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Microbiology
Table of Contents
Unit 22 Overview: Respiratory System Infections
22.1 Anatomy and Normal Microbiota of the Respiratory Tract
22.2 Bacterial Infections of the Respiratory Tract
22.3 Viral Infections of the Respiratory Tract
22.4 Respiratory Mycoses

🦠microbiology review

22.1 Anatomy and Normal Microbiota of the Respiratory Tract

Citation:

The respiratory system is a complex network of structures that work together to facilitate breathing and protect against harmful microbes. From the nasal cavity to the alveoli, each part plays a crucial role in maintaining respiratory health and defending against pathogens.

Our respiratory tract is home to diverse microbial communities that interact with our immune system. While some microbes are beneficial, others can cause infections. Understanding these interactions is key to preventing and treating respiratory diseases.

Anatomy and Microbiota of the Respiratory Tract

Anatomical structures of respiratory tract

  • Upper respiratory tract consists of nasal cavity, pharynx, and larynx
    • Nasal cavity divided into nasal vestibule (anterior portion) and respiratory region (posterior portion) lined with ciliated epithelium and mucus-secreting goblet cells
    • Pharynx has three regions: nasopharynx (behind nasal cavity), oropharynx (behind oral cavity), and laryngopharynx (connects to esophagus and larynx)
    • Larynx contains vocal cords and epiglottis which prevents aspiration of food or liquid into the lower respiratory tract
  • Lower respiratory tract includes trachea, bronchi, bronchioles, and alveoli
    • Trachea (windpipe) is a cartilage-reinforced tube that bifurcates into right and left primary bronchi
    • Bronchi branch into smaller secondary and tertiary bronchi, which further divide into bronchioles
    • Terminal bronchioles are the smallest airways without alveoli, while respiratory bronchioles have some alveoli budding off their walls
    • Alveoli are tiny air sacs arranged in clusters (alveolar sacs) where gas exchange occurs between the lungs and bloodstream
      • Pulmonary surfactant reduces surface tension in alveoli, preventing collapse during exhalation

Microbiota in respiratory regions

  • Nasal cavity harbors skin-associated bacteria such as Staphylococcus spp. (S. aureus, S. epidermidis), Corynebacterium spp., and Propionibacterium spp. (P. acnes)
  • Nasopharynx contains potential pathogens like Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis that can cause upper respiratory infections (otitis media, sinusitis)
  • Oropharynx has a diverse microbiota including Streptococcus spp. (S. salivarius, S. mitis), Neisseria spp., and the fungus Candida albicans
  • Lower respiratory tract was traditionally thought to be sterile, but recent studies using molecular techniques suggest the presence of a lung microbiome
    • Predominant genera in the lung microbiome include Prevotella spp., Veillonella spp., and Streptococcus spp.
    • Composition of the lung microbiome can be altered in respiratory diseases (COPD, asthma, cystic fibrosis)

Respiratory tract defense mechanisms

  • Mechanical defenses:
    1. Mucociliary escalator traps inhaled particles and microbes in mucus
    2. Coordinated beating of cilia sweeps mucus towards the pharynx to be swallowed or expectorated
    3. Epiglottic reflexes prevent microbes from entering the lower respiratory tract during swallowing or vomiting
  • Innate immune defenses include antimicrobial peptides (defensins) in respiratory secretions, alveolar macrophages that phagocytose microbes, and neutrophils recruited during inflammation
    • Innate lymphoid cells contribute to mucosal immunity by producing cytokines and mediating tissue repair
  • Adaptive immune defenses involve secretory IgA antibodies that neutralize microbes and toxins, as well as T cell and B cell-mediated specific immune responses
  • Respiratory epithelium acts as a physical barrier and produces mucus, antimicrobial peptides, and inflammatory mediators

