João Francisco Tomaz Santos Botelho (6010-5A73-CB50)

Curriculum Vitae

João Francisco Tomaz Santos Botelho

My name is João Botelho and I completed my PhD in Pharmaceutical Sciences - Microbiology at the University of Porto in December 2018, studying the molecular basis of antibiotic resistance mediated by different mobile elements in Pseudomonas aeruginosa isolates from clinical settings. I used experimental and computational approaches and worked in the laboratory of Luísa Peixe, funded by a competitive Fundação para a Ciência e Tecnologia (FCT) grant. I also completed a short postdoctoral fellowship in the same laboratory, before moving to Germany in April 2019 to work as a Max Planck postdoctoral researcher in the laboratory of Hinrich Schulenburg. There, I used computational and experimental approaches to study antibiotic resistance in an evolutionary context, and was awarded the Kiel Life Science Award for Early Career Postdocs while in Germany. I was then awarded a Maria Zambrano Fellowship at the end of 2021 and worked at the Centre for Plant Biotechnology and Genomics CBGP (UPM-INIA) in Spain from July 2022 to November 2024, where my research focused on the evolutionary dynamics of bacterial and archaeal genomes, viruses and microbial populations. In 2023, I've secured a competitive contract in the 6th edition of the Individual Call of the Scientific Employment Stimulus (CEEC), funded by the FCT. Since December 2024, I've been working at the Centre for Biotechnology and Fine Chemistry (CBQF) with my CEEC project, which focuses on exploring the role of duplicated core genes in multipartite bacterial genomes. I've produced high quality results and publications in the labs and countries where I've worked and have established myself as a major figure in the field of bacterial evolution, as evidenced by invitations to present my results and ideas at academic institutions. I have also developed strong collaborations with scientists around the world, resulting in international publications and competitive funding. I have recently co-supervised a PhD student, an undergraduate student and am currently a co-supervisor of a PhD student.

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Identification

Personal identification

Full name: João Francisco Tomaz Santos Botelho
Date of birth: 1988/05/16
Gender: Male

Citation names

Botelho, João

Author identifiers

Ciência ID: 6010-5A73-CB50
ORCID iD: 0000-0002-2771-2345
Google Scholar ID: _Sz69QgAAAAJ

Email addresses

joaobotelho9@hotmail.com (Professional)
joao.tbotelho@upm.es (Professional)
botelho@evolbio.mpg.de (Professional)

Websites

Knowledge fields

Natural sciences - Biological Sciences - Microbiology
Exact Sciences - Computer and Information Sciences - Bioinformatics
Natural sciences - Biological Sciences - Evolutionary Biology
Medical and Health Sciences - Health Sciences - Infectious Diseases
Medical and Health Sciences - Health Sciences - Public and Environmental Health

Languages

Language	Speaking	Reading	Writing	Listening	Peer-review
Portuguese (Mother tongue)
English	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)	Proficiency (C2)

Education

	Degree	Classification
2021/06/10 - 2021/06/17 Attended	Introduction to Containers for Scientific Computing (Outros) Christian-Albrechts-Universität zu Kiel, Germany
2021/06/02 - 2021/06/04 Attended	Advanced R (Outros) Max-Planck-Institut für Evolutionsbiologie, Germany
2021/05/27 - 2021/05/28 Attended	R for Beginners (Outros) Max-Planck-Institut für Evolutionsbiologie, Germany
2021/05/17 - 2021/05/20 Attended	Ontologies – statistics, biases, tools, networks, and interpretation (CBNA L2P1) (Outros) European Molecular Biology Laboratory, Germany
2021/04/29 - 2021/04/29 Attended	High-Performance and Parallel Computing introduction course (Outros) Christian-Albrechts-Universität zu Kiel, Germany
2021/01/14 - 2021/01/15 Attended	Research Software Development Workshop (Outros) Max-Planck-Institut für Evolutionsbiologie, Germany
2018/12/19 Concluded	Ciências Farmacêuticas (Doutoramento) Major in Microbiologia Universidade do Porto Faculdade de Farmácia, Portugal "Carbapenemase producers of Pseudomonas aeruginosa: lights on new mobile genetic elements" (THESIS/DISSERTATION)	A
2016/01/20 - 2016/01/22 Attended	2nd ESCMID course on the Principles of Molecular Microbiological Diagnostics (Outros) Maastricht Universitair Medisch Centrum+, Netherlands
2011/11/03 Concluded	Ciências Farmacêuticas (Mestrado integrado) Universidade do Porto Faculdade de Farmácia, Portugal	15

Affiliation

Science

	Category Host institution	Employer
2024/12/01 - Current	Researcher (Research)	Universidade Católica Portuguesa, Portugal
	Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal
2022/07/27 - 2024/11/15	Researcher (Research)	Universidad Politécnica de Madrid, Spain
	Centro de Biotecnología y Genómica de Plantas, Spain
2019/04/24 - 2022/06/23	Postdoc (Research)	Max-Planck-Institut für Evolutionsbiologie, Germany

2019/01/02 - 2019/03/31	Postdoc (Research)	Universidade do Porto Faculdade de Farmácia, Portugal

2012/01/16 - 2012/07/15	Research Trainee (Research)	Universidade de Aveiro CICECO, Portugal

2011/03/01 - 2011/05/31	Research Trainee (Research)	Uniwersytet Mikolaja Kopernika w Toruniu Collegium Medicum im Ludwika Rydygiera w Bydgoszczy Wydzial Farmaceutyczny, Poland

