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- •Contents
- •1.1.9 Laryngeal Atresia
- •1.1.10 Laryngeal Webs
- •1.1.11 Congenital Subglottic Stenosis
- •1.1.12 Laryngeal Cleft
- •1.1.13 Tracheoesophageal Fistula
- •1.1.14 Tracheal Bronchus
- •1.2.2 Mesenchyme Development
- •1.2.4 Lung Development
- •1.2.4.1 Embryonic Stage
- •1.2.4.2 Pseudoglandular Stage
- •1.1.1 Oral Cavity
- •1.1.2 Nasal Cavity
- •1.1.3 Palate
- •1.1.4 Primitive Pharynx
- •1.1.5 Upper Airway Anomalies
- •1.1.6 Cleft Lip/Palate
- •1.1.7 Choanal Atresia
- •1.1.8 Laryngomalacia
- •1.2.4.3 Canalicular Stage
- •1.2.4.4 Saccular Stage
- •1.2.4.5 Alveolar Stage
- •1.2.5 Congenital Respiratory System Defects
- •1.2.5.1 Tracheal Agenesis
- •1.2.5.2 Congenital Tracheal Stenosis
- •1.2.5.3 Lung Agenesis
- •1.2.5.4 Lung Hypoplasia
- •References
- •2.1 Introduction
- •2.2 Nasal Cavity
- •2.2.1 Vestibule
- •2.2.2 Respiratory Mucosa
- •2.2.3 Olfactory Mucosa
- •Supporting Cells
- •Basal Cell
- •Olfactory Receptor Cell (Bipolar Neuron)
- •Brush Cell (Microvillar Cell)
- •2.2.3.2 The Lamina Propria
- •2.2.3.3 Olfactory Glands (Bowman’s Glands)
- •2.3 Paranasal Sinuses
- •2.4 Pharynx
- •2.5 Larynx
- •2.6 Trachea
- •2.6.1.1 Ciliated Columnar Cells
- •2.6.1.2 Goblet Cells
- •2.6.1.3 Brush Cells
- •2.6.1.4 Basal Cells
- •2.6.1.5 Enteroendocrine System Cells (Kulchitsky Cells or DNES Cells)
- •2.6.2 Lamina Propria
- •2.7 Lungs
- •2.7.1 Pleura
- •2.7.2 Bronchi
- •2.7.3 Bronchioles
- •2.7.3.1 Terminal Bronchioles
- •2.7.3.2 Respiratory Bronchioles
- •2.7.4 Ductus Alveolaris
- •2.7.5 Alveoli
- •2.7.5.2 Type II Alveolar Cell (Septal Cell, Large Alveolar Cell)
- •References
- •3.1.1.3 Nerves
- •Ophthalmic Division
- •Maxillary Division
- •Parasympathetic Nerve Supply
- •3.1.1.4 Bony Anatomy
- •3.1.1.5 Cartilaginous Pyramid
- •3.1.1.6 Structure
- •External Nasal Anatomy
- •Internal Nasal Anatomy
- •3.1.2 Nasal Physiology
- •3.1.2.1 Nasal Airflow
- •3.1.2.2 Abnormal Nasal Physiology
- •3.2.1 Larynx Anatomy
- •Cricoid Cartilage
- •Thyroid Cartilage
- •Epiglottis
- •Arytenoid Cartilages
- •Corniculate Cartilages
- •Cuneiform Cartilages
- •Extrinsic Ligaments
- •Intrinsic Ligaments
- •Laryngeal Cavity
- •Piriform Recesses
- •Cricothyroid Muscles
- •Posterior Cricoarytenoid Muscles
- •Lateral Cricoarytenoid Muscles
- •Transverse Arytenoid Muscle
- •Thyroarytenoid Muscles
- •Superior Laryngeal Nerve
- •Arteries
- •Veins
- •Lymphatics
- •Swallowing
- •Respiration
- •Phonation
- •3.2.2.1 Reflex Glottic Closure
- •References
- •4.1 Introduction
- •4.2.1 Choanal Atresia
- •4.2.2 Pyriform Aperture Stenosis
- •4.2.3 Cleft Lip Nasal Deformity
- •4.2.4 Nasolacrimal Duct Cysts
- •4.2.5 Encephaloceles
- •4.3 Craniofacial Anomalies
- •4.3.1 Pierre Robin Syndrome
- •4.3.2 Treacher-Collins Syndrome
- •4.3.3 Crouzon Syndrome
- •4.3.4 Down Syndrome
- •4.3.5 Apert Syndrome
- •4.4.1 Thyroglossal Duct Cyst
- •4.4.2 Laryngomalacia
- •4.4.3 Vocal Fold Paralysis
- •4.4.5 Subglottic Stenosis
- •4.4.6 Subglottic Hemangioma
- •4.4.7 Laryngeal Cysts
- •4.4.8 Laryngeal Cleft
- •4.5 Conclusion
- •References
- •5.1 Innate Immunity
- •5.2 Adaptive Immunity
- •References
- •6.1 Introduction
- •6.2 Innate Immunity
- •6.3 Adaptive Immunity
- •References
- •7.1 Introduction
- •References
- •8: Respiratory Microbiome
- •8.1 Introduction
- •8.2.1 Childhood Asthma
- •8.2.2 Asthma Exacerbation
- •8.3 Bacteriome
- •8.4 Virome
- •8.5 Mycobiome
- •References
- •9.1 Introduction
- •References
- •10.1 Introduction
- •10.3.3 The Appointment Process, Explained
- •10.3.5 Parental Involvement
- •10.4 Coordinating Care When Your Child Is Ill
- •10.4.3 Exhibit Cohesion
- •10.6 Conclusion
- •References
- •11.1 Introduction
- •11.2 Nasal Cavity
- •11.2.1 Choanal Atresia
- •11.2.2 Rhinosinusitis
- •11.2.4 Juvenile Nasopharyngeal Angiofibroma
- •11.3 Pharynx
- •11.4 Nasopharynx
- •11.4.1 Adenoid Hypertrophy
- •11.4.2 Nasopharyngeal Carcinoma
- •11.5 Oropharynx
- •11.5.1 Thyroglossal Duct Cyst
- •11.6 Hypopharynx
- •11.6.1 Retropharyngeal Abscess
- •11.6.2 Lymphatic Malformation