Pathogen bypass of respiratory defenses

  • Pathogens employ various strategies to evade these defenses
    • Adherence to respiratory epithelial cells via adhesins or pili
    • Secretion of toxins that damage epithelial cells and impair ciliary function
    • Resistance to phagocytosis by alveolar macrophages and intracellular killing mechanisms
    • Antigenic variation of surface structures to evade antibody recognition

Microbe-respiratory system interactions

  • Beneficial interactions:
    • Normal microbiota competes with pathogens for nutrients and attachment sites, preventing their overgrowth (colonization resistance)
    • Commensal microbes stimulate the development and regulation of the respiratory immune system
  • Pathogenic interactions:
    • Viral infections cause upper respiratory illnesses (rhinovirus, influenza) and lower respiratory infections in children (RSV)
    • Bacterial pathogens cause pneumonia (S. pneumoniae), tuberculosis (M. tuberculosis), and whooping cough (B. pertussis)
    • Fungal infections like aspergillosis (A. fumigatus) and pneumocystis pneumonia (P. jirovecii) affect immunocompromised individuals
  • Microbiome dysbiosis is associated with chronic respiratory diseases
    • COPD patients have increased Haemophilus spp. and decreased diversity in their lung microbiome
    • Asthma patients display an altered microbiome with increased Proteobacteria and decreased Bacteroidetes
    • Cystic fibrosis lungs are colonized by antibiotic-resistant Pseudomonas aeruginosa and other opportunistic pathogens

Key Terms to Review (82)

