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Rafael Tavares holds a Bachelor’s degree in Biology (2017), a Master’s degree (2019) in Microbiology both from University of Aveiro, Portugal, and a PhD degree in Biosciences (2025) (specialization in Microbiology) from University of Coimbra, Portugal. He is currently working at Laboratório de Microbiologia Aplicada (University of Aveiro, Portugal) in yeast isolation and characterization. His main research interests are focused on the characterization of the microbial community and associated antimicrobial resistance profiles in environmental and nosocomial settings, particularly using next-generation sequencing. He participated in 2 research projects funded by FCT (as a research fellow). He has published 8 papers in WoS journals, with a total of 153 citations by June 2025 and a h-index of 6. He has also presented oral presentations (3) and posters (9) in national and international scientific meetings. He has peer-reviewed for 5 international journals. Key skills include traditional and molecular microbiology techniques as well as bioinformatic skills for data analysis of next generation sequencing data (Illumina and PacBio) for both genome and metagenome sequencing, with emphasis on R language. Key-words: Antimicrobial resistance; Urban wastewater treatment plants (UWTPs); Bacterial communities; Next-generation sequencing; Bioinformatic analysis.
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Identification

Personal identification

Full name
Rafael Tavares
Date of birth
1995/12/21
Gender
Male

Citation names

  • Tavares, Rafael DS

Author identifiers

Ciência ID
E11E-AD60-B527
ORCID iD
0000-0001-9138-5935

Email addresses

  • rafael.tavares@ua.pt (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Upper intermediate (B2) Advanced (C1) Upper intermediate (B2)
Education
Degree Classification
2020/08/01 - 2025/06/05
Concluded
 Biociências (com especialização em microbiologia) (Doutoramento)
Universidade de Coimbra Faculdade de Ciencias e Tecnologia, Portugal
"Integrons and integron-borne antibiotic resistance in clinical settings and wastewater" (THESIS/DISSERTATION)
 Aprovado com louvor e distinção
2020/01/27 - 2020/01/31
Attended
 Experimental Design and Analysis of Multivariate Data (advanced course) (Outros)
Universidade de Aveiro, Portugal
 18
2017/09 - 2019/12/01
Concluded
 Microbiologia (Mestrado)
Universidade de Aveiro, Portugal
"Pathogenic and antibiotic-resistant strains of Escherichia coli in wastewater effluents treated with UV radiation" (THESIS/DISSERTATION)
 19
2019/07/01 - 2019/07/05
Attended
 Fundamentals on Animal Cell Culture (Advanced course) (Outros)
Universidade de Aveiro, Portugal
2018/07/23 - 2018/07/27
Attended
 Microbial diversity: methods and applications (Advanced course) (Outros)
Universidade de Aveiro, Portugal
2018/07/09 - 2018/07/13
Attended
 Bioinformatics for microbiologists (Advanced course) (Outros)
Universidade de Aveiro, Portugal
2018/06/18 - 2018/06/22
Attended
 Antibiotic alternatives against pathogenic bacteria (Advanced course) (Outros)
Universidade de Aveiro, Portugal
2013/09 - 2017/07
Concluded
 Biologia (Licenciatura)
Universidade de Aveiro, Portugal
"Characterization of cefotaxime-resistant strains of Escherichia coli from an effluent treated with ultraviolet radiation" (THESIS/DISSERTATION)
 18
Affiliation

Others

Category
Host institution 		Employer
2025/05/01 - 2055/08/31 Research fellow at Projeto Espumante de Portugal (PRR-C05-i03-I-000194) Universidade de Aveiro, Portugal
2020/08/01 - 2025/06/05 PhD student Universidade de Coimbra, Portugal
2020/02/01 - 2020/07/31 Research Fellow in project GrEAT (BI/CESAM/0086_2019/PTDC/BTA-BTA/29970/2017) Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
Projects

