Prof. Dr. Natacha Couto | Academic Portfolio

Narrative CV

I completed my PhD at the Faculty of Veterinary Medicine, University of Lisbon, supported by an FCT scholarship. My research investigated the dynamics of methicillin‑resistant staphylococci (MRS) in animals, with a focus on Staphylococcus pseudintermedius, the main cause of canine skin infections. I documented an increase in multidrug‑ and pandrug‑resistant strains in a tertiary veterinary hospital and evaluated biocides as effective treatment options in cases where efflux‑mediated resistance limited antimicrobial therapy. Transcriptomic analyses revealed that the ST71 lineage upregulates numerous surface proteins and toxins, which likely contribute to its success as a high‑risk clone. Using serological proteome analysis, I identified four antigenic proteins with strong vaccine potential. My PhD was awarded cum laude and produced seven peer‑reviewed articles and one letter to the editor (part of 26 publications between 2009–2016).

After completing my PhD in 2016, I joined the Department of Medical Microbiology and Infection Control at the University Medical Center Groningen (UMCG‑RUG, NL) under Prof. Alex W. Friedrich and Dr. John W. Rossen, where I led the department's first metagenomics study on clinical samples. I developed and optimised laboratory workflows and bioinformatics pipelines for genomics and metagenomics, producing reproducible next-generation sequencing (NGS) protocols that have been adopted internationally and underpin 31 highly cited publications (including nine as last author and one invited expert review). This work generated numerous invited lectures and media coverage (Genetic Engineering & Biotechnology News, 2022), led to my role as a guest expert for the ENNGS (2020) and election as Secretary of ESGEM (2018–2022), and laid the foundation for sustained international collaborations and my first substantial research funding (JPIAMR and H2020).

In 2020 I joined Prof. Edward J. Feil's group at the Milner Centre for Evolution, University of Bath, contributing to the SpARK (JPIAMR) and OH‑DART (UKRI) projects that investigated the population structure of Klebsiella spp. and Escherichia coli across clinical and non‑clinical settings. Both studies showed that transmission occurs predominantly between humans, with animal and environmental reservoirs playing a limited role in human acquisition. A complementary study with Prof. Jan Maarten van Dijl’s group (UMCG‑RUG) showed that enteric and blood Staphylococcus aureus isolates of the same sequence type are proteomically similar, demonstrating that bacteremia depends more on host barrier integrity than on inherent microbial invasiveness. These results have been highlighted in subsequent publications and support ongoing work (two manuscripts forthcoming). More recently, I have focused on plasmids carrying virulence determinants leading significant work that is aiming to understand the movement of plasmids across different bacterial hosts and ecological niches. This has resulted in one Master of Science thesis (University of Bristol, 2025) and three lectures as invited speaker. From March 2020 until January 2022 I worked remotely from Lisbon due to the COVID‑19 pandemic and in December 2021 I received an Outstanding Contribution Award from the University of Bath and eventhough the contract ended in January 2022, I have continued collaborating with the group as an independent researcher.

Since 2022, I stepped into an independent role as a Consultant, which allowed me to work remotely from Lisbon (UK/USA universities/companies cannot employ staff who are not UK/USA residents). In 2022, I consulted for IDbyDNA (now part of Illumina), a company in the USA, supporting the development of metagenomics workflows to integrate next‑generation sequencing into clinical microbiology. I provided scientific writing and technical expertise to R&D teams and contributed to the design of a reflex‑to‑culture mNGS workflow, resulting in two conference abstracts and a manuscript in preparation. The same year I joined the Centre for Genomic Pathogen Surveillance (Pandemics Science Institute, University of Oxford), led by Prof. David Aanensen. I led the design and implementation of a national whole-genome sequencing survey across four NIHR-funded Global Health Research Units (Colombia, India, Nigeria, Philippines) to characterise the population structure of Klebsiella pneumoniae causing invasive hospital disease. I am also mentoring young researcher across the GHRU units in genomic epidemiology and bioinformatics. This work has resulted in one publication (2024) and is ongoing, with further manuscripts in preparation. Within this framework I coordinated the development of the computational pipelines and visualisation tools that underpin the analyses and reporting. I contributed to the development of two web applications — amr.watch and vaccines.watch — that integrate global genomic data for monitoring, analysis and visualisation of antimicrobial resistance and vaccine-target information to inform public health policy and both platforms are used internationally. During this time, I coordinated and delivered training in bioinformatics, genomic epidemiology, stakeholder engagement and reporting. In 2024, I secured funding as co‑applicant for an international project with Dr. Mike Beeton (Cardiff Metropolitan University), Prof. Mário Ramirez (FMUL) and Dr. Patrick Meyer-Sauteur (University Children's Hospital Zurich) to investigate whether specific Mycoplasma pneumoniae variants confer elevated risk for antimicrobial treatment.

Since 2024, I co‑lead, with Prof. Kathryn Holt (London School of Hygiene and Tropical Medicine [LSHTM]), a global effort to curate antimicrobial-resistance genotypes, an effort now recognized as WHO as a crucial collaboration for the development of a WHO catalogue of AMR Genes for priority pathogens. Alongside WHO, we are seeking funding to link genotypes with phenotypes for underepresented species or drug classes. Since November 2025, I'm now a Consultant for LSHTM, where I'm leading the efforts to integrate S. aureus genomics data into AMRnet and AMRrules. In 2025, I was awarded an Honorary Professorship in Microbial Genomics at Cardiff Metropolitan University. I am Chair of the ESGEM Executive Committee since 2023 and in recognition of professional excellence and service, I was named an ESCMID Fellow and was featured in an ESCMID article for the International Day of Women and Girls in Science (2024).

Work Experience since completing PhD

Position	Period	FTE	Type of Position	Institution
Professor	09/2025-now	NA	Honorary	Cardiff Metropolitan University, UK
Consultant	11/2025-now	NA	Fixed Term	London School of Hygiene and Tropical Medicine, UK
Visiting Researcher/Consultant	03/2022-10/2025	NA	Fixed Term	University of Oxford, UK
Consultant	02/2022-12/2022	NA	Fixed Term	IDbyDNA Inc. (now Illumina), USA
Associate Researcher	01/2020-01/2022	1.0	Fixed Term	University of Bath, UK
Post-doc Researcher	09/2016-12/2019	1.0	Fixed Term	University of Groningen, The Netherlands

Education

PhD

Institution conferring the title: Faculty of Veterinary Medicine, University of Lisbon (FMV-UL), Portugal

Date of PhD award: 13/01/2016

Supervisors: Prof. Constança Pomba (FMV-UL) and Dr. Ana Varela Coelho (ITQB-UNL, Portugal)

Thesis title: "Insights into the dynamics of methicillin-resistant staphylococci in animals - a focus on Staphylococcus pseudintermedius"

PhD obtained with cum laude (Louvor e Distinção).

MSc

Institution conferring the title: Faculty of Veterinary Medicine, University of Lisbon, Portugal

Date of MSc award: 06/06/2010

Supervisors: Prof. Constança Pomba (FMV-UL) and Prof. Luca Guardabassi (University of Copenhagen, Denmark)

Thesis title: "Nasal carriage of methicillin-resistant coagulase-positive staphylococci among cats and dogs hospitalized in the Veterinary Teaching Hospital of the Faculty of Veterinary Medicine – Technical University of Lisbon, Portugal"

MSc obtained with grade 19/20.

Upcoming Events & News

November 4-6, 2026 IUMS 2026 - Program Committee Member

Focusing on AI & Innovation in Microbiology, Lisbon, Portugal.

Event details & registration

November 2-4, 2026 ESCMID-ESGEM-ESGMAP Postgraduate Course Co-Coordinator

Tracking plasmids for clinical and public health use.