2009/09/01 - 2011/03/01	Research Trainee (Research)	Universidade do Porto Faculdade de Farmácia, Portugal

Projects

Grant

	Designation	Funders
2025 - Current	Effective Monitoring and Modelling solutions for data-driven hOlistic management of URBAN water quality HORIZON-CL6-2024-ZEROPOLLUTION-02-2-two-stage Researcher	Horizon 2020
2022/07/27 - Current	Coevolution of virus-host interactions and their effect on the microbiome UP2021-035 Post-doc Centro de Biotecnología y Genómica de Plantas, Spain	Agencia Estatal de Investigación Ongoing
2015/01/02 - 2018/12/19	Carbapenemase producers of Pseudomonas aeruginosa: lights on new mobile genetic elements SFRH/BD/104095/2014 PhD Student Fellow	Governo da República Portuguesa Ministério da Ciência Tecnologia e Ensino Superior Concluded

Contract

	Designation	Funders
2024/12/01 - Current	Exploring core gene redundancy and antibiotic resistance through microbial genomics, mathematical modeling, and deep learning 2023.06600.CEECIND/CP2855/CT0001 Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal	Fundação para a Ciência e a Tecnologia Ongoing
2022/07/27 - Current	Severo Ochoa programme CEX2020-000999-S (2022–2025) Post-doc Centro de Biotecnología y Genómica de Plantas, Spain	Agencia Estatal de Investigación Ongoing
2022/09/01 - 2025/08/31	Optimising Pseudomonas putida as a crop warden. Environmental signals, effector specificity and efficiency of the type VI secretion system biocontrol weapon PID2021-123000OB-I00 Post-doc Universidad de Sevilla, Spain	Agencia Estatal de Investigación Ongoing
2021/01/01 - 2022/12/31	Bacterial responses to evolution-informed antibiotic therapy - resistance and microbiome monitoring in an interventional study EXC 2167 Post-doc	Deutsche Forschungsgemeinschaft
2012/01/16 - 2012/07/15	Development of sustainable selective catalytic oxidation of alkanes FP7-PEOPLE-2009-RG-256509 Master Student Fellow	EU Framework Programme for Research and Innovation Marie Sklodowska-Curie Actions Concluded