Actinobacteria: Actinobacteria are a group of Gram-positive bacteria known for their high G+C content in their DNA. They play crucial roles in soil ecosystems, human health, and the production of antibiotics.
Adhesin: Adhesins are specialized proteins expressed by pathogens to attach to host cells. They play a crucial role in the initial stages of infection by binding to specific receptors on the host cell surface.
Alveoli: Alveoli are tiny air sacs located in the lungs where gas exchange occurs between the air and the blood. They play a critical role in respiration by allowing oxygen to enter the bloodstream and carbon dioxide to be expelled.
Bronchi: The bronchi are major air passages that branch off from the trachea into the lungs. They play a crucial role in conducting air to and from the respiratory zones of the lungs.
Bronchitis: Bronchitis is an inflammation of the bronchial tubes, which carry air to and from the lungs. It often results in coughing, mucus production, and can be caused by bacterial or viral infections.
Bronchiole: Bronchioles are small air passages in the lungs that branch off from the bronchi and lead to the alveoli. They play a crucial role in regulating airflow and gas exchange.
Defensins: Defensins are small, antimicrobial peptides produced by various cells, including epithelial cells and neutrophils. They play a crucial role in the innate immune system by disrupting the membranes of pathogens.
Eikenella: Eikenella is a genus of gram-negative, facultative anaerobic bacteria that are part of the normal microbiota in the human respiratory tract. It is commonly associated with infections following human bites or fistfights.
Endotoxin: Endotoxin is a component of the outer membrane of Gram-negative bacteria, primarily composed of lipopolysaccharides (LPS). It can trigger strong immune responses when released into the host organism.
Epiglottis: The epiglottis is a leaf-shaped flap of cartilage located at the root of the tongue that covers the windpipe during swallowing to prevent food from entering the airway. It plays a crucial role in directing food and liquids into the esophagus.
Epiglottitis: Epiglottitis is a potentially life-threatening inflammation of the epiglottis, often caused by bacterial infection. It can obstruct the airway and requires immediate medical attention.
Firmicutes: Firmicutes are a phylum of predominantly Gram-positive bacteria with thick cell walls. They play a significant role in the human microbiota, particularly in the respiratory and digestive systems.
Exotoxin: Exotoxins are potent, extracellular toxins secreted by certain bacteria that can cause significant damage to the host by disrupting normal cellular processes. Unlike endotoxins, exotoxins are proteins and can be neutralized by antibodies.
Eustachian tube: The eustachian tube is a narrow canal that connects the middle ear to the nasopharynx. It helps to equalize air pressure on both sides of the eardrum.
Goblet cell: Goblet cells are specialized epithelial cells found in the respiratory and intestinal tracts, responsible for secreting mucus to protect and lubricate the lining. They play a crucial role in maintaining the mucosal barrier against pathogens.
Goblet cells: Goblet cells are specialized epithelial cells that secrete mucus to protect mucous membranes. They play a critical role in trapping pathogens and particles, preventing them from entering the body.
Laryngitis: Laryngitis is the inflammation of the larynx, often leading to a hoarse voice or loss of voice. It can be caused by viral, bacterial infections, or other irritants.
Laryngopharynx: The laryngopharynx is the lower part of the pharynx, located behind the larynx and extending to the esophagus. It serves as a pathway for both air and food.
Larynx: The larynx, also known as the voice box, is an organ located in the neck that plays a crucial role in breathing, sound production, and protecting the trachea against food aspiration. It houses the vocal cords and is involved in producing vocal sounds.
Macrophage: Macrophages are large white blood cells within tissues that engulf and digest cellular debris, foreign substances, microbes, and cancer cells. They play a crucial role in the immune system by identifying, phagocytizing, and presenting antigens to T cells.
Microbiota: Microbiota refers to the community of microorganisms, including bacteria, fungi, and viruses, that inhabit a particular environment in or on the body. These microbial communities play essential roles in health and disease.
Mucosa-associated lymphoid tissue (MALT): Mucosa-associated lymphoid tissue (MALT) is a collection of lymphoid tissues found in various mucosal membranes, including those lining the respiratory tract. It plays a crucial role in immune response by protecting mucosal surfaces from pathogens.
Mucous membrane: Mucous membranes are moist linings found in various body cavities and passages that open to the external environment. They play a crucial role in trapping pathogens and particulates, thus serving as a first line of defense.
Mucociliary escalator: The mucociliary escalator is a defense mechanism in the respiratory tract where mucus traps inhaled particles and cilia move them upwards towards the throat to be expelled or swallowed. This process helps keep the respiratory tract clear of pathogens and debris.