Event details & registration

Invited Lectures

Couto N. ESGEM-AMR: a global effort to curate rules for AMR genotyping. Keynote Speaker at the Norwegian Consortium for Microbial Genomics Annual Meeting, 2025, December 4, Oslo, Norway.
Couto N. A novel method for assessing global genetic diversity and molecular surveillance of Mycoplasma pneumoniae. Lecturer at ESCMID-ESGMD-ESGEM course on Enhancing Hospital Surveillance and Rapid Diagnostics of Critical Pathogens through Metagenomics Sequencing, 2025, November 25-27, Groningen, The Netherlands.
Couto N. Population-scale plasmid genomics in One Health. Invited Speaker at ESGEM-EFWISG Webinar 2024, July 11, online.
Couto N. Post-analysis standardization. Invited Speaker at Conference of the Bacterial genome sequencing pan-european network, 2024, February 27 – March 1, Engelberg, Switzerland.
Couto N. Plasmids: the next challenge for epidemiology. Invited Speaker at Semana Mundial de Concienciación sobre la RAM (WAAW), 2023, November 21-22, Bogotá, Colombia (hybrid event).
Couto N. Plasmid typing: are we there yet? Invited Speaker at NIHR GHRU-AMR General Meeting, 2023, September 14-16, Cartagena, Colombia.
Couto N. Metagenomics in the field of emerging infectious diseases: overview and applications. Invited Speaker at Webinar organized jointly by Institute Pasteur and INIA-CISA, 2022, December 14, online.
Couto N. Guidelines for outbreak tracing using Metagenomics. Inivted speaker at Current and Future Challenges in Veterinary Virus Genomics, 2022, June 21-22, The Pirbright Institute, Surrey, United Kingdom.
Couto N. Metagenomics for typing. Lecturer at ESCMID Postgraduate Education Course: Next-generation sequencing in routine clinical microbiology and infectious diseases, 2021, September 27-29, online.
Couto N. Building JPIAMR Careers. Invited Speaker at JPIAMR Junior Researchers Workshop, 2021, June 29-30, online.
Couto N. An update on clinical metagenomics tools. Invited Speaker at International Conference on Clinical Metagenomics, 2019, October 17-18, Geneva, Switzerland.
Couto N. Setting-up diagnostic NGS virology in a University Medical Center. Invited Speaker at ESCV Workshop on Next Generation Sequencing in Clinical Virology, 2019, May 24-25, Valencia, Spain.
Couto N. Clinical Metagenomics and bioinformatics pipelines. Invited Speaker at Genomic Medicine in Action symposium GMS, 2019, May 28, Stockholm, Sweden.
Couto N. Making sense of genome shreds: tools and strategies for straightforward genome data analysis. Invited Speaker at 29th European Congress of Clinical Microbiology and Infectious Diseases, 2019, April 13–16, Amsterdam, The Netherlands.
Couto N. Next generation sequencing for next generation clinical microbiology. Invited Speaker at QIAGEN Nordic Microbiology Forum, 2019, January 21-22, Copenhagen, Denmark.
Couto N. NGS and virology in a University Medical Center. Invited Speaker at ESCV Workshop Next Generations Sequencing in Clinical Virology, 2018, November 20-21, Leiden, The Netherlands.
Couto N. NGS: current and future platforms. Lecturer at ESCMID Capacity-Building Workshop: Metagenomics in the Diagnostic Laboratory, 2018, October 21-24, Groningen, The Netherlands.
Couto N. NGS approaches in Microbiology. Invited Speaker at Roche Sequencing Solutions Sample Preparation EMEA User Meeting, 2018, October 10-11, Riga, Latvia.
Couto N. Unravelling the complex structure of mobile genetic elements through short-and long-read sequencing. Invited Speaker at KNMV DMT meeting Application and challenges of long-read sequencing, 2018, February 1, Utrecht, The Netherlands.
Couto N. Shotgun metagenomics approach for identification and typing of pathogens in clinical samples. Lecturer at Medical Sciences Summer School Antimicrobial Resistance, 2017, August 20-24, Groningen, The Netherlands.
Couto N. Anaerobic bacteria in animals – relevant species, epidemiology and antimicrobial resistance. Lecturer at ESCMID Postgraduate Technical Workshop, 2016, September 26-28, Groningen, The Netherlands.
Couto N. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by serological proteomic analyses. Invited Speaker at SCAN Seminar ITQB, 2015, May 13, Oeiras, Portugal.
Couto N, Pomba C. Interpretação dos testes de suscetibilidade aos Antibióticos e Biocidas. Lecturer at I Curso de Pós-Graduação: Estratégias de Antibioterapia em Animais de Companhia, Faculty of Veterinary Medicine – University of Lisbon, 2015, March 7-8, Lisbon, Portugal.
Lourenço AM, Couto N. MRSA e MRSP em Dermatologia: como tratar? Lecturer at I Curso de Pós-Graduação: Estratégias de Antibioterapia em Animais de Companhia, Faculty of Veterinary Medicine – University of Lisbon, 2015, March 7-8, Lisbon, Portugal.
Couto N. Transferência da resistência aos antibióticos dos animais ao homem. Invited Speaker at IV Congresso Científico de Saúde, Antibióticos – Que futuro? 2013, November 21-22, Lisbon, Portugal.
Couto N. Frequência de colonização por staphylococci coagulase-positivos meticilina-resistentes em cães e gatos internados no Hospital Escolar da Faculdade de Medicina Veterinária. Invited Speaker at CIISA Seminar, Faculty of Veterinary Medicine – University of Lisbon, 2010, July 16, Lisbon, Portugal.

Oral Communications at International Conferences

Rudman TR, Couto N, Rowlands RS, Beeton ML. Optimising DNA extraction methods for urinogenital mycoplasmas for future use in direct sequencing. Early Career Mycoplasma and Chlamydia Researcher Conference 2024, March 6, online.
Couto N, Argimón S, Diaz-Caballero J, Yeats C, Abudahab K, Connor D, Aanensen D. Dynamics of carbapenemase-encoding genes in a global large-scale genomic dataset of WHO priority pathogens (AMRwatch). Proceedings of the 33rd European Congress of Clinical Microbiology and Infectious Diseases 2023, April 15-18, Copenhagen, Denmark.
Gibbon M, Couto N, Cozens K, Coates A, Thiry D, Breurec S, Brisse S, Feil EJ. The plasmid-borne virulence factor aerobactin (lineage iuc3) is strongly associated with isolates of Klebsiella pneumoniae from pigs and ducks. Proceedings of the 32nd European Congress of Clinical Microbiology and Infectious Diseases 2022, April 23-26, Lisbon, Portugal.
Couto N, Thorpe H, Gibbon M, Philips R, Brisse S, Rodrigues CP, David S, Merla C, Corbella M, Ferrari C, Sassera D, Corander J, Feil EJ. The CHASRI element, encoding resistance to heavy-metals, is associated with Klebsiella isolates from hospital patients and may be co-selected alongside antibiotic resistance. Proceedings of the 31st European Congress of Clinical Microbiology and Infectious Diseases 2021, July 9-12, online.
Peker N, Björnberg A, Nestor D, Sinha B, Couto N, Rossen J, Sundqvist M, Mölling P. Whole blood or plasma? Shotgun metagenomics-based diagnosis of bloodstream infections using long-read MinION sequencing. Proceedings of the 31st European Congress of Clinical Microbiology and Infectious Diseases 2021, July 9-12, online.
Lizarazo E, Couto N, Silva D, Vincenti-Gonzalez M, Camacho D, Comach G, Bethencourt S, Jaenisch T, Friedrich AW, Carriço J, Ramirez M, Rossen JWA, Tami A. Understanding dengue genetic dynamics in the context of consecutive outbreaks in Venezuela. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Fleres G, Couto N, Chlebowicz M, Rossen JW, Friedrich A, Garcia-Cobos S. Detection of a mobile colistin resistance (mcr-5) gene in hospital tap water using short- and long-read shotgun metagenomics sequencing. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Mendes CI, Lizarazo E, Machado MP, Silva DN, Tami A, Ramirez M, Couto N, Rossen JWA, Carriço JA. DEN-IM: Dengue Virus Identification from Metagenomic Sequencing Data. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Chlebowicz MA, Zhou XW, Couto N, Raangs EC, Arends JP, Bathoorn E, Friedrich AW, Rossen JW. Insights into vancomycin-resistant enterococci outbreaks through short- and long-read sequencing. Proceedings of the Oxford Nanopore Community Meeting London Calling, 2018, May 24-25, London, United Kingdom.
Couto N, Chlebowicz M, Cruz Campos AC, Raangs EC, Friedrich AW, Rossen JWA. Unravelling the complex structure of mobile genetic elements through short- and long-read sequencing. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Raangs EG, Vincenti-Gonzalez M, Bethencourt S, Jaenisch T, Friedrich AW, Tami A, Couto N, Rossen JWA. Optimization of a shotgun metagenomics protocol for identification and typing of dengue. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Vincenti-Gonzalez M, Bethencourt S, Jaenisch T, Grillet M, Friedrich AW, Tami A, Couto N, Rossen JWA. Higher resolution of dengue phylogenetic trees from Venezuela using the whole genome sequence. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Mölling P, Hedberg ST, Eriksson L, Johansson M, Paulander W, Couto N, Rossen JWA, Krause J, Herbig A, Sundqvist M. Shotgun metagenomics and typing of bacterial DNA in 5 mL whole blood from patients with suspected bloodstream infection. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Couto N, Raangs E, Vincenti-Gonzalez M, Tovar R, Bethencourt S, Grobusch MP, Jaenisch T, Friedrich A, Tami A, Rossen J. Shotgun metagenomics as a tool for the rapid diagnosis and genotyping of dengue. Proceedings of the 10th European Congress of Tropical Medicine and International Health 2017, October 16-20, Antwerp, Belgium.
Couto N, Raangs E, Friedrich A, Rossen J. Evaluation of shotgun metagenomics and sequence classification methods for the diagnosis of bacterial pathogens in patients' samples. Proceedings of the 27th European Congress of Clinical Microbiology and Infectious Diseases 2017, April 22-25, Vienna, Austria.
Lizarazo Forero E, Couto N, Raangs E, Vincenti-Gonzalez M, Friedrich A, Tami A, Rossen J. Shotgun metagenomics as a tool for the rapid diagnosis and genotyping of dengue. Proceedings of the 27th European Congress of Clinical Microbiology and Infectious Diseases 2017, April 22-25, Vienna, Austria.
Couto N, Monchique C, Marques C, Belas A, Telo da Gama L, Pomba C. Insights into the evolution of antimicrobial resistance in staphylococci isolated from companion animals: a 16-year study in Portugal. Proceedings of the 25th European Congress of Clinical Microbiology and Infectious Diseases 2015, April 25–28, Copenhagen, Denmark.
Marques C, Couto N, Belas A, Aboim C, Fernandes L, Telo da Gama L, Pomba C. Spread of highly successful human multidrug-resistant clones causing urinary tract infections in companion animals. Proceedings of the 25th European Congress of Clinical Microbiology and Infectious Diseases 2015, April 25–28, Copenhagen, Denmark.
Couto N, Martins J, Martins AM, Pomba C, Coelho AV. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by serological proteomic analyses. Proceedings of the 1st National Symposium on Biomarkers in Animal Science and Veterinary Sciences – An Interdisciplinary Approach, March 31, Évora, Portugal.
Pomba C, Belas A, Salazar ASS, Gama LT, Couto N. Risk factors for faecal colonization with Escherichia coli producing extended-spectrum and plasmid-mediated AmpC beta-lactamases in dogs without antimicrobial pressure. Proceedings of the 24th European Congress of Veterinary Internal Medicine 2014, September 4-6, Mainz, Germany.
Marques C, Couto N, Belas A, Saial D, Delgado M, Pomba C. Emergence of Multidrug-Resistant Bacteria Causing Urinary Tract Infections in Companion Animals: A 14¬Year Retrospective Study in Portugal. Proceedings of the 24th ECVIM-CA 2014, September 4-6, Mainz, Germany.
Couto N, Kadlec K, Schwarz S, Pomba C. High frequency of the vga(A) gene among MRSA ST398 from pigs and humans in Portugal. Proceedings of the 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans, and the Environment 2012, June 26-29, Aix-en-Provence, France.
Centeno M, Loução F, Baptista FM, Couto N, Saraiva-Lima M, Pomba C. Fluoroquinolones selective pressure induces the increase of multidrug-resistant Escherichia coli isolates from calves. Proceedings of the 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans, and the Environment 2012, June 26-29, Aix-en-Provence, France.

