Respiratory Infection and Antimicrobial Resistance

Group leader: Jose María Marimón Ortiz De Zárate, M.D., Ph.D.

Donostialdea IHO
Dr. José María Marimón Ortiz De Zárate completed his Degree in Pharmacy at the University of Santiago de Compostela (1989) and is a Doctor in Microbiology from the University of the Basque Country (UPV/EHU) in 2000. He is a Specialist in Clinical Microbiology and Parasitology via FIR (1992-1995). He has been Attending Physician of the Microbiology Service at the Donostia University Hospital (Donostialdea IHO) since 1997 and Head of the Molecular Biology and Automation Section since 2013.
Author of 95 publications in indexed journals ( (90 in international journals and 5 in national journals), 1 book chapter and director of 3 doctoral theses. More than 20 competitive national and international projects granted, one international patent and one diagnostic test commercialised.
Since 2011, he has been a teacher of the Master’s Degree of the Department of Preventive Medicine and Public Health at the UPV/EHU Faculty of Medicine. Collaborator with group 26 of the CIBERes (Network Centre for Biomedical Research in Respiratory Diseases) since June 2006 and its Head in 2017 and 2018. Member of the Board of Directors of the SEIMC from 2012 to 2015.
Dr. Marimón has been Head of the Respiratory Infection and Antimicrobial Resistance Group of the Infection Diseases Area of the Biodonostia HRI since 2017.

Strategic Objectives

Respiratory infection:

Main objective: to study the epidemiology of respiratory infection.

Streptococcus pneumoniae infection.

  • Invasive pneumococcal infection in children and adults: incidence, serotypes and genotypes.
  • Non-invasive pneumococcal infection: otitis and conjunctivitis. Serotypes and genotypes. Antibiotic resistance.
  • Vaccine studies. Impact of the 13-valent conjugate vaccine. Comparison with the 7-valent vaccine. Influence of child vaccination with the new 13-valent vaccine on invasive infections and on the naso-pharyngeal carriage in the early years of life.
  • Design of new pneumococcus typing techniques.
  • The role of pneumococcal biofilm in chronic respiratory infections (COPD).

Streptococcus pyogenes infection.

  • Incidence and characterisation of the strains causing non-invasive diseases: otitis and vaginitis resulting from S. pyogenes.
  • Pneumonia caused by S. pyogenes. Clinical-epidemiological aspects.
  • Phenotypic and genotypic characterisation of the isolated causes of pharyngitis. Study of antibiotic susceptibility.

Respiratory infection caused by a virus.

  • Infections caused by the influenza virus. Genetic characterisation of seasonal strains.
  • Epidemiology of the viruses causing flu syndrome other than the flu virus. Seasonality, hospitalisation and ages of maximum incidence of each one.
  • Value of viral infections in acute exacerbation of COPD.
  • Microbiological characteristics of emerging respiratory viruses: pandemic H1N1 influenza virus and H3N2 swine influenza virus, human metapneumovirus, bocavirus. Diagnosis and epidemiology of their infections
  • Characteristics of mixed infections from two or more respiratory viruses or between viruses and bacteria in cases of pneumonia.

Chronic obstructive pulmonary disease (COPD).

  • Value of new infections and re-infections in the exacerbation of COPD.
  • Bacterial or viral persistence in the respiratory tract of patients with COPD.
  • Role of antibiotic and antiviral treatment in the exacerbation.


  • Epidemiological study of tuberculosis in Gipuzkoa.
  • Application of molecular techniques to the diagnosis and study of anti-tuberculosis resistance directly carried out on clinical samples.
  • Comparison of phenotypic and genotypic techniques of antibiotic susceptibility in strains of Mycobacterium tuberculosis.
  • Molecular characterisation of the M. tuberculosis isolates: spoligotyping and MIRU-VNTR.

Bacterial resistance:

Main objective: epidemiology of antimicrobial resistance and the mechanisms (presence and dissemination) responsible for them.

Bacterial resistance in Gram-positive bacteria.

  • To determine the evolution of the antibiotic resistance of Streptococcus pneumoniae over time: new serotypes causing infection and their genetic determining factors of resistance; the influence of antibiotic consumption in the general population on resistance; the dissemination of multi-resistant clones after incorporating conjugate vaccines.
  • To verify the replacement of “resistant serotypes” as a result of the commercialisation of the 13-valent conjugate vaccine in 2010; influence of childhood vaccination on antibiotic resistance.
  • To establish the mechanisms of Streptococcus pyogenes resistance to macrolide, tetracycline and fluoroquinolone antibiotics.

The effect of prophylaxis with oral antiseptics in ICUs to prevent aspiration pneumonia. Prevalence and selection capacity of resistant microorganisms.

  • To discover the prevalence of resistance to disinfectants and resistances associated with other antimicrobials in Intensive Care Units (ICU).
  • Induction of resistance to in vitro antiseptics. Characterisation of the genes and mutations associated with resistance.
  • Phenotypic and genotypic characterisation of resistant isolates. To determine the phenomena of phenotypic adaptation or stable resistance and the biofilm formation capacity. Comparison of the metabolic profiles between sensitive and resistant strains.

Bacterial resistance in other microorganisms.

  • Prevalence of antimicrobial resistance in commensal microbiome and in zoonotic gastrointestinal pathogens. Molecular mechanisms responsible for resistance.
  • Characterisation of community-acquired bacterial pathogens and of the multidrug-resistant bacteria included in the PRAN (Action Plan on Microbial Resistance) by means of Whole Genome Sequencing (WGS).
  • Resistance in bacteria of hospital origin. Research into other multi-resistant bacteria with new resistance mechanisms: new carbapenemases, plasmid and constituent beta-lactamases.

Main lines of research

  • Respiratory infection:
    • Streptococcus pneumoniae infection.
    • Streptococcus pyogenes infection.
    • Respiratory infection caused by less common viruses and agents (Nocardia and Coxiella).
  • Antimicrobial resistance:
    • Bacterial resistance in respiratory pathogens.
    • Bacterial resistance in zoonotic pathogens that cause gastroenteritis.
    • Bacterial resistance. Other microorganisms.

Team Members

Name Surname
Center E-mail
Marta Alonso Asencor OSI Donostialdea
Maitane Aranzamendi Zaldunbide OSI Donostialdea
María Ercibengoa Arana Biodonostia HRI
Pedro Idigoras Viedma OSI Donostialdea
Ane Sorarrain Zarraga Biodonostia HRI
Diego Vicente Anza OSI Donostialdea
Loreto Vidaur Tello OSI Donostialdea

Scientific Output