Grant

Designation Funders
2025/05/01 - 2025/08/31 Projeto Espumante de Portugal
PRR-C05-i03-I-000194
Research Fellow
Universidade de Aveiro, Portugal
2020/08 - 2024/07 Effect of anthropogenic pollution on bacterial integron’s dynamics in aquatic systems
74802DFA
 Fundação para a Ciência e a Tecnologia
2020/02/01 - 2020/07/31 Project GReAT - Granular microalgae-bacterial sludge for aquaculture wastewater treatment
PTDC/BTA-BTA/29970/2017
Research Fellow
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Conference poster
  1. Tavares, Rafael DS; Rodrigues, ET; Tacão, Marta; Henriques, Isabel. "One-year surveillance of pathogens in a full-scale Municipal Wastewater Treatment Plant". 2023.
  2. Tavares, Rafael DS; Rodrigues, Elsa Teresa; Tacão, Marta; Henriques, Isabel. "Identification of indicator genes for monitoring antibiotic resistance and pathogens in wastewater". Paper presented in FEMS2023, 2023.
  3. Tavares, Rafael DS; Rodrigues, Elsa Teresa; Tacão, Marta; Henriques, Isabel. "A year-long monitorization of the resistome of a Municipal Wastewater Treatment Plant". Paper presented in Ciência 2023, 2023.
  4. Dias, Joana; Tavares, Rafael DS; Tacão, Marta; Henriques, Isabel. "Unveiling the diversity of Vibrio species in Ria de Aveiro: along the estuary we go!". Paper presented in One Health Day, CESAM, 2020.
  5. Tavares, Rafael DS; Tacão, Marta; Figueiredo, Ana Sofia; Duarte, Ana; Manaia, Célia; Henriques, Isabel. "Characterization of multi-drug resistant Escherichia coli in the UV-treated outflow of an Urban Wastewater Treatment Plant.". Paper presented in Microbiotec19, 2019.
  6. Tavares, Rafael DS; Tacão, Marta; Figueredo, Ana Sofia; Duarte, Ana; Manaia, Célia; Henriques, Isabel. "Multi-drug resistant Escherichia coli released in the UV-C irradiated effluent of a Wastewater Treatment Plant". Paper presented in One Health Day, CESAM, 2019.
  7. Tavares, Rafael DS; Tacão, Marta; Manaia, Célia; Henriques, Isabel. "Whole-genome sequencing as a tool to predict the risk of E. coli strains released by an Urban Wastewater Treatment Facility". Paper presented in GenomePT Symposium, 2019.
  8. Tavares, Rafael DS; Silva, Isabel; Figueiredo, Ana Sofia; Manaia, Célia; Henriques, Isabel. "Antibiotic-resistant E. coli in an UV-treated effluent: troubled waters ahead?". Paper presented in Microbiotec17, 2017.
  9. Tavares, Rafael DS; Tacão, Marta; Teixeira, Pedro; Roxo, Inês; Ramalheira, Elmano; Ferreira, Sónia; Henriques, Isabel. "Report on a multi-drug resistant Escherichia coli ST744 carrying mcr-1 and blaKPC-3 isolated from a patient in Portugal after colistin treatment". Paper presented in 2nd International Caparica Conference in Antibiotic Resistance, 2017.
Journal article
  1. Rafael D.S. Tavares; Elsa T. Rodrigues; Marta Tacão; Isabel Henriques. "Temporal dynamics of class 1 and class 3 integron pools in treated wastewater". Water Research (2025): https://doi.org/10.1016/j.watres.2025.123718.
    10.1016/j.watres.2025.123718
  2. Rafael D. S. Tavares; Marta Tacão; I Henriques. "Integrons are key players in the spread of beta-lactamase-encoding genes". International Journal of Antimicrobial Agents (2025): http://dx.doi.org/10.1016/j.ijantimicag.2024.107421.
    10.1016/j.ijantimicag.2024.107421
  3. Tavares, Rafael D.S.; Fidalgo, Cátia; Rodrigues, Elsa T.; Tacão, Marta; Henriques, Isabel. "Integron-associated genes are reliable indicators of antibiotic resistance in wastewater despite treatment- and seasonality-driven fluctuations". Water Research 258 (2024): 121784. http://dx.doi.org/10.1016/j.watres.2024.121784.
    10.1016/j.watres.2024.121784
