i.e., toxins and fimbriae) of enterotoxigenic E. coli (ETEC)	Ana Ferraz
2021/09/06 - 2021/09/24	Characterization of resistance/virulence genes by PCR of Staphylococcus aureus isolates obtained from raw milk samples.	Ana Campos
2021/01 - 2021/07	Aptamers for Staphylococcal enterotoxin A: effects on incorporating nucleic acid mimics	Roberto Miguel Pais Pinto

Distinctions

Award

2024	Best Project Proposal at 5th FEMS Summer School for Postdocs 2024 Federation Of European Microbiological Societies, Netherlands
2023	FEMS Early Career Scientist Meeting Grant - Microbiotec'23 Federation Of European Microbiological Societies, Netherlands
2023	5ª edição do concurso comunicação de ciência em microbiologia - Vencedor na categorial geral Sociedade Portuguesa de Microbiologia, Portugal
2021	Best Oral Presentation Award - LEPABE Talks Universidade do Porto Laboratorio de Engenharia de Processos Ambiente Biotecnologia e Energia, Portugal Universidade do Porto Faculdade de Engenharia, Portugal
2017	2nd Best Scientific Poster Award - V AEICBAS Biomedical Congress Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal
2015	Prize Prof. Doutor Fernando Serrão Universidade do Porto Faculdade de Ciências, Portugal

Other distinction

2024	Top 20 of the most talented and promising researchers from across the world - Invitation to FEMS Summer School for Postdocs 2024 Federation Of European Microbiological Societies, Netherlands
2018	FCT PhD Studentship - SFRH/BD/138883/2018 Fundação para a Ciência e a Tecnologia, Portugal
2015	Erasmus+ Scholarship - Stockholm University, Sweden Universidade do Porto Instituto de Ciências Biomédicas Abel Salazar, Portugal