Global Research Network

Interactive visualization of research institutions and collaborators.

Collaborators by Institution

Lisbon, Portugal: Mário Ramirez, Rafael Mamede, FMUL
Porto, Portugal: Ana Freitas, Ângela Novais, FFUP
Oxford, UK: David Aanensen, Sophia David, Nabil-Fareed Alikhan, Georgina Lewis-Woodhouse, Emanuelle Kumaran, Philip M Ashton, University of Oxford
Groningen, Netherlands: John WA Rossen, Bhanu Sinha, Jan Maarten van Dijl, UMCG-RUG
Bath, UK: Ed Feil, Marjorie Gibbon, Zam Iqbal, University of Bath
Cardiff, UK: Mike Beeton, Charlotte Dixon, Cardiff Metropolitan University
Copenhagen, Denmark: Louise Roer, Lina Cavaco, SSI
Bengaluru, India: Varun Shamana, Geetha Nagaraj, Ravikumar K Lingegowda, KIMS
Bogotá, Colombia: Tatiana Camacho, Angela Sofia Garcia, Pilar Donado-Gody, Agrosavia
Manila, Philippines: June Gayeta, Faye Ablola, Sonia Sia, RITM
Ibadan, Nigeria: Abeeb Adeniyi, Joseph Adegoke, Iruka Okeke, University of Ibadan
Melbourne, Australia: Jane Hawkey, Monash University
London, UK: Kathryn Holt, London School of Hygiene and Tropical Medicine
Berlin, Germany: Guido Werner, Birgit Strommenger, RKI
Melbourne, Australia: Sarah Baines, Torsten Seeman, Benjamin P. Howden, University of Melbourne
Madrid, Spain: Teresa M. Coque, Rafael Cantón, Val Lanza, Hospital Ramón y Cajal
Orebro, Sweden: David Nestor, Paula Molling, Martin Sundqvist, Orebro Hospital
Freiburg, Germany: Sandra Reuter, University Medical Center Freiburg
Oslo, Norway: Harry Thorpe, Jukka Corander, University of Oslo

Grants

Year	Project	Funding Body	Amount	Status
2025	Education Course	ESCMID	€40,000	Ongoing
2024	ESGEM-AMR	NA	NA	Ongoing
2023	NIHR CADA ref.33690	NIHR	£29,981	Completed
2023	Education Course	ESCMID	€38,000	Completed
2023	Genomic Diversity of Mycoplasma pneumoniae	ESCMID	€180,000	Ongoing
2023	Get Started Fund	ESCMID	€38,000	Completed
2023	Education Course	ESCMID	€38,000	Completed
2022	Global Genomic Surveillance of AMR [16/136/111]	NIHR	£6.9M	Ongoing
2018	Tools for the Epidemiology of AMR Plasmids, One-Health Transmission and Surveillance [TEAPOTS]	JPIAMR	€50,000	Completed
2021	Education Course	ESCMID	€2500	Completed
2018	Surveillance Of mobiLome meDiated aNtibiotic rEsiStance Spread [SOLIDNESS]	JPIAMR	€50,000	Completed
2018	SECRETERS (MSCA-ITN)	Horizon 2020	€4.08M	Completed
2018	One Health Drivers of AMR in Thailand (MR/S004769/1)	UKRI	£2.9M	Completed
2017	FoodProTects	Interreg Europe	€666,263.66 (TIC2)	Completed
2016	Rates and routes of transmission of multidrug resistant Klebsiella clones and genes into the clinical from environmental sources [SpARK]	JPIAMR	€1,865,784	Completed
2015	EurHealth-1Health	JPIAMR	€4,992,999.44	Completed
2012	Immunogenicity of vaccine candidate antigens from Staphylococcus pseudintermedius [PTDC/CVT-EPI/4345/2012] in Canis canis	FCT	€195,600	Completed

Education Course (ESCMID)

Role: Co-Coordinator

Coordinating, alongside, Louise Roer (SSI), the development and delivery of the course entitled Tracking plasmids for clinical and public health use.

ESGEM-AMR

Role: Co-Lead

Co-leads the design of technical guidance, specifications, AMRgen package and coordinated the Staph subgroup.

Genomic Diversity of Mycoplasma pneumoniae (ESCMID)

Role: Co-Applicant

Designed the bioinformatics workflows, led analyses of genomic diversity and population structure, and translated findings into surveillance recommendations.

Global Genomic Surveillance of AMR (NIHR)

Role: Work package Lead

Led the implementation of a national survey on carbapenem-resistant Klebsiella pneumoniae (Kpn), a genomic survey to assess the diversity of KPn in low and middle-income countries. Coordinated multi-country data integration, developed the reporting framework, and supported capacity building for genomic surveillance partners.

SECRETERS (MSCA-ITN, Horizon 2020)

Role: Co-Applicant

Helped develop the project proposal.

Education Course (ESCMID)

Role: Co-Coordinator

Coordinating, alongside, John WA Rossen (UMCG-RUG) and Sandra Reuter (UMCFreiburg), the development and delivery of the course entitled Enhancing hospital surveillance and rapid diagnostics of critical pathogens through metagenomics sequencing.

TEAPOTS (JPIAMR)

Role: Co-Applicant

Helped develop the project proposal. Communicated with collaborators. Analysed results.

One Health Drivers of AMR in Thailand (UKRI)

Role: Researcher

Led the genomic analyses linking sources and transmission pathways.

SOLIDNESS (JPIAMR)

Role: Co-Applicant

Designed the project, coordinated with collaborators, analysed the results, wrote the white papers.

FoodProTects

Role: Work package Lead

Led the design, optimization and implementation of shotgun and targeted metagenomics protocols, from sample preparation to data analysis. Supervised two PhD students within the project. Communicated with collaborators in Germany.

Scholarships, Grants and Awards

Year	Award	Organization	Amount
2024	ESCMID Fellowship	ESCMID	NA
2022	ECCMID Travel Grant	ESCMID	€500
2021	Outstanding Contribution Award	University of Bath	NA
2021	ECCMID Travel Grant	ESCMID	€500
2015	ECCMID Travel Grant	ESCMID	€500
2015	ESCMID Observership Grant	ESCMID	€924.64
2014	ESCMID Attendance Grant	ESCMID	€1350
2011	ESCMID Attendance Grant	ESCMID	€850
2011	PhD Scholarship	FCT	€47,040
2011	ERASMUS Scholarship	ERASMUS	€1050

