Microbial Infections Affecting the Respiratory System: Structure, Pathogens, and Clinical Syndromes

CHAPTER 19: Respiratory System Structure and Normal Biota

Anatomy of the Respiratory System

The respiratory system is divided into the upper and lower tracts, each with distinct anatomical features and clinical significance. Understanding these divisions is essential for identifying the sites of infection and the pathogens involved.

• Upper respiratory tract: Includes the mouth, nose, nasal cavity, sinuses, pharynx, epiglottis, and larynx.

• Lower respiratory tract: Comprises the trachea, bronchi, bronchioles, and alveoli.

Normal Biota of the Respiratory Tract

The respiratory tract harbors a diverse normal microbiota, predominantly Gram-positive bacteria. While many are harmless, some can become opportunistic pathogens under certain conditions.

• Common genera: Streptococcus, Staphylococcus

• Potential pathogens: Streptococcus pyogenes, Haemophilus influenzae, Streptococcus pneumoniae, Neisseria meningitidis, Staphylococcus aureus

• Fungi: Candida albicans colonizes the oral mucosa

Microbial Diseases of the Upper Respiratory Tract

Pharyngitis

Pharyngitis is an inflammation of the throat, often presenting with redness, swelling, and sometimes white exudates. It can be caused by viruses or bacteria, with Streptococcus pyogenes being a significant bacterial agent.

• Symptoms: Sore throat, swollen mucosa and tonsils, foul breath, white patches (streptococcal disease)

• Causative agents: Common cold viruses, Streptococcus pyogenes

• Transmission: Respiratory droplets, direct contact, fomites

• Complications: Scarlet fever (sandpaper rash, high fever), rheumatic fever (heart valve damage, arthritis)

• Diagnosis: Rapid diagnostic tests, culture confirmation

• Treatment: Antibiotics

• Prevention: Good hand hygiene

Rhinitis (Common Cold)

Rhinitis, or the common cold, is a self-limiting viral infection affecting the upper respiratory tract. It is highly contagious and caused by a variety of viruses.

• Causative agents: Over 200 viruses, including rhinoviruses, coronaviruses, adenoviruses, RSV

• Transmission: Indirect contact, droplets

• Symptoms: Sneezing, runny nose, scratchy throat, low fever (especially in children)

Sinusitis

Sinusitis is the inflammation of the sinuses, which can be caused by viruses, bacteria, fungi, or noninfectious factors such as allergies or structural abnormalities.

• Causative agents: Mixed viral, bacterial, or fungal infections

• Treatment: Broad-spectrum antibiotics (bacterial), antifungals/surgery (fungal)

Acute Otitis Media (Ear Infection)

Acute otitis media is a common complication of upper respiratory infections, especially in children. It involves infection and inflammation of the middle ear.

• Causative agents: Mixed viral and bacterial, notably Streptococcus pneumoniae and Haemophilus influenzae

• Pathogenesis: Bacteria enter the middle ear, multiply, and cause inflammation and fluid accumulation

• Prevention: Vaccines (Prevnar for S. pneumoniae, Hib for H. influenzae)

• Treatment: Watchful waiting, antibiotics, tympanic membrane tubes

Diphtheria

Diphtheria is a potentially life-threatening infection of the upper respiratory tract caused by Corynebacterium diphtheriae. The disease is characterized by the formation of a pseudomembrane in the throat.

• Causative agent: Corynebacterium diphtheriae

• Transmission: Droplet, direct contact, fomites

• Virulence factor: Diphtheria exotoxin

• Symptoms: Sore throat, formation of a grayish membrane (fibrin, tissue, bacteria)

• Prevention: DTaP vaccine (diphtheria toxoid)

• Treatment: Penicillin

Microbial Diseases of the Upper and Lower Respiratory Tract

Influenza

Influenza is a highly contagious viral infection that affects both the upper and lower respiratory tracts. It is caused by influenza viruses A, B, and C, which are enveloped RNA viruses with surface glycoproteins hemagglutinin (H) and neuraminidase (N).