Nasopharynx: The nasopharynx is the upper part of the pharynx, located behind the nasal cavity and above the soft palate. It serves as a passageway for air from the nose to the throat and plays a role in respiratory functions.
Nasolacrimal ducts: Nasolacrimal ducts are small channels that drain tears from the lacrimal sac into the nasal cavity. They play a crucial role in maintaining eye moisture and can be pathways for respiratory infections.
Nasal cavity: The nasal cavity is a large, air-filled space above and behind the nose in the middle of the face. It functions as the main pathway for inhaled air to be filtered, warmed, and humidified before reaching the lungs.
Otitis: Otitis is an inflammation or infection of the ear, commonly caused by bacterial or viral pathogens. It can affect the outer, middle, or inner ear and often results in pain, swelling, and potential hearing loss.
Palatine tonsils: Palatine tonsils are two lymphoid tissues located at the back of the throat, one on each side. They play a role in immune defense by trapping and destroying pathogens entering through the mouth or nose.
Pharyngitis: Pharyngitis is the inflammation of the pharynx, causing a sore throat. It can be caused by viral or bacterial infections.
Pharynx: The pharynx is a muscular tube that connects the nasal and oral cavities to the larynx and esophagus. It plays a role in both respiratory and digestive systems by facilitating the passage of air and food.
Pneumonia: Pneumonia is an infection that inflames the air sacs in one or both lungs, which may fill with fluid or pus. It can be caused by bacteria, viruses, or fungi and results in symptoms such as cough, fever, and difficulty breathing.
Proteobacteria: Proteobacteria are a major phylum of Gram-negative bacteria that includes a wide variety of pathogenic and non-pathogenic species. They are characterized by their diverse metabolic capabilities and roles in various environments.
Pseudomonas: Pseudomonas is a genus of Gram-negative, rod-shaped bacteria known for their metabolic diversity and ability to thrive in various environments. They are often opportunistic pathogens, particularly Pseudomonas aeruginosa, which can cause infections in humans.
Respiratory system: The respiratory system consists of organs and structures involved in gas exchange, including the nose, throat, larynx, trachea, bronchi, and lungs. It serves as a primary entry point for pathogens causing respiratory infections.
Rhinitis: Rhinitis is the inflammation of the nasal mucous membranes, often resulting in symptoms such as sneezing, nasal congestion, and runny nose. It can be caused by infections, allergens, or other irritants.
Secretory IgA: Secretory IgA (sIgA) is an immunoglobulin found predominantly in mucosal areas, such as the gut, respiratory tract, and urogenital tract. It plays a crucial role in immune function by preventing colonization by pathogens.
Sinusitis: Sinusitis is the inflammation or swelling of the tissue lining the sinuses, often caused by infections. It can be classified as acute, subacute, chronic, or recurrent based on its duration and frequency.
Streptococcus: Streptococcus is a genus of Gram-positive bacteria that often occur in chains or pairs. They are known for causing a variety of infections in humans, ranging from mild throat infections to life-threatening diseases.
Staphylococcus aureus: Staphylococcus aureus is a Gram-positive bacterium commonly found on the skin and in the nasal passages. It can cause a range of infections from minor skin conditions to severe diseases like pneumonia and sepsis.
Trachea: The trachea, also known as the windpipe, is a tube that connects the larynx to the bronchi of the lungs and allows air passage. It plays a crucial role in providing airflow to and from the respiratory system.
Tonsillitis: Tonsillitis is an inflammation of the tonsils, typically caused by viral or bacterial infections. It results in sore throat, difficulty swallowing, and swollen tonsils.
Tympanic membrane: The tympanic membrane, also known as the eardrum, is a thin membrane that separates the external ear from the middle ear. It plays a crucial role in hearing by transmitting sound vibrations to the ossicles.
Viridans group streptococci: Viridans group streptococci are a heterogeneous group of alpha-hemolytic and non-hemolytic streptococci that are part of the normal microbiota of the human oral cavity and upper respiratory tract. They are generally non-pathogenic but can cause serious infections like endocarditis under certain conditions.
Pneumocystis jirovecii: Pneumocystis jirovecii is an opportunistic fungal pathogen that can cause a severe form of pneumonia, known as Pneumocystis pneumonia (PCP), in individuals with weakened immune systems. This microscopic fungus primarily infects the alveoli, or air sacs, of the lungs, leading to respiratory distress and potentially life-threatening complications.
Secretory IgA: Secretory IgA (sIgA) is a specialized antibody that plays a crucial role in the body's mucosal immune defense system. It is the predominant immunoglobulin found in external secretions, such as saliva, tears, and respiratory and intestinal fluids, where it helps protect against pathogens and maintain a healthy microbiome.
