Isabel Portugal

Bacterial Pathogenomics and Drug Resistance

Our research activity is focused on the molecular epidemiology, clinical impact of strain diversity and laboratory diagnosis of infectious diseases caused by bacterial pathogens, namely, mycobacteria and Gram-negative pathogens. Moreover, we also focus on the translation of genomic diversity and in-depth knowledge of resistance mechanisms towards development of novel products and computational tools.

Tuberculosis and other infectious diseases of bacterial etiology comprise still today a major cause of public health concern. This is further aggravated when the underlying pathogens acquire or evolve de novo resistance mechanisms and become unaffected by most treatment regimens and drugs that are available. We focus on this very problem and, with an area of interest spanning across the fields of clinical microbiology and genomics, we wish to elucidate bacterial mechanisms underlying diversification and adaptation processes with epidemiological and clinical relevance, along with the translation towards product development and novel computational tools or approaches.

Presently, our research area builds upon three main interconnected themes: i) translation of Mycobacterium tuberculosis Evolutionary Epidemiology and Diversity to Public Health and Product Development; ii) understanding the Clinical Impact of Bacterial Persistence and Latency on Drug Tolerance; and iii), Healthcare-associated Antimicrobial Resistance. These themes intend to bring together research carried on mycobacteria (including Mycobacterium tuberculosis and Non-Tuberculous Mycobacteria) and Gram-negative pathogens with the goal of providing an integrated and comprehensive approach towards the understanding of bacterial pathogenesis and adaptation. For this purpose, we employ not only state-of-the-art genome-wide approaches that encompass a strong computational component but also, high-throughput phenotypic characterization. We also focus on developing the potential of this approach to generate novel insights on the fundamental biology of these pathogens, which can be translated to a more adequate management of these infections at the public health level or through translational research towards new product development.

Moreover, the laboratory holds a large collection of clinically relevant bacterial strains and actively collaborates with different institutions and laboratories worldwide in the screening of active compounds with anti-bacterial or anti-tubercular activity as well as the elucidation of the mechanisms of action via genomic analysis.

Perdigão J, Silva C, Maltez F, Machado D, Miranda A, Couto I, Rabna P, Florez de Sessions P, Phelan J, Pain A, McNerney R, Hibberd M, Mokrousov I, Clark TG, Viveiros M, Portugal I. Emergence of multidrug resistant Mycobacterium tuberculosis of the Beijing lineage in Portugal and Guinea-Bissau: a snapshot of moving clones by whole-genome sequencing. Emerg Microbes Infect 2020 9(1). DOI: 10.1080/22221751.2020.1774425
Perdigão J, Modesto A, Pereira AL, Neto O, Matos V, Godinho A, Phelan J, Charleston J, Spadar A, Florez de Sessions P, Hibberd M, Campino S, Costa A, Fernandes F, Ferreira F, Correia AB, Gonçalves L, Clark TG, Duarte A. Whole genome sequencing resolves a polyclonal outbreak by extended-spectrum beta-Lactam and carbapenem resistant Klebsiella pneumoniae in a Portuguese tertiary-care hospital. Microbial Genomics; 2020, 7 (6). DOI: 10.1099/mgen.0.000349.
Perdigão J, Gomes P, Miranda A, Maltez F, Machado D, Silva C, Phelan JE, Brum L, Campino S, Couto I, Viveiros M, Clark TG, Portugal I. Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal. Scientific Reports; 2020, 10(2600) DOI: 10.1038/s41598-020-59558-3.
Brynilsrud O, Pepperell C, Suffys P, Grandjean L, Monteserin J, Debech N, Bohlin J, Alfsnes K, Petterson J, Kirkleite I, Fandinho F, da Silva M, Perdigao J, Portugal I, Viveiros M, Clark T, Caws M, Dunstan S, Thai P, Lopez B, Ritacco V, Kitchen A, Brown T, van Soolingen D, O’neill M, Holt K, Feil E, Mathema B, Balloux F, Eldholm V. Global expansion of Mycobacterium tuberculosis Lineage 4 shaped by colonial migration and local adaptation. Sci Adv; 2018, 4(10). DOI: 10.1126/sciadv.aat5869.
Coll F, Phelan J, Hill-Cawthorne GA, Nair M, Mallard K, Ali S, Abdallah A, Alghamdi S, Alsomali M, Ahmed A, Portelli S, Oppong Y, Alves A, Bessa T, Campino S, Caws M, Chatterjee A, Crampin A, Dheda K, Furnham N, Glynn J, Grandjean L, Há D, Hasan R, Hasan Z, Hibberd M, Joloba M, Jones-López, Matsumoto T, Miranda A, Moore D, Morcillo N, Panaiotov S, Parkhill J, Portugal I, Penha C, Perdigão J, Rchiad Z, Robledo J, Sheen P, Sesha N, Sirgel F, Sola C, Sousa E, Streicher E, Viveiros M, Warren R, McNerney R, Pain A, Clark T. Genome-wide analysis of multi- and extensively drug-resistant Mycobacterium tuberculosis. Nat Genet 2018 50(2. DOI: 10.1038/s41588-017-0029-0.

Isabel Portugal

Group Leader


Phone: (+351) 217946400 (Ext. 205)

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Faculdade de Farmácia da Universidade de Lisboa | Av. Professor Gama Pinto
1649-003 Lisboa | Portugal

Phone | +351 217 946 400
Fax | +351 217 946 470
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