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SCI papers since 2009


Publications of the "Antibiotic Resistance Lab" team members


Ferreira, C., Costa, S.S., Serrano, M., Oliveira, K., Trigueiro, G., Pomba, C., Couto, I., 2021. Clonal Lineages, Antimicrobial Resistance, and PVL Carriage of Staphylococcus aureus Associated to Skin and Soft-Tissue Infections from Ambulatory Patients in Portugal. Antibiotics-Basel 10, 345.


Belas, A., Menezes, J., Gama, L.T., Pomba, C., Consortium, P.E.-R., 2020. Sharing of clinically important antimicrobial resistance genes by companion animals and their human household members. Microbial Drug Resistance 26, 1174-1185.

Brilhante, M., Menezes, J., Belas, A., Feudi, C., Schwarz, S., Pomba, C., Perreten, V., 2020. OXA-181-Producing Extraintestinal Pathogenic Escherichia coli Sequence Type 410 Isolated from a Dog in Portugal. Antimicrobial Agents and Chemotherapy 64.

Cremers, N., Belas, A., Costa, S.S., Couto, I., de Rooster, H., Pomba, C., 2020. In vitro antimicrobial efficacy of two medical grade honey formulations against common high-risk meticillin-resistant staphylococci and Pseudomonas spp. pathogens. Vet. Dermatol. 31, 90-96. 

Lo Piccolo, F., Belas, A., Foti, M., Fisichella, V., Marques, C., Pomba, C., 2020. Detection of multidrug resistance and extended-spectrum/plasmid-mediated AmpC beta-lactamase genes in Enterobacteriaceae isolates from diseased cats in Italy. J. Feline Med. Surgery 22:613-622.

Rodrigues, I.B.B.E., Silva, R.L., Menezes, J., Machado, S.C.A., Rodrigues, D.P., Pomba, C., Abreu, D.L.C., Nascimento, E.R., Aquino, M.H.C., Pereira, V.L.A., 2020. High Prevalence of Multidrug-Resistant Nontyphoidal Salmonella Recovered from Broiler Chickens and Chicken Carcasses in Brazil. Brazilian J. Poultry Sci. 22.


Belas, A., Marques, C., Aboim, C., Pomba, C., 2019. Emergence of Escherichia coli ST131 H30/H30-Rx subclones in companion animals. J. Antimicrob. Chemother. 74, 266-269.

Khemiri, M., Abbassi, M.S., Elghaieb, H., Zouari, M., Dhahri, R., Pomba, C., Hammami, S., 2019. High occurrence of enterotoxigenic isolates and low antibiotic resistance rates of Staphylococcus aureus isolated from raw milk from cows and ewes. Lett. Appl. Microbiol. 68, 573-579.

Marques, C., Belas, A., Aboim, C., Cavaco-Silva, P., Trigueiro, G., Gama, L.T., Pomba, C., 2019. Evidence of sharing of Klebsiella pneumoniae strains between healthy companion animals and cohabiting humans. J. Clin. Microbiol. 57.

Marques, C., Belas, A., Aboim, C., Trigueiro, G., Cavaco-Silva, P., Gama, L.T., Pomba, C., 2019. Clonal relatedness of Proteus mirabilis strains causing urinary tract infections in companion animals and humans. Vet Microbiol 228, 77-82.

Marques, C., Menezes, J., Belas, A., Aboim, C., Cavaco-Silva, P., Trigueiro, G., Gama, L.T., Pomba, C., 2019. Klebsiella pneumoniae causing urinary tract infections in companion animals and humans: population structure, antimicrobial resistance and virulence genes. J. Antimicrob. Chemother. 74, 594-602.



Costa, S.S., Viveiros, M., Pomba, C., Couto, I., 2018. Active antimicrobial efflux in Staphylococcus epidermidis: building up of resistance to fluoroquinolones and biocides in a major opportunistic pathogen. J. Antimicrob. Chemother. 73, 320-324.

Francisco, M., Costa, S.S., Belas, A., Ramos, J., Couto, I., Pomba, C., Viveiros, M., 2018. First report on antimicrobial resistance and molecular characterisation of Salmonella enterica serotype Typhi isolated from human specimens in Luanda, Angola. J. Glob. Antimicrob. Resist. 13, 246-249.

Marques, C., Belas, A., Franco, A., Aboim, C., Gama, L.T., Pomba, C., 2018. Increase in antimicrobial resistance and emergence of major international high-risk clonal lineages in dogs and cats with urinary tract infection: 16 year retrospective study. J. Antimicrob. Chemother. 73, 377-384.