Outputs

Publications

Conference poster	Botelho, João; Iranzo, Jaime. Corresponding author: Botelho, João. "Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance". Paper presented in SMBE 2023, 2023. Grosso, Filipa; Botelho, João; Silva, Liliana; Lood, Cédric; van Noort, Vera; Lavigne, Rob; Luísa Vieira Peixe. "Unraveling the Genetic Mechanisms of blaIMP-5 Dissemination in Acinetobacter Species: Insights and Unanswered Questions". Paper presented in 13th International Symposium on the Biology of Acinetobacter, 2023. Botelho, João; Schulenburg, Hinrich. Corresponding author: Botelho, João. "The ESKAPE pathogens mobilome: a systematic analysis". Paper presented in Microbiotec 19, 2019. Rocha, Joana; Botelho, João; Ksiezarek M; Ribeiro TG; Machado MP; Carriço JA; Pimentel L; et al. "Lactobacillus femina sp. nov., a new species of Lactobacillus delbrueckii group". Paper presented in 8th Congress of European Microbiologists (FEMS 2019), 2019. Botelho, João; Rocha J; Lood, Cédric; Carriço JA; Ribeiro TG; van Noort, Vera; Lavigne, Rob; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Pseudomonas catumbelensis sp. nov. is a novel species within the Pseudomonas putida phylogenetic group isolated from a septic tank in Angola and carrying several antimicrobial resistance genes". Paper presented in 8th Congress of European Microbiologists (FEMS 2019), 2019. Botelho, João; Rocha J; Lood, Cédric; Partridge, Sally R.; Carriço JA; Ribeiro TG; van Noort, Vera; et al. "Characterization of a large blaVIM-2-carrying plasmid in Pseudomonas portuensis sp. nov., a novel species within the Pseudomonas putida phylogenetic group". Paper presented in 8th Congress of European Microbiologists (FEMS 2019), 2019. Botelho, João; Roberts, AP; Mourão, Joana; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Integrative and conjugative elements, the neglected drivers of carbapenemase-encoding genes". Paper presented in ASM Microbe, 2019. Botelho, João; Lood, Cédric; Partridge, Sally R.; van Noort, Vera; Lavigne, Rob; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Megaplasmids on the rise: combining sequencing approaches to fully resolve a carbapenemase-encoding plasmid in a novel Pseudomonas species". Paper presented in 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2019. Grosso, F; Botelho, João; Lira, A; Lameirão, A; Selaru, A; Abreu, G; Lopes, P; Mota, M; Peixe, L. Corresponding author: Grosso, F. "GES-6 Pseudomonas aeruginosa producers more common than expected questioning ceftolozane/tazobactam efficacy". Paper presented in 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2019. Botelho, João; Roberts, AP; León-Sampedro, R; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "An in silico approach to explore the link between carbapenemase-producing Pseudomonas spp. and ICE". Paper presented in Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies, 2018. Botelho, João; Roberts, AP; León-Sampedro, R; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Carbapenemases on the move: it’s good to be on ICE". Paper presented in Copenhagen Bioscience Conference 15 - Averting the post-antibiotic era, 2018. Botelho, João; Roberts, AP; Grosso, F; Peixe, L. "A wide array of integrative conjugative elements associated with carbapenemase-encoding genes in Pseudomonas genomes is disclosed by in silico analysis". Paper presented in 28th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2018. Botelho, João; Grosso, F; Ribeiro TG; Peixe, L. Corresponding author: Botelho, João. "Whole-genome sequencing of a potentially new Pseudomonas species from a non-clinical niche in Angola uncovers a wide array of antimicrobial resistance genes and mobile genetic elements". Paper presented in MicroBiotec 17, 2017. Botelho, João; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Unraveling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 exposes a putative integrative conjugative element housing a blaGES-6 carbapenemase". Paper presented in 16th International Conference on Pseudomonas, 2017. Botelho, João; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Two decades of relentless blaVIM-2 producing Pseudomonas aeruginosa dissemination: the decisive role of mobile genetic elements and successful clones". Paper presented in 16th International Conference on Pseudomonas, 2017. Botelho, João; Grosso, F; Peixe, L. Corresponding author: Botelho, João. "Whole-genome sequencing unveils a potentially new Pseudomonas species associated with Tn6372, a novel blaVIM-2-transposable element". Paper presented in 7th Congress of European Microbiologists (FEMS 2017), 2017. Botelho, João; Grosso, F; Mabrouk, Aymen; Peixe, L. Corresponding author: Botelho, João. "Complete nucleotide sequence of pJB58, a blaVIM-2-harboring plasmid from Pseudomonas aeruginosa". Paper presented in 7th Congress of European Microbiologists (FEMS 2017), 2017. Botelho, João; Grosso, F; Mabrouk, Aymen; Peixe, L. Corresponding author: Botelho, João. "Complete nucleotide sequence of an IncP-2 blaVIM-2-harboring megaplasmid from Pseudomonas aeruginosa". Paper presented in 27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2017. Mabrouk, Aymen; Grosso, F; Botelho, João; Silva, Liliana; Achour, Wafa; Ben Hassen, Assia; Peixe, L. Corresponding author: Mabrouk, Aymen. "Regional clones and carbapenemases associated with carbapenem-resistant Acinetobacter baumannii in nosocomial settings in Tunis, Tunisia". Paper presented in 27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2017. Botelho, João; Grosso, F; Rocha, C; Brilhante, M; Sousa, Clara; Peixe, L. Corresponding author: Botelho, João. "High-risk clones among carbapenemase-producing Pseudomonas aeruginosa in a Portuguese hospital". Paper presented in 25th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2015. Pires, J; Novais, Ângela; Silva, Liliana; Campos, Joana; Botelho, João; Czobor, I; Gheorghe, I; Peixe, L. "Further validation of Blue-Carba, a recently described quick and reliable method for carbapenemase detection". Paper presented in 24th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2014. Sousa, Clara; Botelho, João; Silva, Liliana; Grosso, F; Lopes, João; Peixe, L. "MALDI-TOF MS and FTIR-ATR: Different Biomolecules and Distinct Outputs in Acinetobacter baumannii Typing". Paper presented in 24th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), 2014. Botelho, João; Sousa, Clara; Silva, Liliana; Grosso, F; Nemec, A.; Lopes, João; Peixe, L. Corresponding author: Botelho, João. "Acinetobacter calcoaceticus-Acinetobacter baumannii