Microbiological diagnosis of respiratory tract infections

"We start with the most suitable treatment according to the suspected microorganism. Once the result of the cultures is received, if necessary, it is changed to the most suitable medicine".


Microscopic examination and culture of respiratory secretions are essential for the rational treatment of respiratory infections, so efforts must be made to obtain adequate samples.

  • The lower respiratory tract (below the epiglottis) is sterile under normal conditions.
  • To make the diagnosis it is necessary to collect a good sample that is not contaminated with microorganisms from the mouth and pharynx.
  • Secretions of the lower respiratory tract are contaminated with the microbiota of the upper respiratory tract, unless the sample is obtained by an invasive technique (transtracheal puncture, bronchoscopy).
Imagen del icono de la consulta de Segunda Opinión. Clínica Universidad de Navarra

Do you need our help?
Contact with us

When is the culture of respiratory samples indicated?

Lower respiratory tract infections can affect the trachea and bronchial tree:

  • Tracheitis.
  • Bronchitis, bronchiolitis.
  • Lung tissue: pneumonia, alveolitis.

These are very common infections in the general population and in most cases, they resolve satisfactorily. Often without the need for antibiotic treatment.

What are the most common germs?

  • Streptococcus pneumoniae (pneumococcus).
  • Haemophilus influenzae.
  • Legionella spp.
  • Aspergillus spp.
  • Mycobacterium tuberculosis.
  • Adenovirus.

Do you suspect you have a respiratory infection?

Microbiological diagnostic tests may be required

How is the cultivation of respiratory samples performed?

Once the samples arrive at the laboratory, an extension of these samples is stained after being placed on a slide.

In this way, the morphology of the microorganisms present in the sample and the staining characteristics can be observed.

After this, different culture mediums are inoculated and incubated in ovens at different temperatures.

These culture media will be examined daily to detect the growth of possible microorganisms in the samples.

Once the growth of any microorganism is detected, it is identified by means of different biochemical tests and an antibiogram is carried out (to study the sensitivity of the isolated microorganism to different antibiotics).

Where do we do it?


The Infectious Diseases Service
of the Clínica Universidad de Navarra

This area works on the diagnosis and treatment of diseases produced by an infectious agent, which can be bacteria, virus, fungus and protozoa. Infections affect people by causing very different processes that can be located in any tissue of the human body, so it requires a specific approach.

This area carries out its activity on three fronts: care work, focused on the diagnosis and treatment of infectious diseases; teaching, with training of medical students, resident doctors and nurses; and research vocation, through the development of clinical and laboratory studies.

Organized in care units

  • Infections associated with biomaterials.
  • Nosocomial infections (multi-resistance).
  • Infections in immunosuppressed patients.
  • Community infection.
  • Traveler's medicine.
  • Prudent use and optimization program of anti-infective therapy.
  • Control of infection by multi-resistant microorganisms.
Imagen de la fachada de consultas de la sede en Pamplona de la Clínica Universidad de Navarra

Why at the Clinica?

  • We perform the traveler's assessment and analytical tests in less than 24 hours.
  • Second opinion consultation when the infection has not yet been resolved.
  • We ensure the prudent use of antibiotics.