Publications in peer-reviewed journals

Gibbon M*, Couto N*, Habib S, Cowley L, Aanensen D, Corander J, Thorpe H, Hetland MAK, Sassera D, Merla C, Corbella M, Ferrari C, Turner KME, Sirikancha K, Dulyayangkul P, Alhusein N, Charoenlap N, Thamlikitikul V, Avison MB, Feil EJ (2025). Convergence and global epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus. Lancet Microbe, online first.
David S*, Caballero JD*, Couto N*, Abudahab K*, Alikhan NF, Yeats C, Underwood A, Molloy A, Connor D, Shane HM, Ashton PM, Grundmann H, Holden MTG, Feil EJ, Sia SB, Donado-Godoy P, Lingegowda RK, Okeke IN, Argimón S, Aanensen DM; NIHR Global Health Research Unit on Genomics and enabling data for the Surveillance of AMR (2025). Monitoring antimicrobial resistance trends from global genomics data: amr.watch. PLOS Glob Public Health 5(11):e0005256.
Nestor D, Peker N, Couto N, Hiss AN, Herbig A, Krause J, Rossen JWA, Mölling P, Sundqvist M (2025). Performance of shotgun metagenomics on whole blood from patients with suspected bloodstream infection: Challenges remain. Journal of Microbiological Methods 237:107231.
Medina VA, García-Vega AS, Rodríguez F, Triviño-García ES, Robledo JA, Leal AL, Galvis JC, Reyes LF; Genomic Epidemiology of Antimicrobial Resistance Consortium (GEAR); Okeke IN, Couto N, Kumaran EA, Lewis-Woodhouse G, Argimon S, Arevalo SA, Underwood AP, Fargetton X, Aanensen DM, Donado-Godoy MP (2025). Epidemiological Genomics of Klebsiella pneumoniae isolates from hospitals across Colombia. NPJ Antimicrobial Resistance 3(1):64.
Fleres G, Mirabile A, Lokate M, Rossen JWA, Couto N, Friedrich AW, García-Cobos S (2025). Surveillance and Genomic Characterisation of Colistin-Resistant Gram-Negative Bacteria in the Drains of High-Risk Hospital Units. Journal of Global Antimicrobial Resistance 42:127-134.
Björnberg A, Nestor D, Peker N, Sinha B, Couto N, Rossen J, Sundqvist M, Mölling P (2025). Critical Steps in Shotgun Metagenomics-Based Diagnosis of Bloodstream Infections Using Nanopore Sequencing. APMIS 133(1):e13511.
Germuskova Z, Sosa E, Lagos AC, Aamot HV, Beale MA, Bertelli C, Björkmann J, Couto N, Feige L, Greub G, Hallbäck ET, Hodcroft EB, Harmsen D, Jacob L, Jolley KA, Kahles A, Mather AE, Neher RA, Neves A, Niemann S, Nolte O, Peacock SJ, Razavi M, Roloff T, Schrenzel J, Sikora P, Sundqvist M, Mölling P, Egli A (2024). Conference report: the first bacterial genome sequencing pan-European network conference. Microbes and Infection 105410.
Mutschler E, Roloff T, Neves A, Vangstein Aamot H, Rodriguez-Sanchez B, Ramirez M, Rossen J, Couto N, Novais Â, Howden BP, Brisse S, Reuter S, Nolte O, Egli A, Seth-Smith HMB; ESCMID Study Group for Epidemiological Markers (ESGEM), and ESCMID Study Group for Genomic and Molecular Diagnostics (ESGMD) (2024). Towards unified reporting of genome sequencing results in clinical microbiology. PeerJ 12:e17673.
Shamanna V, Srinivas S, Couto N*, Nagaraj G, Sajankila SP, Krishnappa HG, Kumar KA, Aanensen DM, Lingegowda RK, NIHR Global Health Research Unit On Genomic Surveillance-India Consortium (2024). Geographical distribution, disease association and diversity of Klebsiella pneumoniae KL and O antigens in India: roadmap for vaccine development. Microbial Genomics 10(7):001271.
Werner G, Aamot HV, Couto N (2024). Antimicrobial susceptibility prediction from genomes: a dream come true?. Trends in Microbiology 32(4):317-318.
Werner G, Couto N, Feil EJ, Novais A, Hegstad K, Howden BP, Friedrich AW, Reuter S (2023). Taking hospital pathogen surveillance to the next level. Microbial Genomics 9(4):mgen001008.
Habib S, Gibbon MJ, Couto N, Kakar K, Habib S, Samad A, Munir A, Fatima F, Mohsin M, Feil E (2023). The Diversity, Resistance Profiles and Plasmid Content of Klebsiella spp. Recovered from Dairy Farms Located around Three Cities in Pakistan. Antibiotics (Basel) 12(3):539.
Raineri EJM, Maaß S, Wang M, Brushett S, Palma Medina LM, Sampol Escandell N, Altulea D, Raangs E, de Jong A, Vera Murguia E, Feil EJ, Friedrich AW, Buist G, Becher D, García-Cobos S, Couto N*, van Dijl JM* (2022). Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity. Microbiome 10(1):239.
Aamot HV, Claas ECJ, Couto N, Westh H, Greub G, Rossen JWA (2022). Next-generation sequencing in routine clinical microbiology and infectious diseases: an ESGMD-ESGEM ESCMID postgraduate course. New Microbes and New Infections 49-50:101046.
Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ (2022). A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nature Microbiology 7(12):2054-2067.
Kok NA, Peker N, Schuele L, de Beer JL, Rossen JWA, Sinha B, Couto N* (2022). Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum. Frontiers in Microbiology 13:949328.
Cassidy H, Schuele L, Lizarazo-Forero E, Couto N, Rossen JWA, Friedrich AW, van Leer-Buter C, Niesters HGM (2022). Exploring a prolonged enterovirus C104 infection in a severely ill patient using nanopore sequencing. Virus Evolution 8(1): veab109.
Ditz B, Boekhoudt J, Couto N, Brandsma CA, Hiemstra PS, Tew GW, Neighbors M, Grimbaldeston MA, Timens W, Kerstjens HAM, Rossen JWA, Guryev V, van den Berge M, Faiz A (2022). The Microbiome in Bronchial Biopsies from Smokers and Ex-Smokers with Stable COPD - A Metatranscriptomic Approach. COPD: Journal of Chronic Obstructive Pulmonary Disease 19(1): 81-87.
Schuele L, Cassidy H, Peker N, Rossen JWA, Couto N* (2021). Future potential of metagenomics in clinical microbiology laboratories. Expert Review on Molecular Diagnostics 21(12): 1273-1285.
Peker N, Schuele L, Kok N, Terrazos M, Neuenschwander SM, de Beer J, Akkerman O, Peter S, Ramette A, Merker M, Niemann S, Couto N*, Sinha B, Rossen JWA (2021). Evaluation of whole-genome sequence data analysis approaches for short- and long-read sequencing of Mycobacterium tuberculosis. Microbial Genomics 7(11): 000695.
Lisotto P, Raangs E, Couto N, Rosema S, Lokate M, Zhou X, Harmsen HJM, Friedrich AW, Rossen JWA, Bathoorn E, Chlebowicz-Fliss M (2021). Long-read sequencing-based in silico phage typing of vancomycin-resistant Enterococcus faecium. BMC Genomics 22(1):758.
Lisotto P, Couto N, Rosema S, Lokate M, Zhou X, Bathoorn E, Harmsen HJM, Friedrich AW, Rossen JWA, Chlebowicz-Fliss M (2021). Molecular characterisation of vancomycin-resistant Enterococcus faecium isolates belonging to the lineage ST117/CT24 causing hospital outbreaks. Frontiers in Microbiology 12:728356.
Schuele L, Lizarazo-Forero E, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N* (2021). Application of shotgun metagenomics sequencing and targeted sequence capture to detect circulating porcine viruses in the Dutch-German border region. Transboundary and Emerging Diseases 69(4):2306-2319.
Schuele L, Lizarazo-Forero E, Cassidy H, Strutzberg-Minder K, Boehmer J, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Rossen JWA, Couto N* (2021). First detection of porcine respirovirus 1 in Germany and the Netherlands. Transboundary and Emerging Diseases 68(6):3120-3125.
de Vries JJC, Brown JR, Couto N, Beer M, Le Mercier P, Sidorov I, Papa A, Fischer N, Oude Munnink BB, Rodriquez C, Zaheri M, Sayiner A, Hönemann M, Cataluna AP, Carbo EC, Bachofen C, Kubacki J, Schmitz D, Tsioka K, Matamoros S, Höper D, Hernandez M, Puchhammer-Stöckl E, Lebrand A, Huber M, Simmonds P, Claas ECJ, López-Labrador FX; ESCV Network on Next-Generation Sequencing (2021). Recommendations for the introduction of metagenomic next-generation sequencing in clinical virology, part II: bioinformatic analysis and reporting. Journal of Clinical Virology 138:104812.
Gibbon MJ, Couto N, David S, Barden R, Standerwick R, Jagadeesan K, Birkwood H, Dulyayangkul P, Avison MB, Kannan A, Kibbey D, Craft T, Habib S, Thorpe HA, Corander J, Kasprzyk-Hordern B, Feil EJ (2021). A high prevalence of blaOXA-48 in Klebsiella (Raoultella) ornithinolytica and related species in hospital wastewater in South West England. Microbial Genomics 7(3):mgen000509.
López-Labrador FX, Brown JR, Fischer N, Harvala H, Van Boheemen S, Cinek O, Sayiner A, Madsen TV, Auvinen E, Kufner V, Huber M, Rodriguez C, Jonges M, Hönemann M, Susi P, Sousa H, Klapper PE, Pérez-Cataluňa A, Hernandez M, Molenkamp R, der Hoek LV, Schuurman R, Couto N, Leuzinger K, Simmonds P, Beer M, Höper D, Kamminga S, Feltkamp MCW, Rodríguez-Díaz J, Keyaerts E, Nielsen XC, Puchhammer-Stöckl E, Kroes ACM, Buesa J, Breuer J, Claas ECJ, de Vries JJC; ESCV Network on Next-Generation Sequencing (2021). Recommendations for the introduction of metagenomic high-throughput sequencing in clinical virology, part I: Wet lab procedure. Journal of Clinical Virology 134:104691.
Schuele L, Cassidy H, Lizarazo E, Strutzberg-Minder K, Schuetze S, Loebert S, Lambrecht C, Harlizius J, Friedrich AW, Peter S, Niesters HGM, Rossen JWA, Couto N* (2020). Assessment of Viral Targeted Sequence Capture Using Nanopore Sequencing Directly from Clinical Samples. Viruses 12(12):1358.
da Cruz Campos AC, Couto N, Andrade NLS, Friedrich AW, Rosa ACP, Damasco PV, Chlebowicz-Flissikowska MA, Rossen JWA, the SOLIDNESS Working Group (2020). Virulence and resistance properties of E. coli isolated from urine samples of hospitalized patients in Rio de Janeiro, Brazil – The role of mobile genetic elements. International Journal of Medical Microbiology 310(8):151453.
da Cruz Campos AC, Andrade NL, Couto N, Mutters N, de Vos M, Rosa ACP, Damasco PV, Lo Ten Foe JR, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA (2020). Characterization of fosfomycin heteroresistance among multidrug-resistant Escherichia coli isolates from hospitalized patients in Rio de Janeiro, Brazil. Journal of Global Antimicrobial Resistance 22:584-593.
Benulič K, Pirš M, Couto N, Chlebowicz M, Rossen JWA, Zorec TM, Seme K, Poljak M, Zupanc TL, Ružić-Sabljić E, Cerar T (2020). Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates. PLoS ONE 15(4):e0231503.
Mendes CI, Lizarazo E, Machado MP, Silva DN, Tami A, Ramirez M, Couto N, Rossen JWA, Carriço JA (2020). DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing. Microbial Genomics 6(3):e000328.
da Cruz Campos AC, Cavallo FM, Andrade NL, van Dijl JM, Couto N, Zrimec J, Lo Ten Foe JR, Rosa ACP, Damasco PV, Friedrich AW, Chlebowicz-Flissikowska MA, Rossen JWA (2019). Determining the virulence properties of Escherichia coli ST131 containing bacteriocin-encoding plasmids using short-and long-read sequencing and comparing them with those of other E. coli lineages. Microorganisms 7(11):534.
Trigo da Roza F, Couto N, Carneiro C, Cunha E, Rosa T, Magalhães M, Tavares L, Novais A, Peixe L, Rossen JW, Lamas L, Oliveira M (2019). Commonality of multidrug-resistant Klebsiella pneumoniae ST348 isolates in horses and humans in Portugal. Frontiers in Microbiology 10:165.
Lizarazo E, Couto N, Vincenti-Gonzalez M, Raangs EC, Velasco Z, Bethencourt S, Jaenisch T, Friedrich AW, Tami A, Rossen JW (2019). Applied shotgun metagenomics approach for the genetic characterization of dengue viruses. Journal of Biotechnology: X 2: 100009.
Peker N, Garcia-Croes S, Dijkhuizen B, Wiersma HH, van Zanten E, Wisselink G, Friedrich AW, Kooistra-Smid M, Sinha B, Rossen JW, Couto N* (2019). A comparison of three different bioinformatics analyses of the 16S-23S rRNA encoding region for bacterial identification. Frontiers in Microbiology 10:620.
Couto N*, Schuele L, Raangs EC, Machado MP, Mendes CI, Jesus TF, Chlebowicz M, Rosema S, Ramirez M, Carriço JA, Autenrieth IB, Friedrich AW, Peter S, Rossen JW (2018). Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens. Scientific Reports 8(1):13767.
Zhou X, Chlebowicz MA, Bathoorn E, Rosema S, Couto N, Lokate M, Arends JP, Friedrich AW, Rossen JWA (2018). Elucidating vancomycin-resistant Enterococcus faecium outbreaks: the role of clonal spread and movement of mobile genetic elements. Journal of Antimicrobial Chemotherapy 73(12):3259-67.
Peker N, Couto N, Sinha B, Rossen JW (2018). Diagnosis of bloodstream infections from positive blood cultures and directly from blood samples: recent developments in molecular approaches. Clinical Microbiology and Infection 24(9):944-955.
Fleres G, Couto N, Lokate M, van der Sluis LWM, Ginevra C, Jarraud S, Deurenberg RH, Rossen JW, García-Cobos S, Friedrich AW (2018). Detection of Legionella anisa in water from hospital dental chair units and molecular characterization by whole-genome sequencing. Microorganisms 6(3). pii: E71.
Khemiri M, Abbassi MS, Couto N, Mansouri R, Hammami S, Pomba C (2018). Genetic characterisation of Staphylococcus aureus isolated from milk and nasal samples of healthy cows in Tunisia: First report of ST97-t267-agrI-SCCmecV MRSA of bovine origin in Tunisia. Journal of Global Antimicrobial Resistance 14: 161-165.
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AMD, Raangs EC, Rosema S, Veloo ACM, Zhou K, Friedrich AW, Rossen JWA (2017). Reprint of "Application of next generation sequencing in clinical microbiology and infection prevention". Journal of Biotechnology 250: 2-10.
Deurenberg RH, Bathoorn E, Chlebowicz MA, Couto N, Ferdous M, García-Cobos S, Kooistra-Smid AMD, Raangs EC, Rosema S, Veloo ACM, Zhou K, Friedrich AW, Rossen JWA (2017). Application of next generation sequencing in clinical microbiology and infection prevention. Journal of Biotechnology 243: 16-24.
Couto N, Monchique C, Belas A, Marques C, Gama LT, Pomba C (2016). Trends and molecular mechanisms of antimicrobial resistance in clinical staphylococci isolated from companion animals over a 16-year period. Journal of Antimicrobial Chemotherapy 71: 1479-1487.
Couto N, Belas A, Oliveira M, Almeida P, Clemente C, Pomba C (2016). Comparative RNA-seq-based transcriptome analysis of the virulence characteristics of methicillin-resistant and -susceptible Staphylococcus pseudintermedius strains isolated from small animals. Antimicrobial Agents and Chemotherapy 60: 962-7.
Couto N, Martins J, Lourenço AM, Pomba C, Coelho AV (2016). Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by whole proteome characterization and serological proteomic analyses. Journal of Proteomics 133: 113-24.
Fernandes L, Centeno MM, Couto N, Nunes T, Almeida V, Alban L, Pomba C (2016). Longitudinal characterization of monophasic Salmonella Typhimurium throughout the pig's life cycle. Veterinary Microbiology 192: 231-7.
Gaglio R, Couto N, Marques C, Lopes MFS, Moschettia G, Pomba C, Settanni L (2016). Evaluation of antimicrobial resistance and virulence of enterococci from equipment surfaces, raw materials and traditional cheeses. International Journal of Food Microbiology 236:107-114.
Ruzauskas M, Couto N, Pavilonis A, Klimiene I, Siugzdiniene R, Virgailis M, Vaskeviciute L, Anskiene L, Pomba C (2016). Characterization of Staphylococcus pseudintermedius isolated from diseased dogs in Lithuania. Polish Journal of Veterinary Science 19(1): 7-14.
Couto N, Belas A, Kadlec K, Schwarz S, Pomba C (2015). Clonal diversity, virulence patterns and antimicrobial and biocide susceptibility among human, animal and environmental MRSA in Portugal. Journal of Antimicrobial Chemotherapy 70(9): 2483-7.
Ruzauskas M, Couto N, Kerziene S, Siugzdiniene R, Klimiene I, Virgailis M, Pomba C (2015). Prevalence, species distribution and antimicrobial resistance patterns of methicillin-resistant staphylococci in Lithuanian pet animals. Acta Veterinaria Scandinava 57:27.
Couto N, Belas A, Couto I, Perreten V, Pomba C (2014). Genetic relatedness, antimicrobial and biocide susceptibility comparative analysis of methicillin-resistant and -susceptible Staphylococcus pseudintermedius from Portugal. Microbial Drug Resistance 20(4): 364-71.
Pomba C, López-Cerero L, Bellido M, Serrano L, Belas A, Couto N, Cavaco-Silva P, Rodríguez-Baño J, Pascual A (2014). Within-lineage variability of ST131 Escherichia coli isolates from humans and companion animals in the south of Europe. Journal of Antimicrobial Chemotherapy 69(1): 271-3.
Belas A, Salazar AS, Gama LT, Couto N, Pomba C (2014). Risk factors for faecal colonisation with Escherichia coli producing extended-spectrum and plasmid-mediated AmpC β-lactamases in dogs. Veterinary Record 175(8): 202.
Ruzauskas M, Couto N, Belas A, Klimiene I, Siugzdiniene R, Pomba C (2013). First report of swine-associated methicillin-resistant Staphylococcus aureus ST398 in Lithuania. Polish Journal of Veterinary Sciences 16(1): 125-7.
Couto N, Belas A, Tilley P, Couto I, Gama LT, Kadlec K, Schwarz S, Pomba C (2013). Biocide and antimicrobial susceptibility of methicillin-resistant staphylococcal isolates from horses. Veterinary Microbiology 166(1-2): 299-303.
Couto N, Tilley P, Simões J, Sales Luis JP, Pomba C (2012). First Report of Methicillin-Resistant Staphylococcus aureus ST5 and ST398 from Purebred Lusitano Horses. Journal of Equine Veterinary Science 32(5): 300-4.
Kadlec K, Feßler AT, Couto N, Pomba CF, Schwarz S (2012). Unusual small plasmids carrying the novel resistance genes dfrK or apmA isolated from methicillin-resistant or -susceptible staphylococci. Journal of Antimicrobial Chemotherapy 67(10): 2342-5.
Couto N, Pomba C, Moodley A, Guardabassi L (2011). Prevalence of methicillin-resistant staphylococci among dogs and cats attending a veterinary teaching hospital in Portugal. Veterinary Record 169:72.
Kadlec K, Pomba C, Couto N, Schwarz S (2010). Small plasmids carrying vga(A) or vga(C) genes mediate resistance to lincosamides, pleuromutilins and streptogramin A antibiotics in methicillin-resistant Staphylococcus aureus ST398 from swine. Journal of Antimicrobial Chemotherapy 65(12): 2692-3.
Pomba C, Couto N, Moodley A (2010). Treatment of a lower urinary tract infection in a cat caused by a multidrug-methicillin-resistant Staphylococcus pseudintermedius and Enterococcus faecalis. Journal of Feline Medicine and Surgery 12(10): 802-6.

