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Lab Overview

Our research focus on the study of the antimicrobial treatment of multidrug-resistant bacterial infections in animals and the public health repercussions of the clonal dispersal of these pathogens, their resistance and virulence genes. By studying the transmission dynamics (animal-to-human and vice-versa) we want to determine if and how this transmission occurs. This knowledge will deliver measures that can be applied to break the transmission cycle and thus support new antimicrobial stewardship polices. Moreover, the group is also interested in host-pathogen interactions, with the aim of identifying new potential targets for the treatment of bacterial infections. We use conventional microbiological and molecular methods, namely next generation sequencing, to:

  • characterize the resistome and microbiome of animals and humans in contact;
  • assess the epidemiological relatedness of animal and human bacterial isolates by whole-genome sequencing;
  • determine risk factors for infection/colonization by multidrug-resistant bacteria in animals;
  • update the surveillance of antimicrobial and biocide resistance in pathogenic bacteria;
  • develop new therapeutic approaches for the treatment of multidrug-resistant bacteria infections.

Highlights in the period


- Antimicrobial-resistance in Gram-negative bacteria.

We described, for the first time, the OXA-23 carbapenemase in Acinetobacter baumanni ST2 from a cat with urinary tract infection (Pomba et al., 2014). Some variation within the E. coli ST131 lineage have been associated with clonal commonality across strains isolated from humans and pets (Pomba et al. , 2014). A multicenter study comprising 16 clinical microbiology laboratories from 14 European countries revealed significant differences in the antimicrobial resistance frequencies of bacteria causing urinary tract infection in companion animals across Europe (Marques et al., 2016). A cross sectional study revealed that prior antimicrobial use (last year) in healthy dogs is a risk factor for colonization by ESBL/AmpC-producing E. coli (Belas et al. , 2014).

- Antimicrobial-resistance in Gram-positive bacteria.

The antimicrobial resistance of staphylococci from companion animal infections increased significantly over the last 16 years (Couto et al., 2016). Methicillin-resistant Staphylococcus aureus (MRSA) clonal complex 5 were described in animals from Portugal for the first time (Couto et al. J Antimicrob Chemother, 2015). Acquisition of the fexA and cfr gene in S. pseudintermedius was observed during florfenicol treatment in a dog (Couto et al., 2016).

- Advances in the therapeutics

We identified 4 highly immunogenic proteins that seem promising vaccine candidate antigens of Staphylococcus pseudintermedius by serological proteome analysis (Couto et al., 2016).

 Selected Publications


Marques C et al. 2016. European multicenter study on antimicrobial resistance in bacteria isolated from companion animal urinary tract infections. BMC Veterinary Research.12(1):213.

Fernandes L et al. 2016. Longitudinal characterization of monophasic Salmonella Typhimurium throughout the pig's life cycle. Vet Microbiol.192:231-237. 

Couto N et al. 2016. Identification of vaccine candidate antigens of Staphylococcus pseudintermediusby whole proteome characterization and serological proteomic analyses. J Proteomics.133:113-124.

Couto N et al. 2016. Trends and molecular mechanisms of antimicrobial resistance in clinical staphylococci isolated from companion animals over a 16 year period. J Antimicrob Chemother.71(6):1479-87.

Couto N et al. 2016 Acquisition of the fexA and cfr genes in Staphylococcus pseudintermediusduring florfenicol treatment of canine pyoderma. J Glob Antimicrob Resist.7:126-127.

Catry B et al. 2015. Use of colistin-containing products within the European Union and European Economic Area (EU/EEA): development of resistance in animals and possible impact on human and animal health. Int J Antimicrob Agents. 46(3):297-306.

Pomba C et al. 2014. First report of OXA-23-mediated carbapenem resistance in sequence type 2 multidrug-resistant Acinetobacter baumanniiassociated with urinary tract infection in a cat. Antimicrob. Agents Chemother.58:1267-1268.

Pomba C et al. 2014. Within-lineage variability of ST131 Escherichia coli isolates from humans and companion animals in the south of Europe. J. Antimicrob.  Chemother.69:271-273.

Belas A et al. 2014. Risk factors for faecal colonisation with Escherichia coli producing extended-spectrum and plasmid-mediated AmpC β-lactamases in dogs. Vet Rec.30;175(8):202.


Relevant cooperations


  • Annete Loeffer- UK - Small Animal Medicine and Surgery Group, The Royal Veterinary College
  • Scott Weese-Canada- Ontario Veterinary College at the University of Guelph
  • Stefan Swartz - Alemanha- Institute of Microbiology and Epizootics Centre of Infection Medicine Department of Veterinary Medicine Freie Universität Berlin
  • Vicent Perreten- Suiça- Institute of Veterinary Bacteriology, University of Bern.
  • José Melo-Cristino, Mário Ramirez, João Carriço -Instituto de Medicina Molecular, Universidade de Lisboa, Portugal.
  • Gabriela da Silva, Faculdade de Farmácia, Universidade de Coimbra, Portugal.
  • Patrícia Cavaco-Silva- Centro de Investigação Interdisciplinar Egas Moniz Instituto Universitário Egas Moniz, Portugal.
  • Miguel Viveiros, Isabel Couto - Instituto de Higiene e Medicina Tropical, Universidade Nova de Lisboa, Portugal.
  • Luís Telo da Gama, Animal Genetic Resources, CIISA, University of Lisbon