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Anatomical barriers (including epithelial barrier function and how this is influenced by pathogens)
Reflex mechanisms (sneezing, cough and dyspnoea)
Mucociliary clearance and fluid homeostasis
Innate defence mechanisms (broad outline): professional phagocytes T and B cells, innate lymphoid cells, etc., and the induction and resolution of inflammatory responses (type 1 and type 2 inflammation). Innate immune defence mechanisms, g. recognition of pathogen-associated molecular patterns by structural cells (airway epithelium) and subsequent anti-microbial and pro-inflammatory responses
Acquired immune reactions with immunoglobulin and the role of IgM, IgG and IgA
Step 1: Evaluate the utility of ABG, capillary blood gas and venous blood gas
Step 2: Diagnosis of A-B disorders: Henderson-Hasselbalch equation and the relationship between arterial pressure of oxygen (PaO2), partial pressure of carbon dioxide (PCO2) and pH
Step 3: A-B disorders: importance of the D(A-a) difference, fraction of inspired oxygen (FiO2), the alveolar gas equation and measuring oxygen shunts
Management of clinical diseases, e.g. COPD and sepsis with A-B disorders in ABG
Common pathogens and their antibiotic sensitivities
Uncommon Respiratory pathogens and their meaning in clinical practice
Samples and specific pathogens
Acid-fast bacilli: number (WHO and CDC USA), interpretation of quality, sputum induction indication and culture versus immunofluorescence (IF) versus PCR
Likelihood of a laboratory report being correct (g. Gram-negative pathogens or gonococcal pharyngitis); Nocardia as an acid-fast organism
Whole-genome sequencing (WGS) and targeted next-generation sequencing of Mycobacterium tuberculosis and other mycobacteria
Conventional microbiological methods such as Gram staining, culture and sensitivity testing for different pathogens, such as atypical bacteria, viruses and fungi, and for Pneumocytis pneumonia (PCP) due to Pneumocytsis jerovecii (previously carinii)
Indications for and collection of biological specimens, Gram staining, culture, molecular methods, IF and genetic testing
Interferon gamma release assay, interpretation of microbiological results provided by BAL, quantitative culture, particularities in immunocompromised patients, particularities in nosocomial infection and types of sputum harvest (spontaneous, induced and bronchial aspirate)
Airway microbiome in relation with/to epigenetic and transcriptomic profiles in lung tissue
Microbiologic diagnosis of TB (smear examination, liquid and solid culture media, molecular study of resistance and phenotypic/genotypic methods)
Differential diagnosis using clinical and radiological findings of infectious diseases (i.e. those caused by bacteria, viruses, fungi, mycobacteria and other difficult-to-treat microorganisms) in contrast with those of non-infectious disorders
Empirical antibiotic selection and treatment particularities in patients with acquired immunodeficiency, neutropenic patients, patients with solid organ malignancy, lung and other solid organ transplant recipients, haematopoietic cell transplant recipients, patients with other haematological conditions, patients with secondary immunodeficiency induced by drugs and biologicals and patients with primary immune deficiency syndromes
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