Research Lab


Research Interests

Our research is focused on two main research topics: i) the ecology, evolution and dynamics of antimicrobial resistant bacteria through different niches and ii) the role of the urinary microbiota in human health and disease. We aim at understanding key fundamental aspects related to the selection and adaptation of bacterial populations to different hosts using conventional and cutting edge methodologies. Applied research is dedicated to the design and production of quick and inexpensive tools for the diagnosis, treatment, and prevention of diseases. Main goals are:

  • Identification of drivers involved or promoting antimicrobial resistance selection and dissemination in different niches - One Health approach
  • Elucidation of significant surface bacterial features as strain signatures and their potential role in host adaptation
  • Improve diagnostic methods for clinically relevant bacteria
  • Identify novel compounds with antimicrobial and anti-biofilm activity, and biotherapeutics
  • Understand the role of human urinary microbiota in health and disease
  • Improve industrial processes for the production of safe, sustainable and high quality food
Research Highlights
IR Bactyping: A bacterial strain typing method to support epidemiology and infection control in real-time

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IR Bactyping is an accurate (>95%), easy to implement and low-cost strain typing tool based on a biochemical fingerprint obtained by Fourier-Transform Infrared spectroscopy that can reduce by >75% the time-to-response (less than 24h) and by 90% the cost of analysis compared to reference typing methods. Because we have proprietary spectral databases, we are able to identify specific strain types that represent main and well-defined lineages involved in local or nationwide epidemics in multiple countries. Precise and timely strain type information is crucial to early identify outbreak events and particular high-risk clones and will contribute to support real-time surveillance, precise and effective infection control measures in healthcare settings.

Transfer of the technology is being supported by Hitech 2019 and BIP Proof 2019 programs. 




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State-of-the-art genomic tools unveiled a common chromosomal hotspot for optrA acquisition within Enterococcus faecalis genomes obtained from different countries

Enterococcus rank as one of the most common causes of nosocomial infections. In recent years, transferable genes conferring resistance to last-resort antibiotics as linezolid, especially optrA, emerged in different regions. We compared the genomes of optrA-carrying E. faecalis strains from disparate origins and countries, and identified phylogenetically related strains from human clinical and animal hosts in different continents. Morevoer, optrA was often associated with the same genetic element embedded within a large chromosomal platform conserved among hundreds of E. faecalis genomes and inserted into the same integration site in different strains, here proposed as a genetic hotspot for optrA integration. Our study suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains, anticipating a dramatic increase of optrA spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.

Comparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes


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AcCNET (Accessory Genome Constellation Network) analysis of the E. faecalis strains. The accessory genome network is represented by the origin of isolates. Each colour indicates a different origin as indicated in the figure key.

Representative Projects

  • SAFE Superbug Awareness for Education. EIT Health. Activity number 210809. Dates: 2021. Budget: 102945€. Luísa Peixe, Filipa Grosso (collaborators).
  • Setting-up biobanks and regenerative medicine strategies to boost research in neurosciences, immunology and infection, musculoskeletal, cardiovascular and oncologic diseases. Funding source: Norte Regional Operational Program. HEALTH-UNorte (NORTE-01-0145-FEDER-000039). 2020 – 2022. Budget: 117616€. Luísa Peixe, Ângela Novais, Filipa Grosso (collaborators).
  • AgriFood XXI. Development and consolidation of research in the agri-food sector in Northern Portugal. NORTE- 01-0145-FEDER-000041. NORTE-45-2020-20 - Sistema de Apoio à Investigação Científica e Tecnológica - “Projetos Estruturados de I&D&I” – UNorte. Dates: 2020-2023. Luísa Peixe, Carla Novais, Patrícia Antunes (collaborators).
  • IR Bactyping – Um serviço de identificação de tipos bacterianos para um apoio à epidemiologia e controlo de infeção em tempo real. BIP Proof award funded by Fundação Amadeu Dias. Dates: 2020-2021. Budget: 10000EUR. Ângela Novais (coordinator). Luísa Peixe, Ana R. Freitas, Teresa G. Ribeiro (collaborators).
  • Enterobacteriaceae multirresistentes: avaliação de um programa de vigilância e controlo implementado num hospital terciário universitário. Financing Source: Grupo de Infeção e Sepsis 2017. Dates: 2019-2020. Budget: 10000EUR. Luísa Peixe, Ângela Novais (collaborators).

Selected Publications

Magdalena Ksiezarek; Teresa Gonçalves Ribeiro; Joana Rocha; Filipa Grosso; Svetlana Ugarcina Perovic; Luisa Peixe. 2021. Limosilactobacillus urinaemulieris sp. nov. and Limosilactobacillus portuensis sp. nov. isolated from urine of healthy women. INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, DOI: 10.1099/ijsem.0.004726
Magdalena Ksiezarek; Svetlana Ugarcina-Perovic; Joana Rocha; Filipa Grosso; Luísa Peixe. 2021. Long-term stability of the urogenital microbiota of asymptomatic European women. BMC MICROBIOLOGY, DOI: 10.1186/s12866-021-02123-3
Freitas, AR; Tedim, AP; Duarte, B; Elghaieb, H; Abbassi, MS; Hassen, A; Read, A; Alves, V; Novais, C; Peixe, L. 2020. Linezolid-resistant (Tn6246::fexB-poxtA) Enterococcus faecium strains colonizing humans and bovines on different continents: similarity without epidemiological link. JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY, 75, DOI: 10.1093/jac/dkaa227
Mourao, J; Rebelo, A; Ribeiro, S; Peixe, L; Novais, C; Antunes, P. 2020. Tolerance to arsenic contaminant among multidrug-resistant and copper-tolerant Salmonella successful clones is associated with diverse ars operons and genetic contexts. ENVIRONMENTAL MICROBIOLOGY, DOI: 10.1111/1462-2920.15016
Antunes, P; Novais, C; Peixe, L. 2020. Food-to-Humans Bacterial Transmission. MICROBIOLOGY SPECTRUM, 8(1), DOI: 10.1128/microbiolspec.mtbp-0019-2016