Khemiria, M., Abbassi, M.S., Couto, N., Mansouri, R., Hammami, S., Pomba, C., 2018. Genetic characterisation of Staphylococcus aureus isolated from milk and nasal samples of healthy cows in Tunisia: First report of ST97-t267-agrI-SCCmecV MRSA of bovine origin in Tunisia. J. Glob. Antimicrob. Resist. 14, 161-165.

Pomba, C., Catry, B., Edo, J.T., Jukes, H., 2018. Licensing and Approval of Antimicrobial Agents for Use in Animals. Microbiol. Spectr. 6.

Rodrigues, A.C., Belas, A., Marques, C., Cruz, L., Gama, L.T., Pomba, C., 2018. Risk Factors for Nasal Colonization by Methicillin-Resistant Staphylococci in Healthy Humans in Professional Daily Contact with Companion Animals in Portugal. Microb Drug Resist 24, 434-446.



Khemiri, M., Alhusain, A.A., Abbassi, M.S., El Ghaieb, H., Costa, S.S., Belas, A., Pomba, C., Hammami, S., 2017. Clonal spread of methicillin-resistant Staphylococcus aureus-t6065-CC5-SCCmecV-agrII in a Libyan hospital. J. Glob. Antimicrob. Resist. 10, 101-105.

Koop, G., Vrieling, M., Storisteanu, D.M.L., Lok, L.S.C., Monie, T., van Wigcheren, G., Raisen, C., Ba, X.L., Gleadall, N., Hadjirin, N., Timmerman, A.J., Wagenaar, J.A., Klunder, H.M., Fitzgerald, J.R., Zadoks, R., Paterson, G.K., Torres, C., Waller, A.S., Loeffler, A., Loncaric, I., Hoet, A.E., Bergstrom, K., De Martino, L., Pomba, C., de Lencastre, H., Ben Slama, K., Gharsa, H., Richardson, E.J., Chilvers, E.R., de Haas, C., van Kessel, K., van Strijp, J.A.G., Harrison, E.M., Holmes, M.A., 2017. Identification of LukPQ, a novel, equid-adapted leukocidin of Staphylococcus aureus. Scientific Reports 7, 40660.

Pomba, C., Rantala, M., Greko, C., Baptiste, K.E., Catry, B., van Duijkeren, E., Mateus, A., Moreno, M.A., Pyorala, S., Ruzauskas, M., Sanders, P., Teale, C., Threlfall, E.J., Kunsagi, Z., Torren-Edo, J., Jukes, H., Torneke, K., 2017. Public health risk of antimicrobial resistance transfer from companion animals. J. Antimicrob. Chemother. 72, 957-968.

Cormican, M., Hopkins, S., Jarlier, V., Reilly, J., Simonsen, G.S., Strauss, R., Vandenberg, O., Zabicka, D., Zarb, P., Catchpole, M., Heuer, O., Iosifidis, E., Monnet, D., Plachouras, D., Weist, K., Ricci, A., Allende, A., Bolton, D., Chemaly, M., Davies, R., Escamez, P.S.F., Girones, R., Herman, L., Koutsoumanis, K., Lindqvist, R., Norrung, B., Robertson, L., Ru, G., Sanaa, M., Simmons, M., Skandamis, P., Snary, E., Speybroeck, N., Ter Kuile, B., Threlfall, J., Wahlstrom, H., Tenhagen, B.A., Teale, C., Schuepbach, G., Beloeil, P.A., Liebana, E., Stella, P., Murphy, D., Hauser, B., Urbain, B., Kozhuharov, E.I., Bozic, F., Michaelidou-Patsia, A., Bures, J., Vestergaard, E.M., Baptiste, K., Tiirats, T., Nevalainen, M., Rouby, J.C., Hahn, G., Schlumbohm, W., Malemis, I., Kulcsar, G., Lenhardsson, J.M., Beechinor, J.G., Breathnach, R., Pasquali, P., Auce, Z., Maciulskis, P., Schmit, M., Spiteri, S., Schefferlie, G.J., Hekman, P., Bergendahl, H., Swiezcicka, A.W., Da Silva, J.P.D., Taban, L.S.C., Hederova, J., Straus, K., Madero, C.M., Persson, E.L., Jukes, H., Weeks, J., Kivilahti-Mantyla, K., Moulin, G., Wallmann, J., Grave, K., Greko, C., Munoz, C., Bouchard, D., Catry, B., Moreno, M.A., Pomba, C., Rantala, M., Ruzauskas, M., Sanders, P., Schwarz, C., Teale, C., van Duijkeren, E., Wester, A.L., Ignate, K., Kunsagi, Z., Torren-Edo, J., 2017. ECDC, EFSA and EMA Joint Scientific Opinion on a list of outcome indicators as regards surveillance of antimicrobial resistance and antimicrobial consumption in humans and food-producing animals. EFSA Journal 15, 70.