complex species depicted by MALDI-TOF MS and multivariate data analysis". Paper presented in MicroBiotec 13, 2013. Sousa, Clara; Botelho, João; Silva, Liliana; Grosso, F; Nemec, A.; Lopes, João; Peixe, L. "Improvement on the discrimination of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species by a combined MALDI-TOF MS and chemometric approach". Paper presented in 10th International Meeting on Microbial Epidemiological Markers (IMMEM-10), 2013. Botelho, João; Silva, AR. "Peroxidative Oxidation of Cyclohexane Catalyzed by Iron(III) Acetylacetonate Anchored onto Amine-Functionalized Solid Supports". Paper presented in IX CICECO Meeting, 2012. Gonçalves, RF; Llopis, A; Félix, CC; Botelho, João; Gaspar, L.; Almada, M; Gonçalves, ML; Guimarães, TM. "Insight into chemistry and biological potential of Osmundea pinnatifida (Rhodophyta)". Paper presented in IJUP'11, 2011. Pereira, DM; Gonçalves, C; Couto, D; Meireles, H; Moreira, P; Mouga, T.; Botelho, João. "Marthasterias glacialis: from chemistry to bioactivity". Paper presented in IJUP'10, 2010.
Journal article	Liu, Yang; Botelho, Joao; Iranzo, Jaime. "Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer". Genome Research (2025): https://doi.org/10.1101/gr.279300.124. 10.1101/gr.279300.124 Tueffers, Leif; Batra, Aditi; Zimmermann, Johannes; Botelho, João; Buchholz, Florian; Liao, Junqi; Mendoza Mejía, Nicolás; et al. "Variation in the response to antibiotics and life-history across the major Pseudomonas aeruginosa clone type (mPact) panel". Microbiology Spectrum 12 7 (2024): https://doi.org/10.1128/spectrum.00143-24. 10.1128/spectrum.00143-24 López-Beltrán, Adrián; Botelho, João; Iranzo, Jaime. "Dynamics of CRISPR-mediated virus–host interactions in the human gut microbiome". The ISME Journal 18 1 (2024): https://doi.org/10.1093/ismejo/wrae134. 10.1093/ismejo/wrae134 Wheatley, Rachel M.; Botelho, João. "Chasing resistance: analyzing the fight against hospital infections". The Lancet Regional Health - Europe 34 (2023): 100740. https://doi.org/10.1016/j.lanepe.2023.100740. 10.1016/j.lanepe.2023.100740 Rocha, Jaqueline; Silva, Vanessa; Poeta, Patrícia; Botelho, João; Manaia, Célia M.. "Searching for links between environmental and clinical mecA Staphylococcus aureus: A comparative genomics study". Science of The Total Environment 895 (2023): 165078. https://doi.org/10.1016/j.scitotenv.2023.165078. Open access • 10.1016/j.scitotenv.2023.165078 Botelho, João. "Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance". Nucleic Acids Research 51 9 (2023): 4385-4397. https://doi.org/10.1093/nar/gkad282. Open access • 10.1093/nar/gkad282 Botelho, João; Tüffers, Leif; Fuss, Janina; Buchholz, Florian; Utpatel, Christian; Klockgether, Jens; Niemann, Stefan; Tümmler, Burkhard; Schulenburg, Hinrich. "Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa". eBioMedicine 90 (2023): 104532. https://doi.org/10.1016/j.ebiom.2023.104532. Open access • 10.1016/j.ebiom.2023.104532 Botelho, João; Cazares, Adrian; Schulenburg, Hinrich. "The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements". Nucleic Acids Research 51 1 (2023): 236-252. https://doi.org/10.1093/nar/gkac1220. Open access • 10.1093/nar/gkac1220 Hall, James P. J.; Botelho, João; Cazares, Adrian; Baltrus, David A.. "What makes a megaplasmid?". Philosophical Transactions of the Royal Society B: Biological Sciences 377 1842 (2021): https://doi.org/10.1098/rstb.2020.0472. Open access • 10.1098/rstb.2020.0472 Botelho, João; Hinrich Schulenburg. Corresponding author: Botelho, João. "The Role of Integrative and Conjugative Elements in Antibiotic Resistance Evolution". Trends in Microbiology 29 1 (2021): 8-18. http://dx.doi.org/10.1016/j.tim.2020.05.011. 10.1016/j.tim.2020.05.011 Botelho, João; Mourão, Joana; Roberts, Adam P.; Peixe, Luísa. "Comprehensive genome data analysis establishes a triple whammy of carbapenemases, ICEs and multiple clinically relevant bacteria". Microbial Genomics 6 10 (2020): https://doi.org/10.1099/mgen.0.000424. Open access • 10.1099/mgen.0.000424 Botelho, João; Grosso, Filipa; Peixe, Luísa. Corresponding author: Botelho, João. "ICEs Are the Main Reservoirs of the Ciprofloxacin-Modifying crpP Gene in Pseudomonas aeruginosa". Genes 11 8 (2020): http://dx.doi.org/10.3390/genes11080889. Open access • 10.3390/genes11080889 Nikolaou, Elissavet; Hubbard, Alasdair T. M.; Botelho, João; Marschall, Taylor A. M.; Ferreira, Daniela M.; Roberts, Adam P.. "Antibiotic Resistance Is Associated with Integrative and Conjugative Elements and Genomic Islands in Naturally Circulating Streptococcus pneumoniae Isolates from Adults in Liverpool, UK". Genes 11 6 (2020): 625. http://dx.doi.org/10.3390/genes11060625. Open access • 10.3390/genes11060625 Hubbard, Alasdair T. M.; Newire, Enas; Botelho, João; Reiné, Jesús; Wright, Elli; Murphy, Emma A; Hutton, William; Roberts, Adam P.. "Isolation of an antimicrobial-resistant, biofilm-forming, Klebsiella grimontii isolate from a reusable water bottle". MicrobiologyOpen 9 6 (2020): 1128-1134. http://dx.doi.org/10.1002/mbo3.1023. Open access • 10.1002/mbo3.1023 Joana Rocha; Botelho, João; Magdalena Ksiezarek; Svetlana Ugarcina Perovic; Miguel Machado; João André Carriço; Lígia L. Pimentel; et al. "Lactobacillus mulieris sp. nov., a new species of Lactobacillus delbrueckii group". International Journal of Systematic and Evolutionary Microbiology 70 3 (2020): 1522-1527. https://doi.org/10.1099/ijsem.0.003901. Open access • 10.1099/ijsem.0.003901 Monárrez, Rubén; Braun, Molly; Coburn-Flynn, Olivia; Botelho, João; Odetoyin, Babatunde W.; Otero-Vera, Jose I.; Quartey, Naa Kwarley Eyiram; et al. "A large self-transmissible resistance plasmid from Nigeria contains genes that ameliorate a carrying cost". Scientific Reports 9 1 (2019): http://dx.doi.org/10.1038/s41598-019-56064-z. Open access • 10.1038/s41598-019-56064-z Botelho, João; Grosso, Filipa; Peixe, Luísa. Corresponding author: Botelho, João. "Antibiotic resistance in Pseudomonas aeruginosa – Mechanisms, epidemiology and evolution". Drug Resistance Updates 44 (2019): http://dx.doi.org/10.1016/j.drup.2019.07.002. 