Infectious Diseases Manifesting in the Respiratory System: Microbiology Study Notes

Chapter 22: Infectious Diseases Manifesting in the Respiratory System

22.1 The Respiratory Tract, Its Defenses, and Normal Biota

The respiratory tract is a major portal of entry for pathogens and is divided into upper and lower sections, each with specialized defenses and resident microbiota. Understanding these components is essential for recognizing how infections develop and are prevented.

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

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

Anatomical Defenses

• Nasal hairs: Trap larger particles and pathogens.

• Ciliated epithelium (ciliary escalator): Moves mucus and trapped particles upward toward the throat for removal.

• Mucus: Traps microbes and debris.

• Coughing and sneezing: Expel irritants and pathogens.

• Swallowing: Moves trapped microbes to the stomach for destruction.

Normal Biota of the Respiratory Tract

The respiratory tract harbors a diverse microbiome, with certain bacteria considered part of the normal flora but capable of causing disease under specific conditions.

• Streptococcus pyogenes

• Haemophilus influenzae

• Streptococcus pneumoniae

• Neisseria meningitidis

• Staphylococcus aureus

Research indicates that the composition of the lung microbiome can be altered in patients with certain lung disorders.

Defenses	Normal Biota
Nasal hair, ciliary escalator, mucus, involuntary responses (coughing, sneezing), secretory IgA, alveolar macrophages, cytokines, complement	Large number of genera. Most abundant: Streptococcus, Prevotella, Sphingomonas, Pseudomonas, Acinetobacter, Fusobacterium, Megasphaera, Veillonella, Staphylococcus. Note: Streptococcus pyogenes, Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Staphylococcus aureus often present as "normal biota".

22.2 Infectious Diseases Manifesting in the Upper Respiratory Tract

Several infectious diseases primarily affect the upper respiratory tract, including the common cold, sinusitis, otitis media, and pharyngitis.

The Common Cold

• Causative organisms: Approximately 200 viruses (rhinoviruses, adenoviruses, coronaviruses)

• Transmission: Indirect contact, droplet contact

• Virulence factors: Attachment proteins; symptoms mainly due to host immune response

• Prevention: Hygiene practices

• Treatment: Symptomatic relief only

• Epidemiology: Highest incidence among preschool and elementary schoolchildren; adults average 2–4 colds/year

Causative Organism(s)	Most Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Epidemiological Features
~200 viruses (rhinoviruses, adenoviruses, coronaviruses)	Indirect contact, droplet contact	Attachment proteins; host response	Not necessary	Hygiene	Symptomatic	Preschool/elementary: 3–8 colds/year; adults: 2–4/year

Sinusitis

• Causative organisms: Viruses, various bacteria (often mixed), various fungi

• Transmission: Direct/indirect contact (viruses), endogenous (bacteria), trauma/opportunistic (fungi)

• Distinctive features: Viral and bacterial much more common than fungal; suspect fungi in immunocompromised patients

Causative Organism(s)	Most Common Modes of Transmission	Culture/Diagnosis	Prevention	Treatment	Distinctive Features	Epidemiological Features
Viruses	Direct/indirect contact	Not usually performed; diagnosis based on clinical presentation	Hygiene	None	Viral/bacterial more common than fungal	Commonly follows cold
Bacteria	Endogenous (opportunism)	Clinical presentation; imaging if needed	N/A	Antibiotics for severe cases	Viral/bacterial more common than fungal	1/7 adults in US; 12–30 million diagnoses/year
Fungi	Trauma/opportunistic	Same as above	N/A	Antifungals if needed	Suspect in immunocompromised	Rare in healthy; more common in India, North Africa, Middle East

Otitis Media (Middle Ear Infection)

• Causative organisms: Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Streptococcus pyogenes, Staphylococcus aureus, Candida auris

• Transmission: Endogenous (may follow upper respiratory tract infection)

• Virulence factors: Capsule, hemolysin (bacteria); biofilm formation (Candida auris)

• Prevention: Pneumococcal conjugate vaccine (PCV13)

• Treatment: Wait for resolution or antibiotics if needed; consult CDC for Candida auris

• Epidemiology: 30% of cases in US children; Candida auris increasing globally

Causative Organism(s)	Most Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Epidemiological Features
Streptococcus pneumoniae	Endogenous	Capsule, hemolysin	Clinical symptoms, failure to resolve in 72 hr	PCV13 vaccine	Wait/antibiotics	30% of US cases
Candida auris	Not known	Biofilm formation	MALDI-TOF/PCR	Consult CDC	Consult CDC	First reported 2009; increasing

Pharyngitis

• Definition: Inflammation of the throat causing pain and swelling

• Causative organisms: Viruses, Streptococcus pyogenes, Fusobacterium necrophorum

• Symptoms: White packets on throat, difficulty swallowing, foul breath; viral is mild, bacterial is more severe with fever, headache, nausea

