Microbiology of the Respiratory System

Normal Microbiota of the Respiratory System

• Suppress pathogens through competitive inhibition in the upper respiratory system
• The lower respiratory system is generally sterile, primarily due to alveolar macrophages

Test Your Understanding (Respiratory Tract)

• Nasal hairs function to filter inhaled air
• Lower respiratory tract is mostly sterile due to the actions of alveolar macrophages

Test Your Understanding (Respiratory Diseases)

• The lower respiratory system is comprised of the lungs, bronchi, and trachea
• The pharynx is part of the upper respiratory system

Streptococcal Pharyngitis (Strep Throat)

• Causative agent: Streptococcus pyogenes
• Resistant to phagocytosis
• Symptoms: local inflammation and fever; swelling of tonsils and potential ear infections
• Diagnosis via enzyme immunoassay (EIA) tests
• Treatment: penicillin
• Scarlet fever: related condition with pink-red rash and fever, produced by erythrogenic toxins from lysogenized S. pyogenes.

Diphtheria

• Causative agent: Corynebacterium diphtheriae, gram-positive rod
• Symptoms: sore throat, fever, malaise, swelling of the neck; gray membrane formation
• Diagnosis via tests for presence of diphtheria toxin
• Treatment: antibiotics and antitoxins
• Prevention through DTaP vaccine (diphtheria toxoid)

Otitis Media

• Common bacterial causes:
  • S. pneumoniae
  • H. influenzae
  • M. catarrhalis
  • S. pyogenes
  • S. aureus
• Incidence of S. pneumoniae reduced by vaccine

Common Cold

• Primarily caused by rhinoviruses (~30-50%) and coronaviruses (~10-15%)
• Symptoms last about a week, with complications possible such as laryngitis and otitis media
• Cough suppressants and antihistamines can ease discomfort, but don't hasten recovery

Upper Respiratory Diseases

• Pharyngitis (sore throat)
• Laryngitis (inflammation of larynx)
• Tonsillitis (inflammation of tonsils)
• Sinusitis (inflammation of sinuses)
• Epiglottitis (inflammation of epiglottis), often due to H. influenzae type b

Lower Respiratory System Diseases- Pertussis (Whooping Cough)

• Causative agent: Bordetella pertussis
• Symptoms characterized by stages including catarrhal, paroxysmal, and convalescent
• Severity in paroxysmal stage with prolonged coughing
• Transmission through airborne droplets
• Prevention through DTaP vaccine (acellular Pertussis cell fragments)

Tuberculosis

• Causative agent: Mycobacterium tuberculosis
• Transmitted human-to-human, with a <1% rate from M. bovis
• Symptoms can vary from initial infection to a mature tubercle
• Diagnosis involves microscopic examination of sputum, blood tests, and skin tests.
• Treatment is prolonged (6+ months) multiple antibiotic treatment

Detection of Tuberculosis

• Microscopic examination of sputum
• Blood tests, measuring release of IFN-y from white blood cells
• Nucleic acid amplification tests (NAATs)
• Skin test

Pneumonia (General)

• Infectious inflammation of the alveoli (air sacs of lungs) characterized by fluid accumulation.
• Bacterial, viral, or fungal causes

Haemophilus influenzae Pneumonia

• Predisposing factors: alcoholism, poor nutrition, cancer, diabetes
• Symptoms resemble pneumococcal pneumonia
• Diagnosis by isolation, special media (X and V factors)
• Treatment: cephalosporins

Pneumococcal Pneumonia

• Causative agent: Streptococcus pneumoniae (encapsulated diplococci)
• Symptoms: infected alveoli, fluid accumulation interfering with oxygen uptake
• Diagnosis: optochin-inhibition test, bile solubility test, or serological typing tests on bacteria
• Treatment: macrolides, fluoroquinolones
• Prevention: pneumococcal vaccines

Mycoplasmal Pneumonia

• Causative agent: Mycoplasma pneumoniae (wall-less bacteria)
• Symptoms: generally mild, respiratory symptoms, cough, headache
• Diagnosis: PCR, serological (IgM) testing
• Treatment: tetracyclines

Legionellosis

• Causative agent: Legionella pneumophila
• Transmitted by inhaling aerosols; not by person-to-person
• Symptoms: potentially fatal pneumonia
• Diagnostic methods: culture on selective media, DNA probe
• Treatment: erythromycin

Psittacosis (Ornithosis)

• Causative agent: Chlamydophila psittaci
• Transmitted to humans by elementary bodies from bird droppings; reorganizes into reticulate body in host cells
• Symptoms: fever, headache, chills
• Diagnosis via bacteria growth in eggs or cell cultures
• Treatment: tetracyclines

Pontiac Fever

• Causative agent: Legionella pneumophila
• Mild respiratory infection characterised by fever, muscle aches, and cough
• Self-limiting condition

Chlamydial Pneumonia

• Causative agent: Chlamydophila pneumoniae
• Transmitted from person to person
• Affects mostly young people
• Symptoms resembling mycoplasmal pneumonia
• Diagnosis via serological tests
• Treatment: tetracyclines

Q Fever

• Causative agent: Coxiella burnetii
• Reservoir: large mammals; can be contracted from unpasteurized milk
• Symptoms: mild respiratory disease, complications include endocarditis
• Diagnosis by detection in cell culture
• Treatment: doxycycline

Melioidosis

• Causative agent: Burkholderia pseudomallei
• Reservoir: soil
• Symptoms are pneumonia or tissue abscesses, and severe sepsis
• Diagnosis: bacterial culture
• Treatment: ceftazidime

Pneumocystis Pneumonia

• Causative agent: Pneumocystis jirovecii
• Symptoms: Pneumonia, few symptoms if unaffected immune system
• Diagnosis: microscopy
• Treatment: trimethoprim

Blastomycosis

• Causative agent: Blastomyces dermatitidis
• Reservoir: soil in the Mississippi valley
• Symptoms: abscesses, cutaneous ulcers, extensive tissue damage
• Diagnosis: Isolation of pathogen from pus or biopsy specimens.
• Treatment: amphotericin B

Coccidioidomycosis

• Causative agent: Coccidioides immitis (Valley fever)
• Reservoir: desert soils of the southwestern U.S.
• Symptoms: chest pain, fever, and cough
• Diagnosis: serological tests.
• Treatment: amphotericin B.

Case Studies

(These are presented in the provided text but need details for specific notetaking)

COVID-19

• Causative agent: Betacoronavirus SARS-CoV-2
• Transmission: droplets or aerosols
• Symptoms: range from minor to severe
• Diagnostic methods: home ELISA test kits, PCR
• Treatment: varying, including remdesivir, Paxlovid, and convalescent plasma

Respiratory Syncytial Virus (RSV)

• Common in infants; causes significant respiratory infections
• Causes cell fusion (syncytium) in cell culture
• Symptoms: pneumonia in infants
• Diagnosis: serological test
• Treatment: ribavirin, palivizumab

Influenza (Flu)

• Symptoms: chills, fever, aches.
• Transmission: airborne droplets
• Diagnosis: PCR or serological test
• Treatment: zanamivir, oseltamivir
• Prophylaxis: multivalent vaccine