- •11.6.4 Lymphoma
- •11.6.5 Rhabdomyosarcoma
- •11.7 Larynx
- •11.7.1 Subglottic Stenosis
- •11.7.2 Laryngotracheal Papillomatozis
- •11.7.3 Croup
- •11.7.4 Epiglottitis
- •11.7.5 Foreign Body Aspiration
- •References
- •12.2.1 Plain Radiography
- •12.2.1.1 The Thymus
- •Tracheal Buckling
- •Hilum
- •Diaphragm
- •Mediastinal Borders
- •Lung Opacities
- •Cystic Lung Diseases
- •Pulmonary İnterstitial Emphysema (PIE)
- •Unilateral Hyperlucent Lung
- •12.2.2 Fluoroscopy
- •12.2.3 Ultrasound
- •12.2.4 Computed Tomography
- •12.2.5 Magnetic Resonance Imaging (MRI)
- •12.2.6 Angiography
- •12.2.7 Positron Emission Tomography (PET)
- •12.3 Conclusion
- •References
- •13.1 Introduction
- •13.2 Nasal Diagnostic Procedures
- •13.2.1 Indications
- •13.2.2 Contraindications
- •13.2.3 Anatomical Features
- •13.2.4 Technical Considerations
- •13.2.5 Technique
- •13.2.5.1 First Pass
- •13.2.5.2 Second Pass
- •13.2.5.3 Third Pass
- •13.3 Flexible Laryngoscopy
- •13.4 Direct Laryngoscopy
- •13.5 Video Laryngoscopy
- •13.5.1 Indications
- •13.5.2 Contraindications
- •13.5.3 Outcomes
- •13.5.4 Equipment
- •13.5.5 Approach Considerations
- •References
- •14.1 Upper Airways
- •14.2.3 Laryngeal Pathologıes
- •References
- •15.1 Introduction
- •15.2 Airway Measurements
- •References
- •16.1 Introduction
- •16.2 Background
- •References
- •17: Allergen Testing: Purpose, Procedure, Interpretation
- •17.1 Introduction
- •17.2 Tests
- •17.2.1 Skin Tests
- •17.2.3 Component Resolved Diagnosis (CRD)
- •17.2.4 Tryptase
- •17.2.5 Basophil Activation Test (BAT)
- •17.2.6 Provocation Tests
- •17.2.7 Nasal sIgE
- •17.2.8 Nasal Smear Eosinophilia
- •17.2.9 Eosinophilic Cationic Protein (ECP)
- •References
- •18: Smell Testing: Purpose, Procedure, Interpretation
- •18.1 Introduction
- •18.2 Possible Olfactory Disorder Diagnosis
- •18.2.1 Conductive Defects
- •18.2.3 Inherited Disorders
- •18.2.3.1 Hormonal Disturbances
- •18.4 Odor Threshold Tests
- •18.8.1 Butanol Threshold Test
- •18.8.1.1 The Penn State University Odor Identification Exam
- •18.8.2 Cross-Cultural Smell Identification Test
- •18.8.3 Sniffin’ Sticks
- •References
- •19: Taste Testing: Purpose, Procedure, Interpretation
- •19.1 Introduction
- •19.2 Definitions
- •19.2.1 Taste Dysfunction Abnormalities
- •19.4.1 Taste Dysfunction
- •19.4.2 COVID-19
- •19.5 Taste Disorder Diagnosis
- •19.6.2 Magnitude Matching
- •19.6.3 Spatial Test
- •References
- •20.1 Introduction
- •20.2 Primary Otalgia Causes
- •20.2.1 Auricle
- •20.2.1.1 Infections
- •20.2.1.2 Trauma
- •20.2.1.3 Allergic Angioedema
- •20.2.1.4 Thermal Damage
- •20.2.2 External Auditory Canal
- •20.2.2.1 Otitis Externa
- •20.2.2.2 Malignant Otitis Externa
- •20.2.2.3 Eczematous Dermatitis
- •20.2.2.4 Furunculosis
- •20.2.2.5 Foreign Body
- •20.2.2.6 Cerumen Impaction
- •20.2.2.7 Tumors
- •20.2.3 Middle Ear
- •20.2.3.1 Acute Otitis Media
- •20.2.3.3 Eustachian Tube Dysfunction
- •20.2.3.4 Cholesteatoma
- •20.2.3.5 Trauma
- •20.3 Secondary Otalgia Causes
- •20.3.1 Oropharyngeal Infections
- •20.3.2 Dental Causes
- •20.3.3 Auricular Lymphadenitis
- •20.3.4 Neck Abscess
- •20.3.5 Parotitis
- •20.3.6 Temporomandibular Joint Dysfunction
- •20.3.7 Sinusitis
- •20.4 Differential Diagnosis
- •References
- •21.1 Introduction
- •21.2 Bacterial Otitis Externa
- •21.3 Acute Otitis Media
- •21.4 Chronic Suppurative Otitis Media
- •21.5 Foreign Body
- •21.5.1 Cerumen
- •21.5.2 Tympanostomy Tube Drainage
- •21.5.3 Traumatic Cerebrospinal Fluid Otorrhea
- •21.5.5 Necrotizing Otitis Externa (Malignant External Otitis)
- •21.5.6 Neoplasms
- •21.5.7 Polyps
- •21.5.8 Otomycosis
- •21.5.9 First Branchial Cleft Cysts
- •21.5.10 Cholesteatoma
- •21.5.11 Spontaneous Cerebral Spinal Fluid Otorrhea
- •References
- •22.1 Introduction
- •22.4 Congenital Causes
- •22.4.1 Choanal Atresia
- •22.4.2 Pyriform Apertura Stenosis
- •22.4.3 Nasal Midline Congenital Masses
- •22.4.3.1 Nasal Dermoid Cyst
- •22.4.3.2 Nasal Glioma
- •22.4.3.3 Encephalocele (Encephalo-Meningocele)
- •Differential Diagnosis
- •22.4.3.4 Nasolacrimal Duct Cyst (Dacryocystocele)