10.1016/j.drup.2019.07.002 Botelho, João; Lood, Cédric; Partridge, Sally R.; van Noort, Vera; Lavigne, Rob; Grosso, Filipa; Peixe, Luísa. Corresponding author: Botelho, João. "Combining sequencing approaches to fully resolve a carbapenemase-encoding megaplasmid in a Pseudomonas shirazica clinical strain". Emerging Microbes & Infections 8 1 (2019): 1186-1194. http://dx.doi.org/10.1080/22221751.2019.1648182. Open access • 10.1080/22221751.2019.1648182 Botelho, João; Adam P. Roberts; Ricardo León-Sampedro; Filipa Grosso; Luísa Peixe. Corresponding author: Botelho, João. "Carbapenemases on the move: it’s good to be on ICEs". Mobile DNA 9 1 (2018): https://doi.org/10.1186/s13100-018-0141-4. Open access • 10.1186/s13100-018-0141-4 Beaton, Ainsley; Lood, Cédric; Cunningham-Oakes, Edward; MacFadyen, Alison; Mullins, Alex J; Bestawy, Walid El; Botelho, João; et al. "Community-led comparative genomic and phenotypic analysis of the aquaculture pathogen Pseudomonas baetica a390T sequenced by Ion semiconductor and Nanopore technologies". FEMS Microbiology Letters 365 9 (2018): http://dx.doi.org/10.1093/femsle/fny069. Open access • 10.1093/femsle/fny069 Botelho, João; Grosso, Filipa; Quinteira, Sandra; Brilhante, Michael; Ramos, Helena; Peixe, Luísa. "Two decades of blaVIM-2-producing Pseudomonas aeruginosa dissemination: an interplay between mobile genetic elements and successful clones". Journal of Antimicrobial Chemotherapy 73 4 (2018): 873-882. http://dx.doi.org/10.1093/jac/dkx517. Open access • 10.1093/jac/dkx517 Botelho, João; Grosso, Filipa; Peixe, Luísa. "Unravelling the genome of a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235 reveals an integrative conjugative element housing a blaGES-6 carbapenemase". Journal of Antimicrobial Chemotherapy 73 1 (2017): 77-83. http://dx.doi.org/10.1093/jac/dkx337. Open access • 10.1093/jac/dkx337 Mabrouk, Aymen; Grosso, Filipa; Botelho, João; Achour, Wafa; Ben Hassen, Assia; Peixe, Luisa. "GES-14-Producing Acinetobacter baumannii Isolates in a Neonatal Intensive Care Unit in Tunisia Are Associated with a Typical Middle East Clone and a Transferable Plasmid". Antimicrobial Agents and Chemotherapy 61 6 (2017): http://dx.doi.org/10.1128/aac.00142-17. Open access • 10.1128/aac.00142-17 Botelho, João; Grosso, Filipa; Quinteira, Sandra; Mabrouk, Aymen; Peixe, Luísa. "The complete nucleotide sequence of an IncP-2 megaplasmid unveils a mosaic architecture comprising a putative novel blaVIM-2-harbouring transposon in Pseudomonas aeruginosa". Journal of Antimicrobial Chemotherapy 72 8 (2017): 2225-2229. http://dx.doi.org/10.1093/jac/dkx143. Open access • 10.1093/jac/dkx143 Botelho, João; Grosso, Filipa; Peixe, Luísa. "Characterization of the pJB12 Plasmid from Pseudomonas aeruginosa Reveals Tn 6352 , a Novel Putative Transposon Associated with Mobilization of the bla _VIM-2 -Harboring In58 Integron". Antimicrobial Agents and Chemotherapy 61 5 (2017): http://dx.doi.org/10.1128/aac.02532-16. Open access • 10.1128/aac.02532-16 Sousa, Clara; Botelho, João; Grosso, Filipa; Silva, Liliana; Lopes, João; Peixe, Luísa. "Unsuitability of MALDI-TOF MS to discriminate Acinetobacter baumannii clones under routine experimental conditions". Frontiers in Microbiology 6 (2015): http://dx.doi.org/10.3389/fmicb.2015.00481. Open access • 10.3389/fmicb.2015.00481 Botelho, João; Grosso, F.; Sousa, C.; Peixe, L.. "Characterization of a new genetic environment associated with GES-6 carbapenemase from a Pseudomonas aeruginosa isolate belonging to the high-risk clone ST235". Journal of Antimicrobial Chemotherapy 70 2 (2014): 615-617. http://dx.doi.org/10.1093/jac/dku391. Open access • 10.1093/jac/dku391 Sousa, C.; Botelho, João; Silva, L.; Grosso, F.; Nemec, A.; Lopes, J.; Peixe, L.. "MALDI-TOF MS and chemometric based identification of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex species". International Journal of Medical Microbiology 304 5-6 (2014): 669-677. http://www.scopus.com/inward/record.url?eid=2-s2.0-84903819314&partnerID=MN8TOARS. 10.1016/j.ijmm.2014.04.014 Silva, A.R.; Botelho, João. "Peroxidative oxidation of cyclic and linear hexane catalysed by supported iron complexes under mild and sustainable conditions". Journal of Molecular Catalysis A: Chemical 381 (2014): 171-178. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887283070&partnerID=MN8TOARS. 10.1016/j.molcata.2013.10.020 Gaspar, L.; Oliveira, A.P.; Silva, L.R.; Andrade, P.B.; de Pinho, P.G.; Botelho, João; Valentão, P.. "Metabolic and biological prospecting of Coreopsis tinctoria". Brazilian Journal of Pharmacognosy 22 2 (2012): 350-358. http://www.scopus.com/inward/record.url?eid=2-s2.0-84856898672&partnerID=MN8TOARS. Open access • 10.1590/S0102-695X2011005000224 Ferreres, F.; Pereira, D.M.; Gil-Izquierdo, A.; Valentão, P.; Botelho, João; Mouga, T.; Andrade, P.B.. "HPLC-PAD-atmospheric pressure chemical ionization-MS metabolite profiling of cytotoxic carotenoids from the echinoderm Marthasterias glacialis (spiny sea-star)". Journal of Separation Science 33 15 (2010): 2250-2257. http://www.scopus.com/inward/record.url?eid=2-s2.0-77955345220&partnerID=MN8TOARS. 10.1002/jssc.201000197
Journal issue	Botelho, João. "Special Issue "Mobile Elements and Antibiotic Resistance"". Antibiotics (2021): https://www.mdpi.com/journal/antibiotics/special_issues/mobile_elements. Published • Invited editor
Online resource	Botelho, João. Corresponding author: Botelho, João. Code repository for reproducing the main figures in the paper: "The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements". 2022. https://gitlab.gwdg.de/botelho/eskape_paper. Botelho, João. Corresponding author: Botelho, João. Code repository for reproducing the analyses in the paper: "Defense systems are pervasive across chromosomally integrated mobile genetic elements and are inversely correlated to virulence and antimicrobial resistance". 2022. https://gitlab.gwdg.de/botelho/ices_imes. Botelho, João. Pseudomonas aeruginosa Hannover strains collection. 2022. https://www.ncbi.nlm.nih.gov/bioproject/810040. Botelho, João. Corresponding author: Botelho, João. Code repository for reproducing the analyses in the paper: "Phylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity". 2022. https://gitlab.gwdg.de/botelho/pa_pangenome. Botelho, João. Pseudomonas sp. FFUP_PS_473 Genome sequencing and assembly. 2017. https://www.ncbi.nlm.nih.gov/bioproject/422363. Botelho, João. blaVIM-2-producing Pseudomonas aeruginosa isolates from Portuguese hospitals. 2017. https://www.ncbi.nlm.nih.gov/bioproject/388154.
Preprint	Liu, Yang; Botelho, João; Iranzo, Jaime. "Timescales and genetic linkage explain the variable impact of defense systems on horizontal gene transfer". 2024. http://dx.doi.org/10.1101/2024.02.29.582795. 10.1101/2024.02.29.582795
Thesis / Dissertation	"Carbapenemase producers of Pseudomonas aeruginosa: lights on new mobile genetic elements". 2018. https://ciencia.ucp.pt/en/publications/d78afc96-9528-46af-93b9-9d9326264aea.