Pre-prints

David S, Kohlenberg A, Yeats C, Abudahab K, Albiger B, Fareed-Alikhan N, Alm E, Byfors S, Couto N, Diaz-Caballero J, Giske C, Glasner C, Linkevicius M, Matuschek E, Palm D, Svartström O, Grudmann H, Struelens MJ, Wisell KT, Monnet DL, Fröding I, Aanensen D, Brolund A (2025). Emergence of carbapenemase-producing Escherichia coli in acute care hospitals in 36 European countries: results from the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey), 2019. Preprints with the Lancet by SSRN http://dx.doi.org/10.2139/ssrn.5275520.
Fröding I, David S, Yeats C, Abudahab K, Albiger B, Fareed-Alikhan N, Alm E, Byfors S, Couto N, Diaz-Caballero J, Giske C, Matuschek E, Linkevicius M, Palm D, Svartström O, Struelens MJ, Wisell KT, Monnet DL, Brolund A, Aanensen D, Kohlenberg A (2025). Persistent spread of carbapenemase-producing Klebsiella pneumoniae in acute care hospitals in 36 European countries: results from the survey of carbapenem- and/or colistin-resistant Enterobacterales (CCRE survey), 2019. Preprints with the Lancet by SSRN http://dx.doi.org/10.2139/ssrn.5275521.
David S, Abudahab K, Couto N, Daningrat WOD, Yeats C, Molloy A, Ashton PM, Alikhan NF, Aanensen DM (2025). Monitoring of vaccine targets and interventions using global genome data: vaccines.watch. Preprints with bioRxiv https://doi.org/10.1101/2025.06.13.659488.
David S*, Caballero JD*, Couto N*, Abudahab K*, Alikhan NF, Yeats C, Underwood A, Molloy A, Connor D, Shane HM, Ashton PM, Grundmann H, Holden MTG, Feil EJ, Sia SB, Donado-Godoy P, Lingegowda RK, Okeke IN, Argimón S, Aanensen DM; NIHR Global Health Research Unit on Genomics and enabling data for the Surveillance of AMR (2025). amr.watch - monitoring antimicrobial resistance trends from global genomics data. Preprints with bioRxiv https://doi.org/10.1101/2025.04.17.649298.
Shamanna V, Srinivas S, Couto N*, Nagaraj G, Sajankila SP, Krishnappa HG, Kumar KA, Aanensen DM, Lingegowda RK, NIHR Global Health Research Unit On Genomic Surveillance-India Consortium (2024). Geographical distribution, disease association and diversity of Klebsiella pneumoniae KL and O antigens in India: roadmap for vaccine development. Preprints with bioRxiv https://doi.org/10.1101/2024.03.15.585133.
Gibbon M*, Couto N*, Habib S, Cowley L, Aanensen D, Corander J, Thorpe H, Hetland MAK, Sassera D, Merla C, Corbella M, Ferrari C, Turner KME, Sirikancha K, Dulyayangkul P, Alhusein N, Charoenlap N, Thamlikitikul V, Avison MB, Feil EJ (2025). Convergence and global epidemiology of Klebsiella pneumoniae plasmids harbouring the iuc3 virulence locus. Preprints with bioRxiv https://doi.org/10.1101/2024.01.05.574329.
Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ (2022). One Health or Three? Transmission modelling of Klebsiella spp. reveals ecological barriers to transmission between humans, animals and the environment. Preprints with bioRxiv https://doi.org/10.1101/2021.08.05.455249.