• Symptoms: Headache, chills, dry cough, body aches, fever, sore throat, extreme fatigue

• Causative agents: Influenza A, B, and C viruses

• Transmission: Aerosols, droplets, fomites; facilitated by crowding and dry air

• Prevention: Inactivated and live attenuated vaccines

• Antigenic variation:

  • Antigenic drift: Point mutations in H or N genes, allowing immune evasion

  • Antigenic shift: Genetic reassortment between strains, leading to new subtypes

Type	Antigenic Subtype	Year	Severity
A	H3N2, H1N1, H2N2	1889, 1918, 1957, 1968, 1977	Moderate to Severe
B	None	1940	Moderate
C	None	1947	Very mild

Pertussis (Whooping Cough)

Pertussis is a highly contagious bacterial disease caused by Bordetella pertussis. It is characterized by severe coughing fits and is preventable by vaccination.

• Causative agent: Bordetella pertussis

• Transmission: Droplet contact

• Symptoms: Runny nose (early), followed by paroxysmal coughing

• Prevention: DTaP vaccine, antibiotic prophylaxis for contacts

• Treatment: Supportive care, antibiotics

Respiratory Syncytial Virus (RSV) Disease

RSV is the most common cause of lower respiratory tract infections in infants and young children. It can cause severe bronchiolitis and pneumonia.

• Causative agent: Respiratory syncytial virus (RSV)

• Transmission: Droplets, fomites; peak in winter and early spring

• Symptoms: Cold-like illness, formation of syncytia (giant cells)

• Prevention: Passive antibody for high-risk children

• Treatment: Ribavirin in severe cases

Microbial Diseases of the Lower Respiratory Tract

Tuberculosis

Tuberculosis (TB) is a chronic infectious disease caused by Mycobacterium tuberculosis. It primarily affects the lungs but can disseminate to other organs.

• Forms: Primary (lung granulomas), secondary (reactivation, chronic symptoms), extrapulmonary (spread to other organs)

• Symptoms: Cough, bloody sputum, fever, weight loss, night sweats

• Transmission: Airborne droplets

• Diagnosis: Tuberculin skin test (Mantoux), chest X-ray, acid-fast staining, culture

• Prevention: Isolation, BCG vaccine (not used in US)

• Treatment: Combination antibiotics (isoniazid, rifampin)

Pneumonia

Pneumonia is an inflammatory condition of the lung alveoli, which become fluid-filled. It can be caused by bacteria, viruses, or fungi and is classified as community-acquired or nosocomial (hospital-acquired).

• Community-acquired agents: Streptococcus pneumoniae (most common), Legionella spp., Mycoplasma pneumoniae, viruses (SARS, COVID-19)

• Nosocomial agents: Polymicrobial, including Streptococcus pneumoniae, Klebsiella pneumoniae, anaerobes, coliforms

• Prevention: Vaccines (Pneumovax), infection control in hospitals

• Treatment: Empiric broad-spectrum antibiotics

Coronavirus Infections (SARS, MERS, COVID-19)

Coronaviruses are RNA viruses with crown-like spikes. Several strains cause mild colds, but novel coronaviruses have caused severe respiratory syndromes in recent decades.

• Notable diseases: SARS (10% mortality), MERS (35% mortality), COVID-19 (2% mortality)

• Symptoms: Flu-like illness, cough, fever, fatigue, myalgia, sore throat, congestion

• Transmission: Zoonotic spillover (bats, intermediate hosts), human-to-human via droplets

• Prevention: Masks, social distancing, hand hygiene

• Treatment: Antivirals (remdesivir), steroids (dexamethasone), mRNA vaccines

Summary Table: Major Respiratory Pathogens and Diseases

Disease	Causative Agent	Transmission	Prevention	Treatment
Pharyngitis	Streptococcus pyogenes, viruses	Droplets, contact	Hygiene	Antibiotics (bacterial)
Rhinitis	Rhinoviruses, others	Droplets, contact	Hygiene	Supportive
Sinusitis	Mixed bacteria/viruses/fungi	Varied	None specific	Antibiotics/antifungals
Otitis Media	S. pneumoniae, H. influenzae	Secondary to URIs	Vaccines	Antibiotics
Diphtheria	C. diphtheriae	Droplets, contact	DTaP vaccine	Penicillin
Influenza	Influenza viruses	Droplets, fomites	Vaccines	Antivirals
Pertussis	B. pertussis	Droplets	DTaP vaccine	Antibiotics
RSV	RSV	Droplets, fomites	Passive antibody	Ribavirin
Tuberculosis	M. tuberculosis	Airborne droplets	Isolation, BCG	Combination antibiotics
Pneumonia	S. pneumoniae, others	Droplets, aspiration	Vaccines, hygiene	Antibiotics
COVID-19	SARS-CoV-2	Droplets, contact	mRNA vaccine	Antivirals, supportive