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
Molecular evolution of clinically relevant antimicrobial resistant bacteria by a One Health approach

Main contributions in antimicrobial resistance studies included:


i) the detection of emergent genes conferring resistance to last-resource antibiotics in human medicine (blaKPC-3, mcr, optrA, blaCMY-2) (Mendes et al. 2018, Freitas et al., 2017, Campos et al. 2018);

ii) association of particular virulence gene profiles with colonization/infection potential in Enterococcus faecium and Klebsiella pneumoniae (Freitas et al. 2018a and 2018b, Andrade et al., 2018);

iii) identification of new mobile genetic platforms carrying antibiotic resistance, biocide tolerance and/or virulence genes (Silva et al. 2018, Botelho et al. 2018a and 2018b and 2017);

iv) identification of new bacterial species carrying intrinsic antibiotic resistance genes (Ribeiro et al. 2017a and 2017b);



Alignment of representative IncX4 plasmids carrying the mcr-1 gene conferring resistance to colistin, a last-resource antibiotic. The pM1A_X4 plasmid was used as reference plasmid and comparison was performed using BRIG software.


Development and optimization of tools for diagnosis of disease-associated bacteria

Applied research contributed to the development of methods (MALDI-TOF MS, FT-IR) with increased resolution, turnaround time and sensitivity at a low cost for the differentiation and identification of bacterial groups (clones or serogroups/serotypes) from clinically relevant species with applications in clinical, veterinary or food industry sectors (Campos et al. 2018, Freitas et al. 2017, Rodrigues et al. 2017). Furthermore, the improvement of the sensitivity of culturomics and metagenomics protocols allowed to capture a higher bacterial diversity in urinary microbiota.



Discrimination of main non-typhoid Salmonella serogroups by a Partial Least Square Discriminant Analysis (PLSDA) model using Fourier-Transform Infrared spectral data.


Representative Projects

  • “Enterobacteriaceae multirresistentes: avaliação de um programa de vigilância e controlo implementado num hospital terciário universitário”, Grupo de Infeção e Sepsis. 2018-2019. Total funding: €10,000, Luísa Peixe (Co-PI).
  • “SafeFood: Development of a novel industrial process for safe, sustainable and higher quality foods, using biotechnology and cybernetic approach”, EC-ERA-Net. Total funding: €1.8M, Unit funding: €110,000, Luísa Peixe (PI).
  • “New technologies for three Health Challenges of Modern Societies: Diabetes, Drug Abuse and Kidney (DESignBIOtecHealth)”, FEDER-Norte 2020, Total funding: €3.4M, Unit funding: €401,348, Luísa Peixe (Collaborator).
  • “Qualidade e Segurança Alimentar – uma abordagem (nano)tecnológica”, FEDER-Norte 2020, Total funding: €3,7M, Unit funding: €801,412, Luísa Peixe (Collaborator).
  • “Discrimination of Salmonella non-typhoid high-risk clones by high-throughput spectroscopic techniques (MALDI-TOF and FTIR-ATR)”, ESCMID, Total and Unit funding: €30,000, Luísa Peixe (PI).

Selected Publications

Bender, JK; Cattoir, V; Hegstad, K; Sadowy, E; Coque, TM; Westh, H; Hammerum, AM; Schaffer, K; Burns, K; Murchan, S; Novais, C; Freitas, AR; Peixe, L; Del Grosso, M; Pantosti, A; Werner, G. 2018. Update on prevalence and mechanisms of resistance to linezolid, tigecycline and daptomycin in enterococci in Europe: Towards a common nomenclature. DRUG RESISTANCE UPDATES, 40, DOI: 10.1016/j.drup.2018.10.002
Oravcova, V; Peixe, L; Coque, TM; Novais, C; Francia, MV; Literak, I; Freitas, AR. 2018. Wild corvid birds colonized with vancomycin-resistant Enterococcus faecium of human origin harbor epidemic vanA plasmids. ENVIRONMENT INTERNATIONAL, 118, DOI: 10.1016/j.envint.2018.05.039
Campos, J; Sousa, C; Mourao, J; Lopes, J; Antunes, P; Peixe, L. 2018. Discrimination of non-typhoid Salmonella serogroups and serotypes by Fourier Transform Infrared Spectroscopy: A comprehensive analysis. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY, 285, DOI: 10.1016/j.ijfoodmicro.2018.07.005
Antunes, P; Campos, J; Mourao, J; Pereira, J; Novais, C; Peixe, L. 2018. Inflow water is a major source of trout farming contamination with Salmonella and multidrug resistant bacteria. SCIENCE OF THE TOTAL ENVIRONMENT, 642, DOI: 10.1016/j.scitotenv.2018.06.143
Novais, C; Campos, J; Freitas, AR; Barros, M; Silveira, E; Coque, TM; Antunes, P; Peixe, L. 2018. Water supply and feed as sources of antimicrobial-resistant Enterococcus spp. in aquacultures of rainbow trout (Oncorhyncus mykiss), Portugal. SCIENCE OF THE TOTAL ENVIRONMENT, 625, DOI: 10.1016/j.scitotenv.2017.12.265