Letters

Schuele L, Fleres G, Strutzberg-Minder K, Schütze S, Löbert S, Lambrecht C, Harlizius J, Peter S, Rossen JWA, Couto N (2021). Detection of a small IncX4 plasmid carrying the mcr-1.1 gene in a pig oral fluid sample by shotgun metagenomic sequencing. Journal of Global Antimicrobial Resistance 24:205-206.
Fleres G, Couto N, Schuele L, Chlebowicz MA, Mendes CI, van der Sluis LWM, Rossen JWA, Friedrich AW, García-Cobos S (2019). Detection of a novel mcr-5.4 gene variant in hospital tap water by shotgun metagenomic sequencing. Journal of Antimicrobial Chemotherapy 74(12):3626-3628.
Couto N, Belas A, Rodrigues C, Schwarz S, Pomba C (2016). Acquisition of the fexA and cfr genes in Staphylococcus pseudintermedius during florfenicol treatment of canine pyoderma. Journal of Global Antimicrobial Resistance 7: 126-127.
Couto N, Belas A, Centeno M, Van Duijkeren E, Pomba C (2014). First description of fexA-positive meticillin-resistant Staphylococcus aureus ST398 from calves in Portugal. Journal of Global Antimicrobial Resistance 2(4): 342-3.
Pomba C, Endimiani A, Rossano A, Saial D, Couto N, Perreten V (2014). First report of OXA-23-mediated carbapenem resistance in sequence type 2 multidrug-resistant Acinetobacter baumannii associated with urinary tract infection in a cat. Antimicrobial Agents and Chemotherapy 58(2): 1267-8.
Fernandes L, Centeno M, Belas A, Nunes T, Lopes Alves P, Couto N, Pomba C (2012). Immediate after birth transmission of epidemic Salmonella enterica Typhimurium monophasic strains in pigs is a likely event. Journal of Antimicrobial Chemotherapy 67(12): 3012-4.
Pomba C, Baptista FM, Couto N, Loução F, Hasman H (2010). Methicillin-resistant Staphylococcus aureus CC398 isolates with indistinguishable ApaI restriction patterns in colonized and infected pigs and humans. Journal of Antimicrobial Chemotherapy 65(11): 2479-81.

Book Chapters

Couto N, Rossen JWA. Overview of Microbial NGS for Clinical and Public Health Microbiology. In: Application and Integration of Omics-powered Diagnostics in Clinical and Public Health Microbiology. Editors: J. Moran-Gilad, Y. Yagel. Cham: Springer Nature 2021.
Couto N, Pomba C. Tipagem de Staphylococcus aureus e Staphylococcus pseudintermedius resistentes à meticilina isolados de animais pela sequenciação de múltiplos loci. In: Abordagens moleculares em Veterinária – Como desvendar a etiologia e a epidemiologia da infeção. Editors: Mónica V. Cunha, João Inácio. Lisboa: Lidel 2014.

Genome Announcements

Lizarazo E, Couto N, Vincenti-Gonzalez M, Raangs EC, Jaenisch T, Friedrich AW, Tami A, Rossen JW (2018). Complete coding sequences of five Dengue virus type 2 clinical isolates from Venezuela obtained through shotgun metagenomics. Genome Announcements 6(25). pii: e00545-18.
Couto N, Chlebowicz MA, Raangs EC, Friedrich AW, Rossen JW (2018). Complete genome sequences of two methicillin-resistant Staphylococcus haemolyticus isolates of multilocus sequence type 25, first detected by shotgun metagenomics. Genome Announcements 6(14). pii: e00036-18.

Conference abstracts published in Refereed Journals

Gudipati S, Perri M, Couto N, Herc E, Zervos M (2019). Molecular epidemiology of daptomycin-resistant Staphylococcus aureusß causing bloodstream infections. Open Forum Infectious Diseases 6(Suppl.2):S291.
Lizarazo EF, Couto N, Raangs E, Vincenti-Gonzalez MF, Tovar R, Bethencourt S, Grobusch MP, Jaenisch T, Friedrich A, Tami A, Rossen JW (2017). Shotgun metagenomics as a tool for the rapid diagnosis and genotyping of Dengue. Tropical Medicine & International Health 22: 125.
Marques C, Belas A, Aboim C, Couto N, Telo da Gama L, Pomba C (2015). Multidrug-resistant uropathogenic bacteria in cats: a 13 year retrospective snapshot. Journal of Feline Medicine and Surgery 17: 816-27.
Pomba C, Belas A, Salazar ASS, Gama LT, Couto N (2015). Risk factors for faecal colonization with Escherichia coli producing extended spectrum and plasmid mediated AmpC beta lactamases in dogs without antimicrobial pressure. Journal Veterinary Internal Medicine 29: 423-83.
Pomba C, Rodrigues AC, Couto N (2015). High Frequency of Colonization by Methicillin-Resistant Staphylococci in Healthy Humans in Daily Contact with Animals in Portugal. Journal Veterinary Internal Medicine 29: 423-83.
Marques C, Couto N, Belas A, Saial D, Delgado M, Pomba C (2015). Emergence of Multidrug-Resistant Bacteria Causing Urinary Tract Infections in Companion Animals: A 14¬Year Retrospective Study in Portugal. Journal Veterinary Internal Medicine 29: 423-83.
Couto N, Belas A, Pomba C (2012). Clonality of methicillin-resistant Staphylococcus aureus and methicillin-resistant Staphylococcus pseudintermedius isolated from healthy and sick companion animals and humans in Portugal. Clinical Microbiology and Infection 18(S3): 337.
Belas A, Salazar AS, Fernandes L, Couto N, Pomba C (2012). Colonisation with extended-spectrum and plasmid-mediated AmpC beta-lactamases Escherichia coli producers in healthy dogs without antimicrobial pressure – a cross-sectional study. Clinical Microbiology and Infection 18(S3): 450.
Couto N, Belas A, Fessler A, Costa S, Couto I, Kadlec K, Schwarz S, Pomba C (2012). Diversity of antimicrobial and biocide susceptibility patterns among equine methicillin-resistant staphylococci. Clinical Microbiology and Infection 18(S3): 750.
Couto N, Ruzauskas M, Belas A, Virgailis M, Klimiene I, Siugzdiniene R, Pomba C (2012). Detection and characterisation of methicillin-resistant Staphylococcus aureus strains isolated from pigs in Lithuania – a cross-sectional study. Clinical Microbiology and Infection 18(S3): 760.
Pomba C, Fernandes L, Belas A, Couto N, Dias R, Cavaco-Silva P (2012). Commonality among CTX-M-15-producing ST131-O25b uropathogenic Escherichia coli isolates from companion animals and humans in Portugal. Clinical Microbiology and Infection 18(S3): 801.
Pomba C, Loução F, Couto N, Delgado M, Duarte-Correia J (2011). Cephalosporin and clavulanic acid resistance mechanisms in Escherichia coli isolates from cattle in Portugal. Clinical Microbiology and Infection 17(S4): S122.
Couto N, Tilley P, Simões J, Sales-Luís J, Pomba C (2011). Nasal carriage of methicillin-resistant staphylococci among sick and healthy horses in Portugal. Clinical Microbiology and Infection 17(S4): S339.
Couto N, Guerreiro L, Belas A, Leandro C, Barbosa R, Cavaco-Silva P, Pomba C (2011). High-frequency of the ST131-O25b pandemic Escherichia coli clone among uropathogenic isolates from companion animals and humans in Portugal. Clinical Microbiology and Infection 17(S4): S376.

