Respiratory Infection and Antimicrobial Resistance

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

Donostialdea IHO

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 gastrointestinal pathogens. Molecular mechanisms responsible for resistance.
  • To detect antimicrobial resistance in the isolated zoonotic pathogens of animals or human patients (e.g. metallo beta-lactamases).
  • 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 Donostialdea IHO
María Ercibengoa Arana Donostialdea IHO
María Fernandez-Reyes Silvestre Donostialdea IHO
Eduardo González Pérez – Yarza Donostialdea IHO
Pedro Idigoras Viedma Donostialdea IHO
Jose María Marimón Ortiz De Zárate Donostialdea IHO
Esther Tamayo Oya Donostialdea IHO
Diego Vicente Anza Donostialdea IHO
Loreto Vidaur Tello Donostialdea IHO


Scientific Output


Published: 10 / 105

Helicobacter pylori resistance to antibiotics in Europe and its relationship to antibiotic consumption.

Megraud F, Coenen S, Versporten A, Kist M, Lopez-Brea M, Hirschl AM, Andersen LP, Goossens H, Glupczynski Y, Study Grp Participants.

Gut. 2013; 62: 34-42. FI: 10.732 (Q1).

DALI: defining antibiotic levels in intensive care unit patients: are current ß-lactam antibiotic doses sufficient for critically ill patients?

Roberts JA, Paul SK, Akova M, Bassetti M, De Waele JJ, Dimopoulos G, Kaukonen KM, Koulenti D, Martin C, Montravers P, Rello J, Rhodes A, Starr T, Wallis SC, Lipman J.

Clin Infect Dis. 2014; 58: 1072-1083. FI: 9.416 (Q1).

Influenza Vaccine Effectiveness in Preventing Outpatient, Inpatient, and Severe Cases of Laboratory-Confirmed Influenza.

Castilla J, Godoy P, Dominguez A, Martinez-Baz I, Astray J, Martin V, Delgado-Rodriguez M, Baricot M, Soldevila N, Mayoral JM, Quintana JM, Galan JC, Castro A, Gonzalez-Candelas F, Garin O, Saez M, Tamames S, Pumarola T, CIBERESP Cases Controls Influenza.

Clin. Infect. Dis. 2013; 57: 167-175. FI: 9.374 (Q1).

HTLV Spanish Study Grp. Development of Tropical Spastic Paraparesis in Human T-Lymphotropic Virus Type 1 Carriers Is Influenced by Interleukin 28B Gene Polymorphisms.

Treviño A, López, M, Vispo E, Aguilera A, Ramos JM, Benito R, Roc L, Eiros JM, De Mendoza C, Soriano V.

Clin. Infect. Dis. 2012; 55: 1-4. FI: 9.154 (Q1).

Do fast foods cause asthma, rhinoconjunctivitis and eczema? Global findings from the International Study of Asthma and Allergies in Childhood (ISAAC) Phase Three.

Ellwood P, Asher MI, Garcia-Marcos L, Williams H, Keil U, Robertson C, Nagel G, ISAAC Phase III Study Grp.

Thorax. 2013; 68: 351-360. FI: 8.376 (Q1).

Two Outbreaks of Listeria monocytogenes Infection, Northern Spain.

Perez-Trallero E, Zigorraga C, Artieda J, Alkorta M, Marimon JM.

EMERG INFECT DIS. 2014; 20: 2155-2157. FI: 7.327 (Q1).

Spread of Streptococcus pneumoniae Serotype 8-ST63 Multidrug-Resistant Recombinant Clone, Spain.

Ardanuy C, de La Campa AG, Garcia E, Fenoll A, Calatayud L, Cercenado E, Perez-Trallero E, Bouza E, Linares J.

EMERG INFECT DIS. 2014; 20: 1848-1856. FI: 7.327 (Q1).

Decrease in mortality in severe community-acquired pneumococcal pneumonia: impact of improving antibiotic strategies (2000-2013).

Gattarello S, Borgatta B, Solé-Violán J, Vallés J, Vidaur L, Zaragoza R, Torres A, Rello J.

Chest. 2014; 146: 22-31. FI: 7.132 (Q1).

ISAAC Phase Three Study Grp. The association between tobacco and the risk of asthma, rhinoconjunctivitis and eczema in children and adolescents: analyses from Phase Three of the ISAAC programme.

Mitchell EA, Beasley R, Kei, U, Montefort S, Odhiambo J.