- •22.5 Infectious Causes
- •22.5.1.1 Rhinitis Etiology
- •22.5.2 Neonatal Rhinitis
- •22.5.3 Bacterial or Viral Rhinitis
- •22.5.4 Iatrogenic Rhinitis
- •22.5.5 Infectious Rhinitis (Rhinosinusitis)
- •22.6 Adenoid Hypertrophy
- •22.7 Inflammatory Causes
- •22.7.1 Allergic Rhinitis
- •22.7.2 Nonallergic Rhinitis
- •22.7.3 Eosinophilic Nonallergic Rhinitis (NARES)
- •22.7.4 Nasal Polyp
- •22.7.5 Antrochoanal Polyp
- •22.7.6 Inferior Turbinate Hypertrophy
- •22.8 Neoplasia
- •22.8.1 Benign Tumors (Juvenile Nasopharyngeal Angiofibroma)
- •22.8.2 Malignant Tumors
- •22.9 Systemic Causes
- •22.9.1 Cystic Fibrosis
- •22.9.2 Primary Ciliary Dyskinesia
- •22.10 Trauma/Iatrogenic Causes
- •22.10.1 Nasal Trauma-Septal Hematoma
- •22.10.2 Septum Deviation
- •22.10.3 Nasal Foreign Bodies
- •References
- •23.1 Introduction
- •23.2 Pathophysiology
- •23.3 Allergic Rhinitis
- •23.4 Non-allergic Rhinitis
- •23.5 Infectious Rhinitis
- •23.6.1 Vasomotor Rhinitis
- •23.7 Evaluation
- •23.8 Diagnosis
- •23.9 Treatment
- •23.10 Prognosis
- •23.11 Conclusion
- •References
- •24.1 Introduction
- •24.2 Pathogenesis
- •24.3 Diagnosis
- •24.3.1 History
- •24.3.2 Examination
- •24.4 Differential Diagnoses
- •24.5 CSF Rhinorrhea
- •24.5.1 CSF Physiology
- •24.5.1.1 Pathogenesis
- •24.6 Diagnosis
- •24.6.1 Chemical Diagnosis
- •24.6.2 Imaging Diagnosis
- •24.7 Treatment
- •24.7.1 Surgical Technique
- •References
- •25.1 Introduction
- •25.1.1 Waldeyer Ring
- •25.3 Anatomy
- •25.3.1 Lymphatic Drainage
- •25.3.1.1 Nerve Supply
- •25.6 Tonsillary Hypertrophy
- •25.7 Physical Examination
- •25.8.1 Obstructive Sleep Apnea
- •References
- •26.1 Introduction
- •26.5 Halitosis Physiopathology
- •26.6.1 Oral Halitosis (Intraoral Halitosis, Oral Malodor)
- •26.6.1.1 Periodontal Infections
- •26.6.1.2 Tongue Oriented Halitosis
- •26.6.1.3 Peritonsillar Abscess
- •26.7 Paranasal Sinus Diseases
- •26.8 Adenoid Vegetation
- •26.9 Chronic Pharyngitis
- •26.10 Chronic Tonsillitis
- •26.11 Tonsillolith
- •26.12 Non-Oral Halitosis
- •26.13 Gastroesophageal Reflux
- •26.14 Diagnosis
- •26.14.1 Organoleptic Measurement
- •26.14.2 Sulfur Monitoring
- •26.14.2.1 Indirect Methods
- •26.14.2.3 Ammonia Monitoring
- •26.14.2.4 Polymerase Chain Reaction (PCR)
- •26.15 Physical Examination
- •References
- •27.1 Introduction
- •27.2 Epidemiology
- •27.4 Diagnosis
- •27.5.1 Clinical Assessment
- •27.6 Treatment
- •27.6.1 Voice Therapy
- •27.7 Phonosurgery
- •References
- •28.1 Introduction
- •28.2 Epidemiologic Characteristics
- •28.3 Swallowing Physiologic Phases
- •28.3.1.1 Prematurity
- •28.3.1.2 Neuromuscular
- •28.3.1.5 Cardiopulmonary Disease
- •28.4 Symptoms
- •28.5 Clinical Feeding Assessment
- •28.7 Flexible Endoscopic Swallowing Evaluation
- •28.8 Imaging
- •28.9 Endoscopic Assessments
- •28.9.1 High-Resolution Manometry
- •28.10 Medical Management
- •28.11 Surgical Management
- •28.11.1 Ankyloglossia
- •28.11.2 Laryngomalacia
- •28.11.3 Laryngeal Cleft
- •28.12 Conclusions
- •References
- •29.1 Introduction
- •29.2 Reactive Lymph Node Enlargements
- •29.3 Vaccines
- •29.4 Acute Suppurative Lymphadenitis
- •29.6 Granulomatous Lymphadenitis
- •29.6.1 Mycobacterial Infection
- •29.6.2 BCG Vaccine
- •29.6.3 Cat-Scratch Disease
- •29.6.4 Sarcoidosis
- •29.6.5 Kikuchi-Fujimoto Disease
- •29.7 Malignancies
- •29.8 Diagnosis
- •References
- •30.1 Introduction
- •30.2 Upper Airway Cough Syndrome
- •30.3 Chronic Rhinosinusitis
- •30.5 Otogenic Cough
- •30.6 Laryngeal Clefts
- •30.7 Conclusion
- •References
- •31.1 Introduction
- •31.5.1 Vocal Cord Disfunction (VCD)
- •31.5.2 Obstructive Sleep Apnea Syndrome (OSAS)
- •31.5.3 Allergic or Non-Allergic Rhinitis
- •31.6 Conclusion
- •References
- •32.1 Introduction
- •32.2.1 Non-massive Hemoptysis
- •32.2.2 Massive Hemoptysis
- •32.4 Diagnostic Evaluation
- •32.4.1 History
- •32.4.1.1 Infection Warning Signs
- •32.4.1.2 Choking
- •32.4.1.3 Exposures
- •32.4.1.4 Underlying Medical Problems
- •32.4.2 Physical Examination
- •32.4.3 Laboratory Evaluation
- •32.4.4 Imaging