Alho, A.M., Pontes, J., Pomba, C., 2016. Guardians' Knowledge and Husbandry Practices of Feline Environmental Enrichment. Journal of Applied Animal Welfare Science 19, 115-125.

Couto, N., Belas, A., Oliveira, M., Almeida, P., Clemente, C., Pomba, C. 2016. Comparative RNA-seq-based transcriptome analysis of the virulence characteristics of methicillin-resistant and -susceptible Staphylococcus pseudintermedius strains isolated from small animals. Antimicrob. Agents Chemother. 60:962-967.

Couto, N., Martins, J., Lourenco, A.M., Pomba, C., Varela, A. 2016. Identification of vaccine candidate antigens of Staphylococcus pseudintermedius by whole proteome characterization and serological proteomic analyses. J. Proteomics 133:113-124 

Couto, N., Belas, A., Rodrigues, C., Schwarz, S., Pomba, C., 2016. Acquisition of the fexA and cfr genes in Staphylococcus pseudintermedius during florfenicol treatment of canine pyoderma. J. Glob. Antimicrob. Resist. 7, 126-127.

Couto, N., Monchique, C., Belas, A., Marques, C., Gama, L.T., Pomba, C., 2016. Trends and molecular mechanisms of antimicrobial resistance in clinical staphylococci isolated from companion animals over a 16 year period. J. Antimicrob. Chemother. 71, 1479-1487.

Fernandes, L., Centeno, M.M., Couto, N., Nunes, T., Almeida, V., Alban, L., Pomba, C., 2016. Longitudinal characterization of monophasic Salmonella Typhimurium throughout the pig's life cycle. Vet, Microbiol, 192, 231-237.

Figueiredo, R., Card, R.M., Nunez, J., Pomba, C., Mendonca, N., Anjum, M.F., Da Silva, G.J., 2016. Detection of an mcr-1-encoding plasmid mediating colistin resistance in Salmonella enterica from retail meat in Portugal. J. Antimicrob. Chemother. 71, 2338-2340.

Gaglio, R., Couto, N., Marques, C., Lopes, M.D.S., Moschetti, G., Pomba, C., Settanni, L., 2016. Evaluation of antimicrobial resistance and virulence of enterococci from equipment surfaces, raw materials, and traditional cheeses. Int. J. Food Microbiol. 236, 107-114.

Maruhashi, E., Sao Braz, B., Nunes, T., Pomba, C., Belas, A., Duarte-Correia, J.H., Lourenco, A.M., 2016. Efficacy of medical grade honey in the management of canine otitis externa - a pilot study. Vet. Dermatol. 27, 93-E27.

Ruzauskas, M., Couto, N., Pavilonis, A., Klimiene, I., Siugzdiniene, R., Virgailis, M., Vaskeviciute, L., Anskiene, L., Pomba, C., 2016. Characterization of Staphylococcus pseudintermedius isolated from diseased dogs in Lithuania. Pol. J. Vet. Sci. 19, 7-14.



Couto, N., Belas, A., Kadlec, K., Schwarz, S., Pomba, C. 2015. Clonal diversity, virulence patterns and antimicrobial and biocide susceptibility among human, animal and environmental MRSA in Portugal. J. Antimicrob. Chemother. 70:2483-2487.

Catry, B., Cavaleri, M., Baptiste, K., Grave, K., Grein, K., Holm, A., Jukes, H., Liebana, E., Lopez Navas, A., Mackay, D., Magiorakos, A.-P., Moreno Romo, M.A., Moulin, G., Munoz Madero, C., Matias Ferreira Pomba, M.C., Powell, M., Pyorala, S., Rantala, M., Ruzauskas, M., Sanders, P., Teale, C., Threlfall, E.J., Torneke, K., van Duijkeren, E., Torren Edo, J., 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, 297-306.

Ruzauskas, M., Couto, N., Kerziene, S., Siugzdiniene, R., Klimiene, I., Virgailis, M., Pomba, C., 2015a. Prevalence, species distribution and antimicrobial resistance patterns of methicillin-resistant staphylococci in Lithuanian pet animals. Acta Veterinaria Scandinavica 57.