Thorax. 2012; 67: 941-128. FI: 6.840 (Q1).

Spanish Collaboration Endocarditis, Grp Apoyo Manejo Endocarditis Infe. Valve surgery in active infective endocarditis: A simple score to predict in-hospital prognosis.

Martinez-Selles M, Munoz P, Arnaiz A, Moreno M, Galvez J, Rodriguez-Roda J, de Alarcon A, Cabrera EG, Farinas MC, Miro JM, Montejo M, Moreno A, Ruiz-Morales J, Goenaga MA, Bouza E.

Int. J. Cardiol. 2014; 175: 133-137. FI: 6.175 (Q1).


Published: 1 / 1

IV Spanish Consensus Conference on Helicobacter pylori infection treatment.

Gisbert JP, Molina-Infante J, Amador J, Bermejo F, Bujanda L, Calvet X, Castro-Fernández M, Cuadrado-Lavín A, Elizalde JI, Gene E, Gomollón F, Lanas Á, Martín de Argila C, Mearin F, Montoro M, Pérez-Aisa Á, Pérez-Trallero E, McNicholl AG.

Gastroenterologia Y Hepatologia. 2016; 39: 697-721. FI: 0,917 (Q4).


Published: 2 / 2

Grp Espahol Para Estudio VIH-HTLV. Infection by HIV-2, HTLV and new human retroviruses in Spain.

Treviño A, Soriano V.

Med. Clin. 2012; 138: 541-544. FI: 1.385 (Q2).

Anales de Pediatria: The past, the present and the future.

Perez-Yarza EG, Cabanas F, Garcia-Algar O, Valverde-Molina J.

An Pediatr (Barc). 2013; 79: 277-278. FI: 0.867 (Q3).


Published: 0 / 0


Published: 1 / 1

Increased Susceptibility to Pneumococcal Disease in Sjögren Syndrome Patients.

Ercibengoa M, Alonso M, Marimon JM, Saenz JR, Perez E.

WJV. 2014; 1: 45-49. FI: 0.000 (Q0).


Projects 7 / 7

Investigación estratégica y desarrollo tecnológico en aplicaciones biomédicas de nanoglicotecnología y especitrometría de masas sobre superficies para diagnóstico clínico y seguridad alimentaria. Biomagune 14.

Investigador Principal: Emilio Pérez Trallero. Entidad Financiadora: Gobierno Vasco, Departamento de Desarrollo Económico y Competitividad. Año inicio: 2014. Año final: 2015.

Detección de Helicobacter Pylory en biopsia, hilo de enterotest y heces. Estudio comparativo empleando métodos moleculares, cultivo o inmunocromatografía y elisa.

Investigador Principal: Emilio Pérez Trallero. Entidad Financiadora: ISCIII Instituto de Salud Carlos III. Año inicio: 2014. Año final: 2016.

Biopatrones: Soporte tecnológico a la toma de decisiones basado en patrones bioquímicos y genéticos complejos.

Investigador Principal: Eduardo González Pérez Yarza. Entidad Financiadora: Diputación Foral de Gipuzkoa. Año inicio: 2014. Año final: 2015.

Serotipificado de Streptococcus Pneumoniae mediante Multiplex-PCR e hibridación reversa en tira.

Investigador Principal: José María Marimón Ortiz de Zárate. Entidad Financiadora: ISCIII Instituto de Salud Carlos III. Año inicio: 2014. Año final: 2016.

EASY PCR LAB – Desarrollo preindustrial de nuevas aplicaciones diagnósticas clínicas como plataforma de lanzamiento de una nueva iniciativa empresarial basada en la tecnología EASY-PCR.

Investigador Principal: José María Marimón Ortiz de Zárate. Entidad Financiadora: Gobierno Vasco, Departamento de Desarrollo Económico y Competitividad. Año inicio: 2013. Año final: 2015.

Impacto de las nuevas vacunas frente N. Meningitidis Serogrupo B en Euskadi: ¿Hacia la desaparición de la Meningitis Meningocócica?

Investigador Principal: José María Marimón Ortiz de Zárate. Entidad Financiadora: Gobierno Vasco, Departamento de Salud. Año inicio: 2013. Año final: 2016.

Nuevos productos para la salud reproductiva y prenatal. NEOBIO.

Investigador Principal: Eloy Sánchez Haya. Entidad Financiadora: Gobierno Vasco, Departamento de Desarrollo Económico y Competitividad. Año inicio: 2012. Año final: 2014.