- •32.5.1 Respiratory Illness
- •32.5.3 Trauma
- •32.5.4 Hemoptysis Mimics
- •References
- •33.1 Introduction
- •33.6 Conclusion
- •References
- •34: Pediatric Allergic Rhinitis: Otolaryngology Perspective
- •34.1 Introduction
- •34.2 Epidemiology
- •34.2.1 Prevalence
- •34.2.2 Risk factors
- •34.3.1 Classical Pathway
- •34.3.2 Nasal Pathway
- •34.4.2 Physical Examination
- •34.4.3 Diagnostic Tests
- •34.4.4 Nasal Cytology
- •34.4.5 Imaging
- •34.5.1 Adenoid Hypertrophy
- •34.5.2 Nasal Septal Deviation
- •34.5.3 Chronic Rhinosinusitis
- •34.5.4 Turbinate Hypertrophy
- •34.5.5 Nasal Foreign Body
- •34.5.6 Other Clinical Conditions
- •34.6.1 Saline Irrigation (Douching)
- •34.7 Treatment
- •34.7.1 Oral Antihistamines
- •34.7.2 Intranasal Steroids
- •34.7.3 Leukotriene Inhibitors
- •34.7.5 Oral Steroids
- •34.7.6 Intranasal Antihistamines
- •34.7.7 Immunotherapy (Sublingual-Subcutaneous)
- •34.8 Conclusion
- •References
- •35: Allergic Rhinitis: Pediatric Pulmonologist Perspective
- •35.1 Introduction
- •35.2.1 Epidemiological Relationship
- •35.2.4 Immunopathology
- •35.2.7 Non-pharmaceutical Treatment Method
- •35.2.8 Pharmaceutical Medication Policy
- •35.2.9 Immunotherapy Against Allergens
- •35.6 Conclusion
- •References
- •References
- •37.1 Introduction
- •37.2 Adenoid Hypertrophy
- •37.7 Preoperative Evaluation
- •37.8 Contraindications
- •37.9 Complications
- •37.9.1 Bleeding
- •37.9.2 Hypernasality
- •37.9.3 Surgical Traumas
- •37.9.4 Torticollis
- •37.9.5 Otitis Media
- •37.9.6 Psychological Trauma
- •37.9.7 Nasopharyngeal Stenosis
- •37.9.8 Recurrence
- •37.10 Postoperative Care
- •37.11 Surgery
- •37.12.1 Adenoiditis
- •References
- •38.1 Introduction
- •38.2 Anatomy
- •38.2.1 Palatine Tonsils (Faucial Tonsils)
- •38.2.2 Lingual Tonsil
- •38.2.3 Adenoids (Pharyngeal Tonsil)
- •38.2.4 Tubal Tonsils
- •38.5.1 Viral Tonsillitis
- •38.5.2 Bacterial Tonsillitis
- •38.5.3 Candida
- •38.6.1 Suppurative Complications
- •38.6.1.1 Peritonsillar Abscess (Quincy Tonsil)
- •Lemierre’s Syndrome
- •38.6.2 Nonsuppurative Complications
- •38.6.2.1 Acute Rheumatic Fever
- •38.6.2.2 Poststreptococcal Glomerulonephritis
- •38.6.2.3 Scarlet Fever
- •38.6.2.6 Palmoplantar Pustulosis (PPP)
- •38.6.2.7 IgA Nephropathy
- •38.7 Clinical Manifestation
- •38.7.1 Infection
- •38.7.2 Obstruction
- •38.7.3 Neoplasia
- •38.8 Diagnosis
- •38.8.2 Physical Examination
- •38.8.3 Laboratory
- •38.8.4 Imagining
- •38.8.5 Polysomnography
- •38.9 Treatments
- •38.9.1 Medical Treatment
- •38.9.2 Surgery
- •38.9.2.2 Tonsillectomy
- •38.9.3.1 Intraoperative Complications
- •38.9.3.4 Postoperative Long-Term Complications (>weeks)

7 Immune Responses toRespiratory Infections
93
promoting the stimulation of CD8+ T-cell responses. Some CD4+ T cells exhibit
cytolytic activity mediated by perforin after inuenza infection [11]. The CD8+ T
cells recognize and eliminate virus-infected cells through mechanisms mediated by
perforins and granzymes or apoptosis. Furthermore, virus-specic CD8+ T cells are
capable of generating both anti-inammatory interleukin (IL)-10 and pro-inammatory mediators such as tumor necrosis factor (TNF) and IFN-γ, thereby maintaining the balance with effective antiviral responses [11, 28]. It is observed that,
following the clearance of the virus, these two pro-inammatory mediators are
reduced. For IL-10 to be produced in lung tissues, IL-27 (released by mononuclear
cells and neutrophils) and IL-2 (produced by T CD4+ lymphocytes) are required
[27]. As well as CD4+ and CD8+ T lymphocytes and regulatory T cells (Tregs) are
involved in immune response modulation. A large number of regulatory interleukins
are produced by these cells, such as IL-10 and transforming growth factor-β1 (TGFβ1) and inhibitory molecules such as CTLA-4 (cytotoxic T-lymphocyte-associated
protein) [27]. Following clearance, part of the effector T cells converts into circulating and tissue-resident memory T cells, providing long-term immunity against reinfection, while others undergo apoptosis during the contraction phase [29].