  4. Tavares, RDS; Tacão, Marta; Ramalheira, Elmano; Ferreira, Sónia; Henriques, Isabel. "Report and Comparative Genomics of an NDM-5-Producing Escherichia coli in a Portuguese Hospital: Complex Class 1 Integrons as Important Players in blaNDM Spread". Microorganisms 10 11 (2022): 2243. http://dx.doi.org/10.3390/microorganisms10112243.
    Published • 10.3390/microorganisms10112243
  5. Tavares, RDS; Tacão, Marta; Figueiredo, Ana S.; Duarte, Ana S.; Esposito, Fernanda; Lincopan, Nilton; Manaia, Célia M.; Henriques, Isabel. "Genotypic and phenotypic traits of blaCTX-M-carrying Escherichia coli strains from an UV-C-treated wastewater effluent". Water Research 184 (2020): 116079. http://dx.doi.org/10.1016/j.watres.2020.116079.
    Published • 10.1016/j.watres.2020.116079
  6. Oliveira, Amanda M.S.; Baraúna, Rafael A.; Marcon, Davi J.; Lago, Letícia A.B.; Silva, Artur; Lusio, Joana; Tavares, RDS; et al. "Occurrence, antibiotic-resistance and virulence of E. coli strains isolated from mangrove oysters (Crassostrea gasar) farmed in estuaries of Amazonia". Marine Pollution Bulletin 157 (2020): 111302. http://dx.doi.org/10.1016/j.marpolbul.2020.111302.
    Published • 10.1016/j.marpolbul.2020.111302
  7. Silva, Isabel; Tacão, Marta; Tavares, RDS; Miranda, Rita; Araújo, Susana; Manaia, Célia M.; Henriques, Isabel. "Fate of cefotaxime-resistant Enterobacteriaceae and ESBL-producers over a full-scale wastewater treatment process with UV disinfection". Science of The Total Environment 639 (2018): 1028-1037. http://dx.doi.org/10.1016/j.scitotenv.2018.05.229.
    Published • 10.1016/j.scitotenv.2018.05.229
  8. Tacão, Marta; Tavares, RDS; Teixeira, Pedro; Roxo, Inês; Ramalheira, Elmano; Ferreira, Sónia; Henriques, Isabel. "mcr-1 and blaKPC-3 in Escherichia coli Sequence Type 744 after Meropenem and Colistin Therapy, Portugal". Emerging Infectious Diseases 23 8 (2017): 1419-1421. http://dx.doi.org/10.3201/eid2308.170162.
    Published • 10.3201/eid2308.170162
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2021/11 Report of blaNDM-5 in the Portuguese nosocomial environment: is one integron all it takes? Microbiotec’21
Online format (Portugal)
2019/12/05 Characterization of multi-drug resistant Escherichia coli in the UV-treated outflow of an Urban Wastewater Treatment Plant Microbiotec’19
University of Coimbra (Coimbra, Portugal)
2017 Fate of ESBL-producing Enterobacteriaceae in a full-scale wastewater treatment plant and potential impact of UV disinfection 2nd International Caparica Conference in Antibiotic Resistance
BIOSCOPE GROUP (Lisboa, Portugal)

Event participation

Activity description
Type of event 		Event name
Institution / Organization
2019/04/17 - 2019/04/17 The Perfect Pitch in 5’. Workshop design to provide tips and tools to facilitate the dissemination of scientific information to peers, stakeholders and the general public. This activity encompassed a 3 hours-long hands-on workshop and the following lectures: How to communicate your science in 5’? How to sell your scientific idea to investors? Why and how to communicate to non-scientific publics? How to optimize your pitch using design tips?
Workshop
 The Perfect Pitch in 5’
Universidade de Aveiro, Portugal
Distinctions

Award

2024 Second place at the best scientific pitch contest "Pitch or Perish"
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2019 Best poster at One Health Day with the poster entitled: Multi-drug resistant Escherichia coli released in the UV-C irradiated effluent of a Wastewater Treatment Plant
Universidade de Aveiro Centro de Estudos do Ambiente e do Mar, Portugal
2019 Merit grant for the 2018/2019 academic year
Universidade de Aveiro, Portugal