Goblet Cells: Goblet cells are specialized epithelial cells found in the mucous membranes of the respiratory and gastrointestinal tracts. They are responsible for the production and secretion of mucus, a protective and lubricating substance that helps trap and expel foreign particles, pathogens, and irritants from the body.
Defensins: Defensins are a class of antimicrobial peptides that serve as part of the innate immune system's chemical defenses against pathogens. They are found in various tissues and bodily fluids, playing crucial roles in pathogen recognition, phagocytosis, and protecting the integrity of the skin, eyes, respiratory tract, and oral cavity.
Propionibacterium acnes: Propionibacterium acnes is an anaerobic, gram-positive bacterium that is a common inhabitant of the human skin and is associated with the development of acne. It plays a significant role in the normal microbiota of the skin and eyes, as well as in bacterial infections affecting these areas.
Staphylococcus epidermidis: Staphylococcus epidermidis is a Gram-positive, coagulase-negative bacterium that is a common member of the normal human skin and mucous membrane microbiota. It is considered an opportunistic pathogen, capable of causing infections in immunocompromised individuals or when the skin barrier is breached.
Corynebacterium: Corynebacterium is a genus of Gram-positive, non-spore-forming, rod-shaped bacteria that are commonly found as part of the normal microbiota in various regions of the human body, including the skin, respiratory tract, and urogenital tract.
Oropharynx: The oropharynx is the middle part of the pharynx, the throat cavity located behind the mouth. It plays a crucial role in the anatomy and normal microbiota of the respiratory tract.
Alveoli: Alveoli are the tiny, air-filled sacs located at the end of the respiratory tree within the lungs. They are the primary site of gas exchange, where oxygen is taken in and carbon dioxide is expelled, and are crucial for the respiratory system's normal function and microbiota.
Streptococcus mitis: Streptococcus mitis is a Gram-positive, alpha-hemolytic bacterium that is a common member of the normal microbiota of the human respiratory tract. It is closely related to other streptococcal species and plays a role in maintaining the balance of the respiratory tract ecosystem.
Alveolar Macrophages: Alveolar macrophages are specialized immune cells found in the alveoli of the lungs. They play a crucial role in maintaining the normal microbiota and defending the respiratory tract against pathogens and foreign particles that enter the body through inhalation.
Upper Respiratory Tract: The upper respiratory tract refers to the anatomical region of the respiratory system that includes the nose, nasal cavity, paranasal sinuses, pharynx, and larynx. This area is responsible for the initial processing and filtering of inhaled air before it reaches the lower respiratory tract.
Epiglottis: The epiglottis is a flap of cartilage located at the base of the tongue that acts as a valve, directing the flow of air and food in the respiratory and digestive tracts.
Pulmonary Surfactant: Pulmonary surfactant is a complex mixture of lipids and proteins produced by alveolar type II cells in the lungs. It plays a crucial role in maintaining the structural integrity and functional efficiency of the respiratory system by reducing surface tension within the alveoli, preventing their collapse during expiration, and facilitating gas exchange.
Colonization Resistance: Colonization resistance refers to the ability of the normal microbiota to prevent the establishment and overgrowth of pathogenic or potentially harmful microorganisms within the human body, particularly in the respiratory tract. It is a crucial mechanism that maintains the balance and stability of the microbial community, thereby protecting the host from infections and disease.
Larynx: The larynx is a complex structure located at the upper part of the respiratory tract, responsible for producing voice and protecting the airway. It serves as a critical component in the anatomy and normal microbiota of the respiratory system.
Trachea: The trachea, also known as the windpipe, is a vital part of the human respiratory system. It is a cylindrical tube that connects the larynx (voice box) to the lungs, allowing for the passage of air during breathing.
Bronchioles: Bronchioles are the smallest air passages within the respiratory tract, branching off from the bronchi and leading directly to the alveoli. They play a crucial role in the anatomy and normal microbiota of the respiratory system.
Streptococcus salivarius: Streptococcus salivarius is a gram-positive, facultatively anaerobic bacterium that is a common member of the normal microbiota of the human oral cavity and upper respiratory tract. It is one of the earliest colonizers of the oral cavity in infants and plays a role in maintaining a healthy oral environment.
Lung Microbiome: The lung microbiome refers to the diverse community of microorganisms, primarily bacteria, that reside within the human lungs. This microbial ecosystem plays a crucial role in maintaining respiratory health and immune function.