Bacterial infections sometimes occur as superinfection following viral infections. In this situation, macrophages usually represent the rst line of defense. These
macrophages are also responsible for recruiting and activating other immune cells
and controlling the spread of bacterial infections. Inammatory response to extracellular bacteria, such as S. pneumoniae, is primarily driven by neutrophil inltration and secondarily by a late adaptive immunity regulated by Th1 and Th17 cells.
Additionally, the production of specic antibodies against the microorganisms is
provided by B lymphocytes [27]. Of note, IgM, IgG, and IgA are fundamental in the
response against bacteria, and particularly capsulated bacteria, as shown by the
recurrence of S. pneumoniae and H. inuenzae infections in patients with primary
antibody deciencies (PAD), often leading to airway remodeling and bronchiectasis
[30]. Notably, the evaluation of the antibody response to vaccination is part of the
diagnostic process of common variable immunodeciency. In these patients with a
suspicion of PAD, the assessment of the response to pneumococcal polysaccharide
vaccines is used as a gold standard to assess T-independent antibody responses [31].
In particular, between IgG subclasses, IgG2 plays a prominent role as an antipolysaccharide antibody. Also, specic antibody deciencies are reported, in which
a specic inability to mount an antibody response against puried Streptococcus
pneumoniae capsular polysaccharide antigens is detected. This may occur despite
normal total IgG, IgA, and IgM levels and preserved antibody responses to protein
antigens [32].
Fungi are ubiquitous indoor and outdoor microorganisms that will likely increase
in prevalence and antigenicity with global climate change. Fungi contain cell wall
molecules such as β-glucan and chitin and secrete biologically active proteases and
glycosidases. Innate immune cells, such as airway epithelial cells and dendritic
cells, are equipped with cell surface molecules that respond to these fungal products, leading to the production of cytokines and proinammatory mediators. As a

94
E. Topyildiz et al.
result, protection against fungal infection is enhanced by generating the adaptive
arm of antifungal immunity, including Th1, Th2, and Th17-type CD4+ T cells [33].
In conclusion, immune responses to respiratory infections are complex processes
involving both innate and adaptive components. The immune system’s ability to
recognize, neutralize, and eliminate pathogens is a remarkable defense mechanism
that helps maintain respiratory health. The clinical picture of patients affected by
IEI clearly recapitulates the importance of the different branches of the immune
system in the response against respiratory pathogens and helps in understanding the
mechanisms [34]. The knowledge of these responses is crucial to the development
of effective therapies and preventive strategies for a wide variety of respiratory
infections.
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https://doi.org/10.1016/S1473- 3099(17)30396- 1.
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95

Respiratory Microbiome
ÜlküRabiaKorkmaz, OmerFarukCetiner, AshaRani,
RaviRanjan, andAyşeBilgeÖztürk
8.1 Introduction
The human body hosts a complex community of microorganisms called “microbiota,” the number of which is 10 times more than the total human cell count [1].
Microbial species belonging to this heterogeneous community exhibit different
dynamics according to time and place [2]. They are affected by the environment and
are in active communication both with the host and among themselves [2].
Human microbiota, which has become increasingly popular in the last 20years,
has now begun to be dened as our “last organ” [1]. As only less than 1% of the
bacteria can be cultured in the laboratory [3], therefore, bacterial laboratory culture
is no longer the gold standard for understanding the role of microbiota in greater
detail. Today, genetic molecular analysis of polymorphic bacterial 16SrRNA gene
sequencing is considered the main method to characterize microbiota [2, 3]. Since
8
Ü. R. Korkmaz
Institute of Asthma and Allergy Prevention, Helmholtz Zenter Munich, Neuherberg, Germany
e-mail: ulku-rabia.korkmaz@helmholtz-munich.de
O. F. Cetiner
Istanbul Faculty of Medicine, Istanbul University, Istanbul, Turkey
A. Rani
Department of Food Science, University of Massachusetts Amherst, Amherst, MA, USA
e-mail: arani@umass.edu
R. Ranjan
Genomics Resource Laboratory, Institute for Applied Life Sciences, University of
Massachusetts Amherst, Amherst, MA, USA
e-mail: ranjan@umass.edu
A. B. Öztürk (*)
Department of Allergy and Immunology, Medeniyet University Faculty of Medicine,
Istanbul, Turkey
© The Author(s), under exclusive license to Springer Nature
Switzerland AG 2024
H. Yüksel et al. (eds.), Pediatric Airway Diseases, Comprehensive ENT,
https://doi.org/10.1007/978-3-031-74853-0_8
97

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the beginning of the 2000s, gene sequencing technology with high data output has
been widely used, and its routine use in the elds of proteomics, metabolomics, and
epigenomics has led to the historical microbiology term “microbiota” [2]. This
rapid technological development has also led to promising options in the prevention
of diseases and personalized medicine [3].