Activities

Oral presentation

	Presentation title	Event name Host (Event location)
2024/10/24	Regions of genome plasticity: a comparative analysis of mobility and retention patterns in bacterial and archaeal pangenomes	IUMS 2024 IUMS (Florence, Italy)
2024/10/24	Regions of genome plasticity: a comparative analysis of mobility and retention patterns in bacterial and archaeal pangenomes	IUMS24 (Florence, Italy)
2024/10/23	Timescales and Genetic Linkage Explain the Variable Impact of Defense Systems on Horizontal Gene Transfer - ePoster flash presentation	IUMS 2024 IUMS (Florence, Italy)
2024/10/23	Timescales and Genetic Linkage Explain the Variable Impact of Defense Systems on Horizontal Gene Transfer	IUMS24 (Florence, Italy)
2023/10/25	Regions of Genome Plasticity: A Comparative Analysis of Mobility and Retention Patterns in Bacterial and Archaeal Pangenomes	The Local Pangenome 2023 (Alicante, Spain)
2023/06/27	The Importance Of Recycling The Sheath Of The Type VI Secretion System (T6SS), A Bacterial Killing Machine And Biocontrol Weapon	XXIX SEM congress (Spanish society for Microbiology) (Burgos, Spain)
2023/01	Assembly and disassembly of a bacterial killing machine and biocontrol weapon. The importance of recycling the sheath of the Type VI secretion system	X Meeting of the Plant Microbiology Group (MiP23) Spanish Society for Microbiology (SEM) (Nerja, Spain)
2022/10/20	The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements	SMBEeverywhere GS5 - Evolutionary Genomics of Host-Pathogen Interactions and Antimicrobial Drug Resistance The Society for Molecular Biology and Evolution
2022/10/20	The ESKAPE mobilome contributes to the spread of antimicrobial resistance and CRISPR-mediated conflict between mobile genetic elements	SMBEeverywhere
2022/02/03	The ESKAPE mobilome	Antimicrobial Chemotherapy Virtual Conference The British Society for Antimicrobial Chemotherapy/The Global Antibiotic Research & Development Partnership
2021/05/07	The ESKAPE pathogens mobilome	Microbial Genomics Workshop University of Pittsburgh (Pittsburgh, United States)
2021/05/07	The ESKAPE pathogens mobilome	University of Pittsburgh
2021/03/05	Integrative and conjugative elements (ICEs): what do we know about them?	Seminar at Hildegard Uecker’s lab Max Planck Institute for Evolutionary Biology (Ploen, Germany)
2021/03/05	Integrative and conjugative elements (ICEs): what do we know about them?	Max Planck Institute for Evolutionary Biology
2020/12/02	Crossroads of mobile genetic elements and antibiotic resistance	BLS Seminar Series Lancaster University (Lancaster, United Kingdom)
2020/12/02	Crossroads of mobile genetic elements and antibiotic resistance	Lancaster University
2020/04	Big data analysis of all bacterial genomes establishes a triple whammy of carbapenemases, ICEs and multiple clinically-relevant bacteria	30th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) European Society of Clinical Microbiology and Infectious Diseases (ESCMID) (Paris, France)
2019/08/07	Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution of mobile genetic elements	Seminar at Tal Dagan’s lab CAU Kiel (Kiel, Germany)
2019/08/07	Antibiotic resistance in Pseudomonas aeruginosa – mechanisms, epidemiology and evolution of mobile genetic elements	Kiel University
2018/11	An in silico approach to explore the link between carbapenemase-producing Pseudomonas spp. and ICE	Antimicrobial Resistance – Genomes, Big Data and Emerging Technologies Wellcome (Hinxton, United Kingdom)
2017/09	Two decades of relentless blaVIM-2 producing Pseudomonas aeruginosa dissemination: the decisive role of mobile genetic elements and successful clones	16th International Conference on Pseudomonas Federation of European Microbiological Societies (FEMS) (Liverpool, United Kingdom)
2017/04/23	Sequencing the plasmid pJB12 from Pseudomonas aeruginosa reveals Tn6352, a novel transposon associated with mobilization of blaVIM-2 harbouring In58 integron	27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) European Society of Clinical Microbiology and Infectious Diseases (ESCMID) (Wien, Austria)
2015/12	Unveiling clones and integrons dynamics associated with carbapenemase-producing P. aeruginosa clinical isolates in a Portuguese hospital	Microbiotec’15 Portuguese Society of Microbiology/Portuguese Society of Biotechnology (Evora, Portugal)
2014/02	Molecular characterization of carbapenem-resistant Pseudomonas aeruginosa clinical isolates from a Portuguese Hospital	IJUP'14 University of Porto (Porto, Portugal)
2011/02	Metabolic profiling and bioactivity of Lithospermum diffusum	IJUP'11 University of Porto (Porto, Portugal)