Causative Organism(s)	Most Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Distinctive Features	Epidemiological Features
Streptococcus pyogenes	Droplet/direct contact	LTA, M protein, hyaluronic acid capsule, SLS/SLO, superantigens	Beta-hemolytic on blood agar, rapid tests	Hygiene	Penicillin, cephalexin	More severe than viral	20–30% of pharyngitis in children
Fusobacterium necrophorum	Endogenous	Invasiveness, endotoxin	Cultured anaerobically, CT for abscess	Hygiene	Penicillin	Can lead to Lemierre’s syndrome	15% of teens/adults
Viruses	All forms of contact	N/A	Rule out S. pyogenes/F. necrophorum	Hygiene	Symptomatic	Hoarseness accompanies viral	40–60% of all pharyngitis

Streptococcus pyogenes and Its Complications

• Characteristics: Gram-positive coccus, grows in chains, facultative anaerobe, produces capsules and slime layer

• Complications if untreated: Scarlet fever, rheumatic fever, glomerulonephritis

Virulence Factors of Streptococcus pyogenes

• Surface antigens mimic host proteins

• M protein resists phagocytosis and aids adhesion

• Surface antigens protect from lysozyme

• Streptolysin O and S: injure cells/tissues

• Erythrogenic toxin (lysogenic strains): key for scarlet fever

• Some toxins act as superantigens

Fusobacterium necrophorum

• Gram-negative bacterium

• Causes 15% of acute pharyngitis in >15 years group

• Can cause Lemierre’s syndrome (peritonsillar abscess, life-threatening)

22.3 Infectious Diseases Manifesting in Both the Upper and Lower Respiratory Tracts

Some pathogens can affect both upper and lower respiratory tracts, leading to more severe or systemic disease.

Whooping Cough (Pertussis)

• Causative agent: Bordetella pertussis (small, gram-negative rod, strictly aerobic, fastidious)

• Phases:

  • Catarrhal: cold symptoms

  • Paroxysmal: uncontrollable coughing with "whoop" sound, possible complications (hemorrhage, vomiting)

  • Convalescent: recovery, ciliated epithelia damaged

• Virulence factors: Filamentous hemagglutinin (attachment), pertussis toxin (mucus production), tracheal cytotoxin (ciliated cell destruction), endotoxin (cytokine production)

• Vaccine: Acellular (DTaP); booster needed after age 11

Causative Organism(s)	Most Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Epidemiological Features
Bordetella pertussis	Droplet contact	FHA, pertussis toxin, tracheal cytotoxin, endotoxin	PCR/growth on selective media; symptoms	Acellular vaccine (DTaP), azithromycin for contacts	Azithromycin; drug resistance emerging	US: 19,000 cases (2017); global: millions annually

Respiratory Syncytial Virus (RSV) Disease

• Causative agent: Respiratory syncytial virus (RSV)

• Transmission: Droplet and indirect contact

• Virulence factor: Syncytia formation (fusion of host cells)

• Prevention: Passive antibody (monoclonal) in high-risk children

• Treatment: Ribavirin plus passive antibody in severe cases

• Epidemiology:

Causative Organism(s)	Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Epidemiological Features
RSV	Droplet, indirect contact	Syncytia formation	RT-PCR	Passive antibody (high-risk)	Ribavirin, passive antibody	US:

22.4 Infectious Diseases Manifesting in the Lower Respiratory Tract

Lower respiratory tract infections are often more severe and can be life-threatening, especially in vulnerable populations.

Influenza

• Causative agents: Influenza viruses A, B, or C (family Orthomyxoviridae)

• Reasons for study: High mortality potential, frequent misdiagnosis, rapid viral evolution

• Symptoms: Headache, chills, dry cough, body aches, fever, sore throat, extreme fatigue, risk of secondary infections (e.g., pneumonia)

• High-risk groups: Very young, elderly, pregnant, or those with chronic diseases

Structure and Virulence Factors

• Hemagglutinin (H): Agglutinates red blood cells, binds to host cell receptors

• Neuraminidase (N): Breaks down mucus, assists in viral budding/release, host cell fusion

Mutation of Glycoproteins

• Antigenic drift: Gradual amino acid changes in antigens; reduces host memory cell recognition

• Antigenic shift: Exchange of RNA segments between different influenza viruses; leads to pandemics

Prevention and Epidemiology

• Annual vaccination (inactivated, trivalent or quadrivalent)

• Vaccine does not cause flu; research ongoing for universal vaccines

• Seasonal flu deaths: US (17,000–52,000/year); global (250,000–500,000/year)

Causative Organism(s)	Most Common Modes of Transmission	Virulence Factors	Culture/Diagnosis	Prevention	Treatment	Epidemiological Features
Influenza A, B, C viruses	Droplet, direct/indirect contact	Glycoprotein spikes, antigenic drift/shift	RT-PCR (gold standard)	Annual vaccination	Oseltamivir (Tamiflu), baloxavir (Xofluza)	US: 17,000–52,000 deaths/year; global: 250,000–500,000

Key Terms and Concepts

• Ciliary escalator: Mechanism by which cilia move mucus and trapped particles out of the respiratory tract.

• Superantigen: Toxin that causes excessive activation of the immune system.

• Antigenic drift: Minor genetic changes in viral antigens.

• Antigenic shift: Major genetic reassortment leading to new viral subtypes.

Additional info: These notes are based on textbook slides and are suitable for exam preparation in a college-level microbiology course. For more details on lower respiratory tract diseases (e.g., tuberculosis, pneumonia), refer to subsequent sections of the chapter.