Mentoring & Supervision

Institution	Supervision Role	Student Name	Link to Thesis
University of Bristol	MSc Co-Supervisor	Srikanth Srinivas	NA
UMCG-RUG	PhD Co-Supervisor	Elias Vera Murguia	Link
UMCG-RUG	PhD Co-Supervisor	Nilay Peker	Link
UMCG-RUG	PhD Co-Supervisor	Leonard Schuele	Link
UMCG-RUG	MSc Co-Supervisor	Siobhan Brushett	NA

Teaching

Year	Institution	Subject	Hours	Program
2023	Universidade de Évora	One Health and Antimicrobial Resistance	2h	MSc in One Health
2019	Universidade Lusófona de Humanidades e Tecnologias	Antimicrobial therapy and resistance in Veterinary Medicine	2h	Integrated MSc in Veterinary Medicine - Microbiology
2019	UMCG-RUG	Genomics for Infection prevention and diagnosis	2h	MSc in Medical and Pharmaceutical Drug Innovation – Medical Microbiology
2019	UMCG-RUG	Research Course	8h	Immunology & Infectious Diseases Research Course
2018	UMCG-RUG	Genomics for Infection prevention and diagnosis	2h	MSc in Medical and Pharmaceutical Drug Innovation – Medical Microbiology
2018	UMCG-RUG	Research Course	8h	Immunology & Infectious Diseases Research Course
2017	UMCG-RUG	Research Course	8h	Immunology & Infectious Diseases Research Course
2016	University of Lisbon - Faculty of Veterinary Medicine	Antimicrobial strategies against Gram-positive infections, Antimicrobial strategies against Gram-negative infections, Introduction to antimicrobials and antimicrobial therapy, Coordination	20h	Antibiotic Strategies in Veterinary Medicine
2015	University of Lisbon - Faculty of Veterinary Medicine	Antimicrobial strategies against Gram-positive infections, Practical sessions	4h	Antibiotic Strategies in Veterinary Medicine
2015	University of Lisbon - Faculty of Veterinary Medicine	Practical sessions on Biochemistry, Haematology, Urology and Hepatology	24h	Medical Propaedeutic II
2015	University of Lisbon - Faculty of Veterinary Medicine	Practical sessions on Semiology	24h	Medical Propaedeutic I
2012	University of Lisbon - Faculty of Veterinary Medicine	Clinical cases of respiratory infections	8h	Medicine I

Leadership Roles

2026
Chair – ESCMID Study Group on Epidemiological Markers (ESGEM)
Local Organizing Committee Member – IUMS 2026, Beyond the Microscope: AI & Innovation in Microbiology, Lisbon, Portugal
Coordinator – ESCMID-ESGEM-ESGMAP Postgraduate Course: Tracking plasmids for clinical and public health use, 2-4 November, Copenhagen (DK)
Co-Lead – ESGEM-AMR Working Group
Reviewer – Nature Microbiology, Springer Nature
2025
Chair – ESCMID Study Group on Epidemiological Markers (ESGEM)
Coordinator – ESCMID-ESGEM-ESGMD Postgraduate Course:Enhancing Hospital Surveillance and Rapid Diagnostics of Critical Pathogens through Metagenomics Sequencing, 25-27 November, Groningen (NL)
Program Committee Chair – IMMEM XIV, Microbial Typing: from Fundamental to Daily Microbiology, Porto, Portugal
Co-Lead – ESGEM-AMR Working Group
Reviewer – National Academy of Sciences in Poland (NCN)
Reviewer – UKSHA
Reviewer – ESCMID
Reviewer – Journal of Clinical Microbiology, ASM
Reviewer – Microbial Genomics, Microbiology Society
2024
Chair – ESCMID Study Group on Epidemiological Markers (ESGEM)
Coordinator – ESCMID-ESGEM Postgraduate Course: Digital Epidemiology with Applications in Public Health, 16-18 July, Oxford (UK)
Co-Lead – ESGEM-AMR Working Group
Expert Panellist – JPIAMR
Reviewer – ESCMID
2023
Chair – ESCMID Study Group on Epidemiological Markers (ESGEM)
Program Committee Member –IMMEM XIII, Establishing whole genome sequencing at the core of epidemiological surveillance, Bath, UK
Expert Panellist – JPIAMR
Reviewer – MRC, UKRI
Reviewer – ESCMID
Reviewer – Microbiology Spectrum, ASM
Reviewer – Journal of Clinical Microbiology, ASM
Reviewer – Journal of Global Antimicrobial Resistance, Elsevier
2022
Secretary – ESCMID Study Group on Epidemiological Markers (ESGEM)
Coordinator – ESCMID-ESGEM Education Course: Moving beyond single species outbreaks: the role of mobile genetic elements, 7-8 July 2022, online
Expert Panellist – National Academy of Sciences in Poland (NCN)
Reviewer – ESCMID
Reviewer – Microbiology Spectrum, ASM
Reviewer – The Lancet Microbe, Elsevier
2021
Secretary – ESCMID Study Group on Epidemiological Markers (ESGEM)
Expert Panellist – National Academy of Sciences in Poland (NCN)
2020
Secretary – ESCMID Study Group on Epidemiological Markers (ESGEM)
Expert Panellist – National Academy of Sciences in Poland (NCN)
2019
Secretary – ESCMID Study Group on Epidemiological Markers (ESGEM)
Editor – Scientific Reports, Springer Nature
Reviewer – Journal of Global Antimicrobial Resistance, Elsevier
2018
Coordinator – ESCMID-ESGEM-ESGMD Capacity-Building Workshop: Metagenomics in the Diagnostic Laboratory, 21-24 October, Groningen (NL)
Editor – Scientific Reports, Springer Nature
Reviewer – Frontiers in Microbiology, Frontiers Media
Reviewer – mSystems, ASM

Invited Lectures

Couto N. ESGEM-AMR: a global effort to curate rules for AMR genotyping. Keynote Speaker at Norwegian Consortium for Microbial Genomics Annual Meeting, 2025, December 4, Oslo, Norway.
Couto N. A novel method for assessing global genetic diversity and molecular surveillance of Mycoplasma pneumoniae. Lecturer at ESCMID-ESGMD-ESGEM course on Enhancing Hospital Surveillance and Rapid Diagnostics of Critical Pathogens through Metagenomics Sequencing, 2025, November 25-27, Groningen, The Netherlands.
Couto N, Diaz-Caballero J. Workshop 3: An introduction to data-based surveillance and surveillance tools. Lecturer at ESCMID-ESGEM-ESGCIP-EFWISG-ESGMD-ESGIE-ESGREV-EVASG-ESGVM course on Emerging Infectious Diseases, 2025, October 21-23, Seville, Spain.
Couto N. The bioinformatics conundrum of microbial typing. Invited Speaker at Bioinformatics Horizons 2025 Conference, 2025, April 3-4, Bucharest, Romania.
Couto N. Genomics Epidemiology for Public Health. Invited Speaker at CADA Workshop, 2024, October 7-8, Ibadan, Nigeria.
Couto N. Using genomics to understand Klebsiella pneumoniae transmission between clinical and non-clinical settings. Lecturer at SANBI Training course on Genomic Pathogen Surveillance – Tools & Interpretation, 2024, September 9-11, Cape Town, South Africa.
Couto N. How to make sense of it? Bioinformatics analyses I and II. Lecturer at ESCMID-ESGMD-ESGEM course on The Future of Infection Diagnostics: A Comprehensive Guide to Next-Generation Sequencing, 2024, September 2-4, Lørenskog, Norway (hybrid course).
Couto N. Population-scale plasmid genomics in One Health. Invited Speaker at ESGEM-EFWISG Webinar 2024, July 11, online
Couto N. Post-analysis standardization. Invited Speaker at Conference of the Bacterial genome sequencing pan-european network, 2024, February 27 – March 1, Engelberg, Switzerland.
Couto N. Plasmids: the next challenge for epidemiology. Invited Speaker at Semana Mundial de Concienciación sobre la RAM (WAAW), 2023, November 21-22, Bogotá, Colombia (hybrid event).
Couto N. Plasmid typing: are we there yet? Invited Speaker at NIHR GHRU-AMR General Meeting, 2023, September 14-16, Cartagena, Colombia.
Couto N. Metagenomics in the field of emerging infectious diseases: overview and applications. Invited Speaker at Webinar organized jointly by Institute Pasteur and INIA-CISA, 2022, December 14, online.
Couto N. Guidelines for outbreak tracing using Metagenomics. Inivted speaker at Current and Future Challenges in Veterinary Virus Genomics, 2022, June 21-22, The Pirbright Institute, Surrey, United Kingdom.
Couto N. Metagenomics for typing. Lecturer at ESCMID Postgraduate Education Course: Next-generation sequencing in routine clinical microbiology and infectious diseases, 2021, September 27-29, online.
Couto N. Building JPIAMR Careers. Invited Speaker at JPIAMR Junior Researchers Workshop, 2021, June 29-30, online.
Couto N. An update on clinical metagenomics tools. Invited Speaker at International Conference on Clinical Metagenomics, 2019, October 17-18, Geneva, Switzerland.
Couto N. Setting-up diagnostic NGS virology in a University Medical Center. Invited Speaker at ESCV Workshop on Next Generation Sequencing in Clinical Virology, 2019, May 24-25, Valencia, Spain.
Couto N. Clinical Metagenomics and bioinformatics pipelines. Invited Speaker at Genomic Medicine in Action symposium GMS, 2019, May 28, Stockholm, Sweden.
Couto N. Making sense of genome shreds: tools and strategies for straightforward genome data analysis. Invited Speaker at 29th European Congress of Clinical Microbiology and Infectious Diseases, 2019, April 13–16, Amsterdam, The Netherlands.
Couto N. Next generation sequencing for next generation clinical microbiology. Invited Speaker at QIAGEN Nordic Microbiology Forum, 2019, January 21-22, Copenhagen, Denmark.
Couto N. NGS and virology in a University Medical Center. Invited Speaker at ESCV Workshop Next Generations Sequencing in Clinical Virology, 2018, November 20-21, Leiden, The Netherlands.
Couto N. NGS: current and future platforms. Lecturer at ESCMID Capacity-Building Workshop: Metagenomics in the Diagnostic Laboratory, 2018, October 21-24, Groningen, The Netherlands.
Couto N. NGS approaches in Microbiology. Invited Speaker at Roche Sequencing Solutions Sample Preparation EMEA User Meeting, 2018, October 10-11, Riga, Latvia.
Couto N. Unravelling the complex structure of mobile genetic elements through short-and long-read sequencing. Invited Speaker at KNMV DMT meeting Application and challenges of long-read sequencing, 2018, February 1, Utrecht, The Netherlands.
Couto N. Shotgun metagenomics approach for identification and typing of pathogens in clinical samples. Lecturer at Medical Sciences Summer School Antimicrobial Resistance, 2017, August 20-24, Groningen, The Netherlands.
Couto N. Anaerobic bacteria in animals – relevant species, epidemiology and antimicrobial resistance. Lecturer at ESCMID Postgraduate Technical Workshop, 2016, September 26-28, Groningen, The Netherlands.
Couto N. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by serological proteomic analyses. Invited Speaker at SCAN Seminar ITQB, 2015, May 13, Oeiras, Portugal.
Couto N, Pomba C. Interpretação dos testes de suscetibilidade aos Antibióticos e Biocidas. Lecturer at I Curso de Pós-Graduação: Estratégias de Antibioterapia em Animais de Companhia, Faculty of Veterinary Medicine – University of Lisbon, 2015, March 7-8, Lisbon, Portugal.
Lourenço AM, Couto N. MRSA e MRSP em Dermatologia: como tratar? Lecturer at I Curso de Pós-Graduação: Estratégias de Antibioterapia em Animais de Companhia, Faculty of Veterinary Medicine – University of Lisbon, 2015, March 7-8, Lisbon, Portugal.
Couto N. Transferência da resistência aos antibióticos dos animais ao homem. Invited Speaker at IV Congresso Científico de Saúde, Antibióticos – Que futuro? 2013, November 21-22, Lisbon, Portugal.
Couto N. Frequência de colonização por staphylococci coagulase-positivos meticilina-resistentes em cães e gatos internados no Hospital Escolar da Faculdade de Medicina Veterinária. Invited Speaker at CIISA Seminar, Faculty of Veterinary Medicine – University of Lisbon, 2010, July 16, Lisbon, Portugal.

