Microbiology and Infection UNIT

Pilar Baylina, PhD

Team Coordination

Pilar Baylina, MEng, PhD
Pilar Baylina, MEng, PhD

Group Leader

Public Health Policies, Risk Management, Quality Management, Phage Biotechnologies

Ruben Fernandes, PhD
Ruben Fernandes, PhD

Senior Researcher

Microbial Stress Response, Virology and Cancer

Pedro Barata, PharmD. MD, PhD
Pedro Barata, PharmD. MD, PhD

Senior Researcher

Microbiome, Hyperbaric Oxygen Therapy

Daniela Mendes, MD, PhD
Daniela Mendes, MD, PhD

Senior Researcher

Diabetic Foot Infections, Hyperbaric Oxygen Therapy

Mónica Botelho, PhD
Mónica Botelho, PhD

Senior Researcher

Infection and Cancer, Parasitology


Carina Silva

Coelho Macedo, MD

Carla Guedes

Sara Sá

Claudio Lima

Diogo Ferreira

Cátia Almeida

Marco Oliveira

Rejane Viana

Jacinta Mendonça

Alexandra Aveiro

Marlene Veiga

Clara Dias

Sofia Lopes

Gonçalo Novais

Research Lines

1. Healthcare infection risk management

PI – Pilar Baylina, MEng, PhD

The development of control systems to sustain the level of healthcare-associated infections (HAIs) is an emerging issue for healthcare management. This is partly due to the perception that HAI became a serious negative impact factor on the performance of healthcare organizations and on related public health dimensions. Throughout the decade of 1990 a significant number of international programmes were developed to understand and to promote effective HAIs prevention and control systems. The research group is focus in HAI prevention, diagnostics, treatment and public health policies for its management.

2. Microbiome and dysbiosis

PI – Pedro Barata, MD, PhD

Normal Gut microbiota is an important mediator several physiological processes (eubiosis). Conversely alteration in number and diversity of certain taxa (dysbiosis) has emerged as implicated in the development and the outcomes of certain diseases.  Still far from being completely understood and analyzed is the complexity of this ecosystem. Certain medicines, such as antibiotics, alterations to lifestyle, stress are among the diversity of causes that disturbes microbiota. The research team is focusing in describing microbial biomarkers in dysbiosis of several conditions such as gut-metabolic axis, gut-brain axis, and gut-lung axis: metabolic syndrome, obesity, cardiovascular disease, pneumonia, mood and, neurogenerative diseases.

3. Diabetic foot infections

PI – Daniela Mendes Martins, MD, PhD

The diabetic foot is one of the major complications of this disease, with an estimated 10% to 25% of diabetic patients developing a diabetic foot ulcer (DFU) in their lifetimes causing a considerable burden in health care and patient well-being. Foot infections are common in patients with diabetes and are associated with high morbidity and risk of lower extremity amputation. Diabetic foot infections (DFIs) are classified as mild, moderate, or severe. DFIs aggravate with antibiotic resistance and with increased virulence of bacterial flora in the infected ulcer in particular due to biofilm formation. Staphylococcus aureus but gram-negative such as P. aeruginosa bacteria are most commonly pathogens causing biofilms. The research group is particular interested in new therapeutic approaches such as hyperbaric oxygen therapy, phage therapy and photodynamic therapy.

4. Antimicrobial Resistance

PI – Ruben Fernandes, PhD

The burden of antibiotics in the environment and in medical prescription is still a major matter of concern. Our group is focusing in drug resistance genes in the taxon of γ-proteobacteria in particular Enterobacteriaceae, Pseudomonacea and Vibrionaceae.

This group is interested in the enzymes conferring resistance to broad spectrum cephalosporins such as ESBL or AmpC and in permeation mechanisms such as mutation in porins or drug efflux pumps.

5. Biofilm formation and stress response

PI – Ruben Fernandes, PhD

Bacterial biofilms do serious harm to the diabetic foot ulcer because they play a crucial role in infection invasion and spread. Staphylococcus aureus and Pseudomonas aeruginosa the predominant Gram-positive and Gram-negative bacteria in diabetic foot infection and are often associated with colonization and biofilm formation.

Biofilm formation also prevents the access of the antibiotics to microbial agents that are causing infection.  Thus biofilm formation are bacteria defense mechanisms against antibiotics. Antibiotics trigger a genomic mechanism in bacteria that activate SOS response. Cell signaling in bacteria mediated by recA cascade activates several mechanism such as quorum sensing and biofilm formation.

6. Parasite infections and Cancer

PI – Mónica Botelho, PhD

Schistosoma haematobium, a parasitic flatworm that infects more than 100 million people, mostly in the developing world, is the causative agent of urogenital schistosomiasis, and is associated with a high incidence of squamous cell carcinoma (SCC) of the bladder. During infection, eggs are deposited in the bladder causing an intense inflammatory reaction. Thus, identifying biomarkers of this process plays an important role in the study of cancer. 

7. Viral infection and Cancer

PI – Ruben Fernandes, PhD

Viruses are associated with a great number of cancer cases. The human papillomaviruses (HPVs), cause cervical cancer and several other epithelial malignancies, and the hepatitis viruses HBV and HCV, which are responsible for the majority of hepatocellular cancer. Nevertheless, some viruses have receptor for some types of cancer, thus being considered as oncolytic virus. One recent example of oncolytic virus is SARS-CoV-2 which as been associated to remission of NK lymphomas. The ongoing research is exploring oncolytic effects of SARS-CoV-2.

8. Phage biotechnology

PI – Pilar Baylina, MEng, PhD

Bacteriophages or simply phages are bacteria infecting viruses. In terms of pharmaceutical classification in EU and United States, phages are considered as anti-infectious medicinal products and biological products, given the intended use and their live nature. Phages are envisioned for a variety of uses including (1) the biocontrol of pathogenic bacteria in agriculture and food industries, (2) the modulation of dysbiotic flora, (3) the eradication of pathogenic bacteria infecting humans or animals.

The research group is devoted to the bioprospecting of new phages intending to contribute to the control and phage therapy of drug resistant Gram-negative pathogens such as Pseudomonas spp. and Klebsiella spp., Salmonella entericaEscherichia coli, and Gram-positive Staphylococci and Streptococci.

Associated Facilities

Virology Lab

Microbiology Lab

Molecular Biology Lab

Cell culture Lab

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