Ruzauskas, M., Couto, N., Siugzdiniene, R., Klimiene, I., Virgailis, M., Vaskeviciute, L., Mockeliunas, R., Pomba, C., 2015. Methicillin-resistant coagulase-negative Staphylococcus spp. prevalence in Lithuanian dogs: a cross-sectional study. Veterinarski Arhiv 85, 175-187.



Couto, N., Belas, A., Centeno, M., van Duijkeren, E., Pomba, C. 2014. First description of fexA-positive meticillin-resistant Staphylococcus aureus ST398 from calves in Portugal. J. Global. Antimicrob. Resist.  (in press).

van Duijkeren, E., Greko, C., Pringle, M., Baptiste, K.E., Catry, B., Jukes, H., Moreno, M.A., Pomba, M.C., Pyörälä, S., Rantala, M., Ružauskas, M., Sanders, P., Teale, C., Threlfall, E.J., Torren-Edo, J., Törneke, K. 2014. Pleuromutilins: use in food-producing animals in the European Union, development of resistance and impact on human and animal health. J. Antimicrob. Chemother. 69:2022-2031.

Pyörälä, S., Baptiste, K.E., Catry, B., van Duijkeren, E., Greko, C., Moreno, M.A., Pomba, M.C., Rantala, M., Ružauskas, M., Sanders, P., Threlfall, E.J., Torren-Edo, J., Törneke, K. 2014. Macrolides and lincosamides in cattle and pigs: use and development of antimicrobial resistance. Vet. J. 200:230-239.

Oliveira, M., Dias, F.R., Pomba, C. 2014. Biofilm and fluoroquinolone resistance of canine Escherichia coli uropathogenic isolates. BMC Res. Notes. 7:499.

Belas, A., Salazar, A.S., Gama, L.T., Couto, N., Pomba, C. 2014. Risk factors for faecal colonisation with Escherichia coli producing extended-spectrum and plasmid-mediated AmpC β-lactamases in dogs. Vet. Rec. 175:202.

Pomba, C., Endimiani, A., Rossano, A., Saial, D., Couto, N., Perreten, V. 2014. First report of OXA-23-mediated carbapenem resistance in sequence type 2 multidrug-resistant Acinetobacter baumannii associated with urinary tract infection in a catAntimicrob. Agents Chemother. 58:1267-1268.

Pomba, C., López-Cerero, L., Bellido, M., Serrano, L., Belas, A., Couto, N., Cavaco-Silva, P., Rodríguez-Baño, J., Pascual, A. 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.

Couto, N., Belas, A., Couto, I., Perreten, V., Pomba, C. 2014. Genetic relatedness, antimicrobial and biocide susceptibility comparative analysis of methicillin-resistant and -susceptible Staphylococcus pseudintermedius from Portugal. Microb. Drug Resist. 20:364-371.



Couto, N., Belas, A., Tilley, P., Couto, I., Gama, L.T., Kadlec, K., Schwarz, S., Pomba, C. 2013. Biocide and antimicrobial susceptibility of methicillin-resistant staphylococcal isolates from horses. Vet. Microbiol. 166:299-303.

Ruzauskas, M., Couto, N., Belas, A., Klimiene, I., Siugzdiniene, R., Pomba, C. 2013. First report of swine-associated methicillin-resistant Staphylococcus aureus ST398 in Lithuania. Pol. J .Vet. Sci. 16:125-127.

Pinho, M.D., Matos, S.C., Pomba, C., Lübke-Becker, A., Wieler, L.H., Preziuso, S., Melo-Cristino, J., Ramirez, M. 2013. Multilocus sequence analysis of Streptococcus canis confirms the zoonotic origin of human infections and reveals genetic exchange with Streptococcus dysgalactiae subsp. equisimilis. J. Clin. Microbiol. 51:1099-109.

Braga, T.M., Pomba, C., Lopes, M.F. 2013. High-level vancomycin resistant Enterococcus faecium related to humans and pigs found in dust from pig breeding facilities. Vet. Microbiol. 161:344-349.



Fernandes, L., Centeno, M., Belas, A., Nunes, T., Lopes Alves, P., Couto, N., Pomba, C. 2012. Immediate after birth transmission of epidemic Salmonella enterica Typhimurium monophasic strains in pigs is a likely event. J. Antimicrob. Chemother. 67:3012-3014.