The entire gene summation of all microbes (bacteria, bacteriophage, fungi, protozoa, and viruses) belonging to the microbiota of a specic environment is termed
the “microbiome” [3]. The “Human Microbiome Project-HMP” is one of the most
comprehensive international projects which has led to over 200 scientic studies in
the literature. The HMP project was planned as an open data portal in 2007 [4] and
this project dened the normal microbiomes of the nasal, oral, skin, gastrointestinal
tract, and urogenital regions of healthy people.
When “The Human Microbiome Project-HMP” was planned, human airways
were not sampled because the lungs were thought to be sterile, but the role of airway
microbiota in disease and health is now well established [5]. Since its discovery, the
role of the respiratory microbiome in the pathogenesis of various lung diseases has
been investigated. A growing body of scientic data from observational clinical
studies and laboratory studies supports the role of microbiota in the pathogenesis of
airway disease and healthy lungs [5]. Our microbiota may play a key modulatory
role in immune, metabolic, and cellular functions, activating disease-related inammatory signals, increasing airway disease susceptibility and disease severity, as well
as directing different phenotypes [3, 6].
Airways are directly exposed to allergens, microbes, and other irritants, and
inhaled air contains 104–106 bacterial cells/m3 [7]. Lung microbiota occurs by the
balance of microbial immigration, microbial elimination, and the relative reproduction rates of its members [3]. Temperature, pH, oxygen tension, nutrient availability,
local microbial competition, host epithelial cell interactions, activation of inammatory cells, and concentration of inammatory cells all have an effect on the
microbiota [3]. The healthy lung has a diverse microbiota and the most prevalent
phyla in the airways are Bacteroidetes and Firmicutes. Streptococcaceae
(Firmicutes), Veillonellaceae (Firmicutes), Prevotellaceae (Bacteroidetes),
Fusobacteriaceae (Fusobacteria), Neisseriaceae (Betaproteobacteria),
Porphyromonadaceae (Bacteroidetes), and Lachnospiraceae (Firmicutes) are the
most prevalent bacteria found in healthy lung airways [3].
Although it is well known that the intestinal microbiota has a critical importance
for human physiology, the “lung microbiota” of healthy individuals has been a less
studied subject. Lung microbiota has long been accepted as sterile, and routine sampling encounters various difculties. Despite its low density and reduced bacterial
load, lung microbiota plays a primary role in maintaining a balance between the
immune system and epithelial responses [3]. Local and distant effects of the bacterial load of the lung have a decisive effect on many respiratory diseases, including
asthma [3, 6, 8].
Although the results of childhood asthma studies have been highly variable
because of the different methods used to assess bacterial populations, however,
there are extensive data available on childhood asthma and microbiota. This

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chapter aims to summarize the current literature on airway microbiota, with a
focus on childhood asthma studies, to provide a comprehensive approach to the
respiratory microbiome and its relationship with airway disease. Accumulating
evidence indicates that the airway microbiome may provide valuable predictive
insights for the diagnosis of asthma, a basis for identifying risk factors and
potential targets for treatment options [6]. In this review, we provide the most
essential concepts and recent developments related to the airway microbiome in
the context of pediatric asthma. This review also highlights the noteworthy studies that have contributed signicantly to advancing our understanding of airway
microbiomes.
8.2 Childhood Asthma andRespiratory Microbiome
8.2.1 Childhood Asthma
Childhood asthma, the most prevalent disease of childhood, is identiable by its
phenotype characterized by initial recurrent wheezing, followed by the occurrence
of airway obstruction and narrowing within the initial 6 years of life [9, 10].
Approximately 3–5% of individuals develop persistent wheeze symptoms from
childhood into adulthood [11]. The subsequent existence of numerous proinammatory cells, such as mast cells, eosinophils, T-lymphocytes, macrophages, or neutrophils, leads to bronchial constriction, mucosal edema, and increased mucus
production [12]. Although in older children and adults the prevalence of asthma is
associated with serum IgE level, asthma development is independent of the IgE
level at birth [13]. While there has been signicant advancement in comprehending
the pathogenic mechanisms (risk and protective factors, phenotypes, triggers, etc.)
and distinctions between children and adults in asthma, our understanding of effective prevention strategies remains incomplete.
Microbial colonization starts in utero, and it is inuenced by many factors,
including maternal microbiome, infection, the season of birth, mode of birth, pet
exposure, breastfeeding, farming, the existence of older siblings, and use of antibiotics in early life [14–17]. A delicate balance is maintained by microbes, which
could be benecial or harmful. During early life, chronic microbial (viral, bacterial,
and fungal) infection or colonization by microbial agents in the lower airway could
result in impaired mucociliary clearance that stimulates an increase in mucus production and ultimately contributes to the development of asthma [18, 19].
Newborns born in summer exhibited higher bacterial richness and specic proles, with an increased abundance of Gram-negative α-proteobacteria and Grampositive Bacilli in their nasopharynx at 1 month, contrasting with those born in other
seasons, suggesting that birth season inuences the early colonization of specic
pathogens in the upper airways [20]. Another study highlighted peak colonization
periods for M. catarrhalis in fall/winter and for H. inuenzae in winter/spring,
reecting regular cycles of colonization and clearance in healthy children. The
observed rise in M. catarrhalis and H. inuenzae detection during winter is likely

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attributed to an uptick in viral respiratory infections, such as inuenza, creating
more opportunities for secondary infections by bacterial pathogens [21].