Supervision

	Thesis Title Role	Degree Subject (Type) Institution / Organization
2022/09/01 - Current	Virus-host interaction dynamics in the gut microbiome through the analysis of CRISPR arrays Co-supervisor	Centro de Biotecnología y Genómica de Plantas, Spain
2022/09/01 - 2024/04/15	Quantifying the effect of CRISPR-Cas immunity on gene gain and loss Co-supervisor	Centro de Biotecnología y Genómica de Plantas, Spain
2020/10 - 2021/08	Collateral sensitivity and horizontal gene transfer; an intersection Co-supervisor	Christian-Albrechts-Universität zu Kiel, Germany

Event organisation

	Event name Type of event (Role)	Institution / Organization
2025/04/02 - 2025/04/03	Co-chair a session on "Microbial Warfare: conflicts between species, strains, and mobile genetic elements" at the Microbiology Society Annual Conference in Liverpool (2-3 April 2025) - https://microbiologysociety.org/event/annual-conference/annual-conference-2025.html#tab-2 (2025/03/31) Conference (Other)	Microbiology Society, United Kingdom
2021/05/25 - 2021/05/25	Webinar ‘Mobile Elements and Antibiotic Resistance’ (2021/05/25 - 2021/05/25) Seminar (Other)
2019/05/08 - 2019/05/10	Evolutionary Biology Meets the Antibiotic Crisis (2019/05/08 - 2019/05/10) Workshop (Other)	Max-Planck-Institut für Evolutionsbiologie, Germany

Event participation

	Activity description Type of event	Event name Institution / Organization
2023/06/01 - 2023/06/02	4th Griffith's Legacy Meeting - Today’s models, approaches and concepts Meeting
2021/10/11 - 2021/10/13	AMR Hackathon Workshop	AMR Hackathon Joint Programming Initiative on Antimicrobial Resistance, Sweden
2021/09/28 - 2021/09/30	Genomic population structures of microbial pathogens Conference	Genomic population structures of microbial pathogens The Royal Society, United Kingdom
2021/09/20 - 2021/09/21	Career Steps for Postdocs in Academia & Industry Workshop	Career Steps for Postdocs in Academia & Industry Max-Planck-Institut für Evolutionsbiologie, Germany
2021/05/06 - 2021/06/08	Plasmids Around the Globe 2021 Conference	Plasmid Biology Society
2021/04/26 - 2021/04/30	Annual Conference Online 2021 Conference	Microbiology Society, United Kingdom
2020/06/09 - 2020/08/04	Pseudomonas Seminars, organized by Urvish Trivedi and Cassie Nelson Conference

Jury of academic degree

	Topic Role	Candidate name (Type of degree) Institution / Organization
2022/02/05	Evolutionary Relationships and Interactions of Conjugative Antibiotic Resistance Plasmids (Thesis) Arguer	Miss Aurelie Tsee Woon Yuen (PhD) La Trobe University, Australia
2022/02/05	Evolutionary Relationships and Interactions of Conjugative Antibiotic Resistance Plasmids (Thesis) Main arguer	Aurelie Tsee Woon Yuen (PhD) La Trobe University, Australia

Ad Hoc journal article review

	Journal title (ISSN)	Publisher
2024/07 - Current	Journal of Applied Microbiology
2024/06 - Current	Drug Resistance Updates
2024/05 - Current	Cell Press Community
2023/10 - Current	JAC-Antimicrobal Resistance
2023/09/21 - Current	Nature Communications
2023/08 - Current	iMeta
2023/07 - Current	Microbiology
2023/07 - Current	The Lancet Regional Health - Europe
2023/06/21 - Current	Microbial Biotechnology
2023/04/24 - Current	NAR Genomics and Bioinformatics
2023/02/27 - Current	Chemosphere
2021/10/29 - Current	Computational and Structural Biotechnology Journal
2021/04/26 - Current	Virulence
2021/04/10 - Current	Future Microbiology
2021/04/10 - Current	International Journal of Molecular Sciences
2021/01/05 - Current	Emerging Microbes & Infections
2020/11/18 - Current	Microorganisms
2020/10/16 - Current	BMC Microbiology
2020/10/12 - Current	Communications Biology
2020/09/18 - Current	Expert Review of Anti-Infective Therapy
2020/05/21 - Current	Antibiotics
2020/05/07 - Current	mSystems
2019/12/10 - Current	Microbial Genomics
2019/11/28 - Current	Infection and Drug Resistance
2019/09/27 - Current	Eurosurveillance
2019/08/24 - Current	Plos One
2017/09/11 - Current	Antimicrobial Agents and Chemotherapy
2016/01/04 - Current	Journal of Antimicrobial Chemotherapy