Kadlec, K., Feßler, A.T., Couto, N., Pomba, C.F., Schwarz, S. 2012. Unusual small plasmids carrying the novel resistance genes dfrK or apmA isolated from methicillin-resistant or -susceptible staphylococci. J. Antimicrob. Chemother. 67:2342-2345.

Price, L.B., Stegger, M., Hasman, H., Aziz, M., Larsen, J., Andersen, P.S., Pearson, T., Waters, A.E., Foster, J.T., Schupp, J., Gillece, J., Driebe, E., Liu, C.M., Springer, B., Zdovc, I., Battisti, A., Franco, A., Zmudzki, J., Schwarz, S., Butaye, P., Jouy, E., Pomba, C., Porrero, M.C., Ruimy, R., Smith, T.C., Robinson, D.A., Weese, J.S., Arriola, C.S., Yu, F., Laurent, F., Keim, P., Skov, R., Aarestrup, F.M. 2012. Staphylococcus aureus CC398: host adaptation and emergence of methicillin resistance in livestock. MBio. 3(1). pii: e00305-11.



van Duijkeren, E., Catry, B., Greko, C., Moreno, M.A., Pomba, M.C., Pyörälä, S., Ruzauskas, M., Sanders, P., Threlfall, E.J., Torren-Edo, J., Törneke, K.; Scientific Advisory Group on Antimicrobials (SAGAM). 2011. Review on methicillin-resistant Staphylococcus pseudintermedius. J. Antimicrob. Chemother. 66(12):2705-14.

Couto, N., Pomba, C., Moodley, A., Guardabassi, L. 2011. Prevalence of meticillin-resistant staphylococci among dogs and cats at a veterinary teaching hospital in Portugal. Vet. Rec. 169:72.

Braga, T.M., Marujo, P.E., Pomba, C., Lopes, M.F. 2011. Involvement, and dissemination, of the enterococcal small multidrug resistance transporter QacZ in resistance to quaternary ammonium compounds. J. Antimicrob. Chemother. 66:283-286.



Baptista, F.M., Alban, L., Nielsen, L.R., Domingos, I., Pomba, C., Almeida, V. 2010. Use of herd information for predicting Salmonella status in pig herds. Zoonoses Public Health 57 Suppl 1:49-59.

Kadlec, K., Pomba, C.F., Couto, N., Schwarz, S. 2010. Small plasmids carrying vga(A) or vga(C) genes mediate resistance to lincosamides, pleuromutilins and streptogramin A antibiotics in methicillin-resistant Staphylococcus aureus ST398 from swineJ. Antimicrob. Chemother. 65:2692-2693.

Pomba, C., Baptista, F.M., Couto, N., Loução, F., Hasman, H. 2010. Methicillin-resistant Staphylococcus aureus CC398 isolates with indistinguishable ApaI restriction patterns in colonized and infected pigs and humans. J. Antimicrob. Chemother. 65:2479-2481.

Pomba, C., Couto, N., Moodley, A. 2010. Treatment of a lower urinary tract infection in a cat caused by a multi-drug methicillin-resistant Staphylococcus pseudintermedius and Enterococcus faecalis. J. Feline Med. Surg. 12:802-806.

Catry, B., van Duijkeren, E., Pomba, M.C., Greko, C., Moreno, M.A., Pyörälä, S., Ruzauskas, M., Sanders, P., Threlfall, E.J., Ungemach, F., Törneke, K., Munoz-Madero, C., Torren-Edo, J.; Scientific Advisory Group on Antimicrobials (SAGAM). 2010. Reflection paper on MRSA in food-producing and companion animals: epidemiology and control options for human and animal health. Epidemiol. Infect. 138:626-644.



Pyörälä, S., Greko, C., Pomba, M.C. 2009. Use of glycopeptides in veterinary medicine. Vet. Rec. 165:543.

Pomba, C., Hasman, H., Cavaco, L.M., da Fonseca, J.D., Aarestrup, F.M. 2009. First description of meticillin-resistant Staphylococcus aureus (MRSA) CC30 and CC398 from swine in Portugal. Int. J .Antimicrob. Agents. 34:193-194.

Pomba, C., da Fonseca, J.D., Baptista, B.C., Correia, J.D., Martínez-Martínez, L. 2009. Detection of the pandemic O25-ST131 human virulent Escherichia coli CTX-M-15-producing clone harboring the qnrB2 and aac(6')-Ib-cr genes in a dog. Antimicrob. Agents Chemother. 53:327-328. (DOI: 10.1128/AAC.00896-08).