Interestingly, infants who have experienced respiratory illnesses accompanied by
wheezing in their rst year tend to exhibit lower lung function levels even before the
onset of any lower respiratory diseases than infants without wheezing-related illness [22, 23]. This suggests that respiratory infections are associated with childhood
asthma and may also impact the development and severity of asthma [24]. However,
the crucial factor in shaping host immune responses lies in the nature, type, and timing of exposure to microbes [25, 26]. While viral infections appear to play a signicant role in initiating wheezing and respiratory distress in early life, exposure to
specic bacterial species may have a protective effect [23].
On the other hand, epidemiological studies have indicated that living in a microbial-rich environment in early life protects against developing asthma, particularly
in children exposed to farming [27–31]. Recent data on farming indicate that DNA
from mattress dust consists of Clostridium and Facklamia species which were posi-
tively associated with farming [32]. Whether the inhalation of metabolites of environmental bacteria contributes to this strong inverse association of asthma with
bacterial diversity is not clearly understood [32]. Another outstanding study from
Depner etal. revealed that the presence of asthma was positively correlated with a
particular operational taxonomic unit from the genus Moraxella in children without
exposure to farming. However, in children from farming environments, Moraxella
colonization showed no association with asthma [32]. von Mutius etal. identied 84
farming and nonfarming families in rural regions of Southern Germany and
Switzerland. This study suggested that the degree of environmental exposure to
endotoxins and other bacterial wall components plays a signicant role as a protective determinant in preventing the onset of atopic diseases during childhood [33].
Furthermore, the meta-analyses show that the protective “farm effect” is stronger
than what individuals brought up in inner cities can experience by exposure to pets,
daycare, and siblings.
8.2.2 Asthma Exacerbation
Asthma exacerbations represent a signicant factor contributing to morbidity and,
in severe cases, mortality of children affected by asthma [34]. Various factors can
contribute to asthma exacerbation, including infections, underuse of asthma control
medications, or exposure to allergens or pollutants. Although asthma exacerbations
may occur at any time during the year, seasonal factors play a crucial role in childhood asthma. This is particularly prevalent during autumn and spring in temperate
climates when viral respiratory tract infections are most widespread [34]. Viral
infections play a pivotal role, contributing signicantly to as many as 90% of exacerbations [35]. On the other hand, summer exacerbations were associated with compromised pulmonary function, sensitivity to Alternaria spp., elevated blood
eosinophil counts, increased doses of inhaled corticosteroids (ICS), and a history of
exacerbation in the preceding season [35].

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8.3 Bacteriome
In 2010, the rst distinctive microbiome analysis from bronchoscopy was obtained
using 16S rRNA gene marker sequencing technology in eight healthy individuals
[36]. Interestingly, the identied bacteria in the lower airways were found to be
distinct from those in the upper respiratory tract [36]. The bacteria associated with
lower chronic respiratory conditions might be colonized commensally in the upper
and lower respiratory tracts of healthy individuals [37]. While it is not well dened
whether the upper or lower microbiome is more relevant for asthma occurrence, the
bacterial burden in the upper airway is greater than the lower airway. The inammatory condition in the local airway impacts the lower airway health using postnasal
drip or aspiration, resulting in the downward translocation of pathogens [38, 39].
Colonization of the respiratory tract with bacterial pathogens triggers cell recruitment and inammation in the airways via enhancing inammatory response to
allergens [40].
A study conducted in the Copenhagen Childhood Birth Cohort, involving 321
neonates monitored over their rst 5 years of life, aimed to explore the potential
relationship between bacterial colonization of the hypopharynx in asymptomatic
neonates and the development of asthma [19]. The ndings indicated that colonization with Streptococcus pneumoniae, Haemophilus inuenzae, and Moraxella
catarrhalis in the airway or a combination were at greater risk for recurrent wheeze
and exacerbation, as well as asthma development via an increase in blood eosinophil and serum IgE levels [19, 41]. Subsequent follow-up studies indicated that
these bacteria are associated with asthma exacerbations [42]. Similarly, a prospective cohort study of 234 children with acute respiratory infections revealed that
colonization with Streptococcus in the nasopharynx (NP) during the critical rst
year of life is linked to childhood asthma development [42]. Additionally, the Finish
Birth Cohort Study (STEPS) made signicant progress in understanding the nasal
airway microbiome by identifying ve different microbiota proles in 923 infants at
the age of 2, including Moraxella-dominant, Streptococcus-dominant,
Dolosigranulum-dominant, Staphylococcus-dominant, and Corynebacteriaceaedominant proles [43, 44]. Among these microbiotas, Moraxella species were associated with a greater risk of respiratory diseases later in childhood [44].
A Childhood Asthma birth cohort study involving infants in the rst 2years of
life indicated that the nasopharyngeal Staphylococcus-dominant microbiome in the
rst 6months of life was associated with an increased risk of recurrent wheezing by
age 3years and asthma that persisted throughout childhood [45]. Moreover, this
path was linked with early allergen sensitization. Furthermore, in cases of wheezing, the identication of the prevalence of Moraxella was correlated with the persistence of asthma into later childhood [45]. Upon subsequent follow-up of the same
cohort, the frequency of both upper and lower respiratory tract infections was linked
to asthma development by the age of 7 [46].