Lower Respiratory Tract: The lower respiratory tract refers to the portion of the respiratory system that includes the trachea, bronchi, bronchioles, and alveoli. This region is responsible for the exchange of gases, primarily the intake of oxygen and the removal of carbon dioxide, which is essential for sustaining life.
Nasal Cavity: The nasal cavity is the upper part of the respiratory system, located between the nostrils and the pharynx. It serves as the primary airway for breathing and is responsible for filtering, warming, and humidifying the air before it reaches the lower respiratory tract.
Neisseria: Neisseria is a genus of Gram-negative, oxidase-positive diplococci bacteria that are commonly found as part of the normal microbiota of the human respiratory tract. These bacteria are important in the context of the anatomy and normal microbiota of the respiratory system.
Laryngopharynx: The laryngopharynx is the lower part of the pharynx, located between the oropharynx and the esophagus. It is responsible for the passage of air to and from the lungs, as well as the passage of food and liquids to the esophagus.
Ciliated Epithelium: Ciliated epithelium is a specialized type of tissue found lining the respiratory tract, including the nasal cavity, trachea, and bronchi. It is characterized by the presence of microscopic, hair-like projections called cilia that extend from the surface of the epithelial cells, which work together to move mucus and foreign particles out of the airways.
Respiratory Epithelium: The respiratory epithelium is the specialized lining of the respiratory tract, which includes the nasal passages, trachea, bronchi, and alveoli. This epithelium plays a crucial role in the normal function and defense mechanisms of the respiratory system.
Nasopharynx: The nasopharynx is the upper part of the pharynx, the cavity behind the nose. It connects the nasal passages to the throat and plays a crucial role in the respiratory and immune systems.
Moraxella catarrhalis: Moraxella catarrhalis is a Gram-negative, aerobic, diplococcus bacterium that is commonly found as part of the normal microbiota of the human upper respiratory tract. It is an opportunistic pathogen that can cause various respiratory tract infections in certain populations.
Prevotella: Prevotella is a genus of Gram-negative, anaerobic bacteria that are commonly found in the human microbiome, particularly in the respiratory, reproductive, and digestive systems. These bacteria play important roles in maintaining the balance of the microbial communities in these anatomical regions.
Veillonella: Veillonella is a genus of anaerobic, gram-negative cocci bacteria that are commonly found as part of the normal microbiota in the human respiratory and digestive systems. These bacteria play important roles in maintaining the balance and health of these microbial communities.
Mucociliary Escalator: The mucociliary escalator is a defense mechanism in the respiratory tract that uses a combination of mucus production and the coordinated movement of cilia to clear the airways of inhaled particles, pathogens, and other debris. It is a critical component of the respiratory system's innate immune response.
Respiratory Syncytial Virus (RSV): Respiratory syncytial virus (RSV) is a common respiratory virus that can cause severe illness in infants, young children, and older adults. It is a leading cause of bronchiolitis and pneumonia in young children and is particularly important in the context of the anatomy and normal microbiota of the respiratory tract.
Innate Lymphoid Cells: Innate lymphoid cells (ILCs) are a group of lymphocytes that do not express antigen-specific receptors, but play a crucial role in the innate immune response and the maintenance of tissue homeostasis in the respiratory tract and other mucosal sites.
Bronchi: The bronchi are the primary airway branches that extend from the trachea and carry air into and out of the lungs. They are a critical component of the respiratory system, playing a vital role in both the anatomy and function of the respiratory tract.
Mucosal Immunity: Mucosal immunity refers to the specialized immune defenses that protect the moist, exposed surfaces of the body, such as the respiratory, gastrointestinal, and urogenital tracts. It serves as the first line of defense against pathogens that attempt to enter the body through these vulnerable mucosal sites.
Gas Exchange: Gas exchange is the process by which oxygen and carbon dioxide are exchanged between the body and the environment. It is a crucial physiological function that occurs in the respiratory system, allowing the body to obtain oxygen for cellular respiration and remove carbon dioxide as a waste product.
Aspergillus fumigatus: Aspergillus fumigatus is a ubiquitous fungus that can cause a range of respiratory infections, from mild allergic responses to life-threatening invasive disease. It is a key topic in the study of fungi, the anatomy and microbiota of the respiratory tract, as well as respiratory mycoses.
Rhinovirus: Rhinoviruses are a group of small, non-enveloped RNA viruses that are the primary causative agents of the common cold. They are closely associated with infections of the upper respiratory tract and play a significant role in viral infections discussed in the context of the anatomy and normal microbiota of the respiratory tract, as well as viral infections of the respiratory tract.