Oral Communications at International Conferences

Rudman TR, Couto N, Rowlands RS, Beeton ML. Optimising DNA extraction methods for urinogenital mycoplasmas for future use in direct sequencing. Early Career Mycoplasma and Chlamydia Researcher Conference 2024, March 6, online.
Couto N, Argimón S, Diaz-Caballero J, Yeats C, Abudahab K, Connor D, Aanensen D. Dynamics of carbapenemase-encoding genes in a global large-scale genomic dataset of WHO priority pathogens (AMRwatch). Proceedings of the 33rd European Congress of Clinical Microbiology and Infectious Diseases 2023, April 15-18, Copenhagen, Denmark.
Gibbon M, Couto N, Cozens K, Coates A, Thiry D, Breurec S, Brisse S, Feil EJ. The plasmid-borne virulence factor aerobactin (lineage iuc3) is strongly associated with isolates of Klebsiella pneumoniae from pigs and ducks. Proceedings of the 32nd European Congress of Clinical Microbiology and Infectious Diseases 2022, April 23-26, Lisbon, Portugal.
Couto N, Thorpe H, Gibbon M, Philips R, Brisse S, Rodrigues CP, David S, Merla C, Corbella M, Ferrari C, Sassera D, Corander J, Feil EJ. The CHASRI element, encoding resistance to heavy-metals, is associated with Klebsiella isolates from hospital patients and may be co-selected alongside antibiotic resistance. Proceedings of the 31st European Congress of Clinical Microbiology and Infectious Diseases 2021, July 9-12, online.
Peker N, Björnberg A, Nestor D, Sinha B, Couto N, Rossen J, Sundqvist M, Mölling P. Whole blood or plasma? Shotgun metagenomics-based diagnosis of bloodstream infections using long-read MinION sequencing. Proceedings of the 31st European Congress of Clinical Microbiology and Infectious Diseases 2021, July 9-12, online.
Lizarazo E, Couto N, Silva D, Vincenti-Gonzalez M, Camacho D, Comach G, Bethencourt S, Jaenisch T, Friedrich AW, Carriço J, Ramirez M, Rossen JWA, Tami A. Understanding dengue genetic dynamics in the context of consecutive outbreaks in Venezuela. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Fleres G, Couto N, Chlebowicz M, Rossen JW, Friedrich A, Garcia-Cobos S. Detection of a mobile colistin resistance (mcr-5) gene in hospital tap water using short- and long-read shotgun metagenomics sequencing. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Mendes CI, Lizarazo E, Machado MP, Silva DN, Tami A, Ramirez M, Couto N, Rossen JWA, Carriço JA. DEN-IM: Dengue Virus Identification from Metagenomic Sequencing Data. Proceedings of the 29th European Congress of Clinical Microbiology and Infectious Diseases 2019, April 13-16, Amsterdam, The Netherlands.
Chlebowicz MA, Zhou XW, Couto N, Raangs EC, Arends JP, Bathoorn E, Friedrich AW, Rossen JW. Insights into vancomycin-resistant enterococci outbreaks through short- and long-read sequencing. Proceedings of the Oxford Nanopore Community Meeting London Calling, 2018, May 24-25, London, United Kingdom.
Couto N, Chlebowicz M, Cruz Campos AC, Raangs EC, Friedrich AW, Rossen JWA. Unravelling the complex structure of mobile genetic elements through short- and long-read sequencing. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Raangs EG, Vincenti-Gonzalez M, Bethencourt S, Jaenisch T, Friedrich AW, Tami A, Couto N, Rossen JWA. Optimization of a shotgun metagenomics protocol for identification and typing of dengue. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Vincenti-Gonzalez M, Bethencourt S, Jaenisch T, Grillet M, Friedrich AW, Tami A, Couto N, Rossen JWA. Higher resolution of dengue phylogenetic trees from Venezuela using the whole genome sequence. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Mölling P, Hedberg ST, Eriksson L, Johansson M, Paulander W, Couto N, Rossen JWA, Krause J, Herbig A, Sundqvist M. Shotgun metagenomics and typing of bacterial DNA in 5 mL whole blood from patients with suspected bloodstream infection. Proceedings of the 28th European Congress of Clinical Microbiology and Infectious Diseases 2018, April 21–24, Madrid, Spain.
Lizarazo Forero E, Couto N, Raangs E, Vincenti-Gonzalez M, Tovar R, Bethencourt S, Grobusch MP, Jaenisch T, Friedrich A, Tami A, Rossen J. Shotgun metagenomics as a tool for the rapid diagnosis and genotyping of dengue. Proceedings of the 10th European Congress of Tropical Medicine and International Health 2017, October 16-20, Antwerp, Belgium.
Couto N, Raangs E, Friedrich A, Rossen J. Evaluation of shotgun metagenomics and sequence classification methods for the diagnosis of bacterial pathogens in patients' samples. Proceedings of the 27th European Congress of Clinical Microbiology and Infectious Diseases 2017, April 22-25, Vienna, Austria.
Lizarazo Forero E, Couto N, Raangs E, Vincenti-Gonzalez M, Friedrich A, Tami A, Rossen J. Shotgun metagenomics as a tool for the rapid diagnosis and genotyping of dengue. Proceedings of the 27th European Congress of Clinical Microbiology and Infectious Diseases 2017, April 22-25, Vienna, Austria.
Couto N, Monchique C, Marques C, Belas A, Telo da Gama L, Pomba C. Insights into the evolution of antimicrobial resistance in staphylococci isolated from companion animals: a 16-year study in Portugal. Proceedings of the 25th European Congress of Clinical Microbiology and Infectious Diseases 2015, April 25–28, Copenhagen, Denmark.
Marques C, Couto N, Belas A, Aboim C, Fernandes L, Telo da Gama L, Pomba C. Spread of highly successful human multidrug-resistant clones causing urinary tract infections in companion animals. Proceedings of the 25th European Congress of Clinical Microbiology and Infectious Diseases 2015, April 25–28, Copenhagen, Denmark.
Couto N, Martins J, Martins AM, Pomba C, Coelho AV. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by serological proteomic analyses. Proceedings of the 1st National Symposium on Biomarkers in Animal Science and Veterinary Sciences – An Interdisciplinary Approach, March 31, Évora, Portugal.
Pomba C, Belas A, Salazar ASS, Gama LT, Couto N. Risk factors for faecal colonization with Escherichia coli producing extended-spectrum and plasmid-mediated AmpC beta-lactamases in dogs without antimicrobial pressure. Proceedings of the 24th European Congress of Veterinary Internal Medicine 2014, September 4-6, Mainz, Germany.
Marques C, Couto N, Belas A, Saial D, Delgado M, Pomba C. Emergence of Multidrug-Resistant Bacteria Causing Urinary Tract Infections in Companion Animals: A 14¬Year Retrospective Study in Portugal. Proceedings of the 24th ECVIM-CA 2014, September 4-6, Mainz, Germany.
Couto N, Kadlec K, Schwarz S, Pomba C. High frequency of the vga(A) gene among MRSA ST398 from pigs and humans in Portugal. Proceedings of the 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans, and the Environment 2012, June 26-29, Aix-en-Provence, France.
Centeno M, Loução F, Baptista FM, Couto N, Saraiva-Lima M, Pomba C. Fluoroquinolones selective pressure induces the increase of multidrug-resistant Escherichia coli isolates from calves. Proceedings of the 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans, and the Environment 2012, June 26-29, Aix-en-Provence, France.
Centeno M, Fernandes L, Couto N, Bessa R, Nunes T, Almeida V, Alban L, Pomba C. Effect of at-birth ceftiofur administration on commensal E. coli ESBL CTX-M genes in pigs from Portuguese industrial herds. Proceedings of the 3rd ASM Conference on Antimicrobial Resistance in Zoonotic Bacteria and Foodborne Pathogens in Animals, Humans, and the Environment 2012, June 26-29, Aix-en-Provence, France.
Pomba C, Couto N. Dissemination of the human pandemic ST131-O25B clone among uropathogenic Escherichia coli isolates from companion animals in Portugal. Proceedings of the 21st Annual Congress of Veterinary Internal Medicine (ECVIM-CA) 2011, September 8-10, Seville, Spain.
Kadlec K, Feßler AT, Couto N, Pomba C, Schwarz S. Characterization of a small apramycin resistance plasmid from porcine MRSA ST398 which carries a variant of the apmA gene. Proceedings of the ASM-ESCMID Conference on Methicillin-resistant Staphylococci in Animals: Veterinary and Public Health Implications 2011, September 8-11, Washington, United States of America.