Committee member

	Activity description Role	Institution / Organization
2015 - 2017	Member of the Pedagogic Council Member	Universidade do Porto Faculdade de Farmácia, Portugal

Course / Discipline taught

	Academic session	Degree Subject (Type)	Institution / Organization
2024/11/11 - 2024/11/11	Seminar for the Master’s in Applied Microbiology	(Mestrado)	Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal
2022/11/02 - 2022/11/02	Seminar for the Master’s in Applied Microbiology	(Mestrado)	Universidade Católica Portuguesa Portuguesa Centro de Biotecnologia e Química Fina, Portugal
2015 - 2017	Curricular unit of Clinical Bacteriology	Master in Clinical Analysis	Universidade do Porto Faculdade de Farmácia, Portugal
2015 - 2016	Curricular unit of Microbiological Quality	Master in Quality Control	Universidade do Porto Faculdade de Farmácia, Portugal
2015 - 2016	Curricular unit of Bacteriology	Integrated Master's in Pharmaceutical Sciences	Universidade do Porto Faculdade de Farmácia, Portugal

Evaluation committee

	Activity description Role	Institution / Organization	Funding entity
2024/09/03 - 2024/09/20	Review grant proposal for the National Science Center, Poland Evaluator	Uniwersytet Medyczny w Bialymstoku, Poland
2023/02/02 - 2023/02/15	FWO Call for Junior and Senior post-doctoral Fellowships Evaluator	Universiteit Antwerpen, Belgium	Fonds Wetenschappelijk Onderzoek Vlaanderen
2020/06/30 - 2020/07/21	Medical Research Council (MRC)-funded fellowships Evaluator	Imperial College London, United Kingdom	UK Research and Innovation
2020/01/29 - 2020/03/15	Research Südtirol/Alto Adige 2019 Evaluator	Università degli Studi di Trento, Italy	Provincia autonoma di Bolzano - Alto Adige

Interview (tv / radio show)

	Program	Topic
2020/11/13 - Current	Programme held in Portuguese and named "Conversas de Consultório"	Science communication, focused on the use of antibiotics and how it impacts the society and the environment

Mentoring / Tutoring

	Topic	Student name
2014/09 - 2016/12	Genotypic and phenotypic characterization of Acinetocter baumannii isolates resistant to carbapenems	Aymen Mabrouk
2014/07 - 2014/08	Molecular characterization of clinical isolates of Pseudomonas aeruginosa resistant to carbapenems	Michael Quinta Brilhante
2014/05 - 2014/06	Molecular characterization of clinical isolates of Pseudomonas aeruginosa resistant to carbapenems	Catarina Rocha

Distinctions

Award

2020	Kiel Life Science Award for Early Career Postdocs Christian-Albrechts-Universität zu Kiel, Germany
2019	ASM Infectious Disease Fellows Program Award American Society for Microbiology, United States
2015	Best Oral Presentation at the Microbiotec 15 American Society for Microbiology, United States

Other distinction

2019	ECCMID Travel grant to attend the 29th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), held in Amsterdam, The Netherlands, 13-16 April 2019 European Society of Clinical Microbiology and Infectious Diseases, Switzerland
2019	FEMS Congress Grant for Early Career Scientists to attend Microbiotec¿19, held in Coimbra, Portugal, 5-7 December 2019 Federation Of European Microbiological Societies, United Kingdom
2018	Novo Nordisk Fonden Grant to attend the Copenhagen Bioscience Conference 15 - Averting the post-antibiotic era, held in Hillerød, Denmark, 31 October to 3 November 2018 Novo Nordisk Fonden, Denmark
2018	Wellcome Genome Campus bursary to attend the Antimicrobial Resistance - Bacterial Genomics, Big Data & Emerging Technologies conference, held in Hinxton, UK, 27-29 November 2018 Wellcome Sanger Institute, United Kingdom
2018	Wellcome Genome Campus bursary to attend the Antimicrobial Resistance - Bacterial Genomics, Big Data & Emerging Technologies conference, held in Hinxton, UK, 27-29 November 2018 Wellcome Sanger Institute, United Kingdom
2017	BSAC Travel grant for the 27th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), held in Wien, Austria, 21-25 April 2017 British Society for Antimicrobial Chemotherapy, United Kingdom
2017	FEMS Congress Grant for Early Career Scientists to attend the 7th FEMS Congress of European Microbiologists, held in Valencia, Spain, 9-13 July 2017 Federation Of European Microbiological Societies, United Kingdom
2017	Microbiology Society Conference Grant to attend the 16th International Conference on Pseudomonas, held in Liverpool, UK, 5-9 September 2017 Microbiology Society, United Kingdom
2015	ESCMID Travel grant for the ESCMID Postgraduate Education Course: 2nd Course on Principles of Molecular Microbiological Diagnostics, held in Maastricht, Netherlands, 20-22 January 2016 European Society of Clinical Microbiology and Infectious Diseases, Switzerland