Another study focusing on nasal microbiome highlighted the association of pediatric asthma with Proteobacteria and Moraxella [47]. A study involving nasal blow
samples from 214 children highlighted that airway microbiota colonization is

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differentially associated with the risk of loss of asthma control and severe exacerbation [48]. Specically, airway microbiota dominated by the Corynebacterium and
Dolosigranulum cluster was associated with a lower risk of asthma compared to
microbiota dominated by more pathogenic bacteria such as Staphylococcus,
Streptococcus, and Moraxella [45]. Likewise, a study highlighted that Moraxella
catarrhalis, an opportunistic human respiratory pathogen, has been identied as a
dominant species of nasal airway microbiotas of children (age range 6–17years)
who experience a greater frequency of exacerbation [49]. Furthermore, invitro ndings demonstrate that strains from Moraxella catarrhalis may cause epithelial damage and elevate the expression of IL-8 and IL-33 [44]. Microbial taxonomic analysis
from Chile revealed that the nasal mucosa was dominated by a high abundance of
Moraxella, Dolosigranulum, Haemophilus, Corynebacterium, Streptococcus, and
Staphylococcus, whereas the oral mucosa was characterized by a high abundance of
Streptococcus, Haemophilus, Gemella, Veillonella, Neisseria, and Porphyromonas
in asthmatic children [50]. Kim etal. demonstrated in a cross-sectional case–control
study an elevated proportion of Firmicutes in upper airway samples among individuals with asthma compared to control as well as children with asthma remission
[51]. In addition, atypical bacteria such as Mycoplasma pneumoniae and
Chlamydophila pneumoniae, recognized as common respiratory pathogens, have
been linked to asthma, wheezing, and asthma exacerbations in children [52–54].
Unlike the upper respiratory microbiota, there are only a few studies that have
reported the potential association between the lower airway microbiota and asthma
[36, 55–57]. Hilty etal. collected samples of lower airways from children with and
without asthma [36]. Microbiome analysis indicated that children with asthma are
richer in Firmicutes phyla and Haemophilus genus [36]. The use of a mouse model
of Haemophilus infection demonstrated that corticosteroid treatment, the main
treatment to reduce airway inammation in people with asthma, promotes
Haemophilus inuenzae persistence, which suggests that this bacterium may
respond directly to corticosteroid via inuencing biolm formation [58]. In line,
Ovaalbumin (OVA)-induced Haemophilus inuenzae-infected mouse shows that a
combination of infection and allergic airway disease promotes bacterial persistence,
leading to the development of steroid-resistant neutrophilic asthma [59] via immune
modulation [60]. Moreover, bronchoalveolar lavage (BAL) pellets from children
who underwent bronchoscopy over 20months with severe asthma showed signicantly enriched abundance of Bacteroides, Faecalibacterium, Roseburia,
Ruminococcus, Parabacteroides, Romboutsia, Alistipes, Eubacterium, and other
ve bacteria in comparison to control, whereas Proteus and Capnocytophaga
showed higher abundance in samples from individuals without severe asthma compared to those with the condition [57].
While association with bacteria and its potential risk for asthma development is
already multifarious, an additional layer of complexity might be added by potential
interaction between viruses and bacteria to shape host microbiome relationships by
altering mucosal surfaces. Following virus infection, cells may decrease the antibacterial peptides and induce bacterial colonization and replication both directly
and indirectly via the upregulation of adherence receptors [61]. The nested cohort

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of 118 with conrmed respiratory syncytial virus (RSV), which is one of the most
common causes of upper and lower acute respiratory infections (ARIs), indicated
that higher nasopharyngeal detection and abundance of Lactobacillus during infancy
were consistently associated with a reduced risk of subsequent wheezing illnesses
at age 2 [62].
Evidence has shown that the microbiome is associated with asthma pathogenesis, but how microbiota and their metabolites shape immune pathways to drive
asthma is still not fully understood. Depending on bacterial species, immune modulation alters. While Proteobacteria species provoke T helper (Th) 17 inammation,
which is associated with noneosinophilic asthma, some Acinetobacter species are
associated with Th2/eosinophilic asthma [63]. Bronchoalveolar lavage from children aged from 4 to 32months with wheezing has demonstrated that an increase in
the alveolar macrophages and neutrophil, but not of eosinophil and mast cells, suggests an association between bacterial colonization and initiating event of allergic
asthma [64].
8.4 Virome
Viral infections have been repeatedly and consistently associated with wheezing
[65–67]. Various evidence indicates that viral infections exacerbate asthma [68–70].
Among the plethora of respiratory viruses, in particular, rhinovirus (RV) stands out
as the predominant single trigger for exacerbations, accounting for as much as 76%
of wheezing episodes in children [67, 71–73]. In addition, early-life rhinovirus
wheezing illnesses and aeroallergen sensitization are the most potent risk factors for
asthma at school age [74]. Rhinoviruses (RVs) can induce a range of illnesses, spanning from asymptomatic infections to severe conditions affecting the lower respiratory tract [75]. RV also regulates airway hyperresponsiveness, a key characteristic
feature of asthma [76]. The Copenhagen prospective study on asthma childhood
(COPSAC) has identied RV as a pathogen inducing severe respiratory disease
potential [42, 77]. Data have highlighted that RV-induced bronchiolitis was more
strongly associated with the risk of developing wheeze and childhood asthma [73].
Notably, RV as a cause of rst-time wheezing in children using corticosteroid treatment could be effective. Clinical trials indicate that children who got a short dose of
oral corticosteroids not only wheezed less in the following year [78, 79] but also had
a 30% lower risk of developing asthma over the next 4–7years [79, 80].
Children prone to developing asthma may have a tendency to create an inammatory environment favoring Th2 responses, along with a connection to specic
risk genes like CDHR3 [71]. Factors like weakened interferon responses, a compromised airway barrier, environmental exposures (like an imbalanced airway microbiome), and nutritional deciencies (low vitamin D and sh oil) increase the risk of
infections from viruses, including RV [71]. Whether viral illnesses actually cause
asthma is still a topic of active debate.
Another prevalent respiratory virus, respiratory syncytial virus (RSV), is
among the most significant risk factors for the onset of wheezing in infants and
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