Respiratory Microbiology

• Respiratory tract infections


  • Sinusitis
  • Nasopharyngitis (common cold)
  • Otitis (media and externa)
  • Tonsillitis
  • Pharyngitis
  • Epiglottis
  • Laryngitis
  • Tracheitis
  • Bronchiolitis
  • Bronchitis
  • Pulmonary tuberculosis
  • Pneumonia
  • Empyema
• The respiratory tract is a continuum, but we make a distinction
• Like many human emotions, the deeper they go the more difficult to get rid of them (if at all)
• There is a direct link to the environment through the oral cavity
• Whatever starts up top has a chance to reach the bottom
• We breathe 12 times/minute, 0.5 liters of air each time, inhaling 860,000 bacteria/day from 200-300 different species from at least 7 different phyla
• 100 times more bacteria at night, think when you jog
• Infectious disease

  The science of likelihood & intent
• A "multiphase turbulent buoyant cloud" (no need to learn the term)
• Fungi can remain in suspension 30 meters away
• Types of respiratory tract pathogens

  • Microbiota
  • The professionals (invaders)
  • Secondary invaders
• The professionals (invaders)


  • Mycobacterium tuberculosis
  • Influenza virus
  • Rhinovirus (Picornaviridae)
  • Streptococcus pneumoniae
  • Streptococcus pyogenes
  • Bordetella pertussis
  • Legionella pneumophila
  • Corynebacterium diphteriae
• Secondary invaders


  • Streptococcus pneumoniae
  • Streptococcus pyogenes
• S. pneumoniae depressed immune responses (e.g. HIV)

  Pneumonia
• Secondary invaders initial infection (e.g., influenza)

  S. aureus
• Impaired local responses (e.g. CF)

  Pseudomonas aeruginosa
• Depressed resistance (e.g., alcoholism, elderly, organ dysfunction)


  Haemophilus influenza, Mycobacterium tuberculosis, Pneumocystis jirovecii, CMV
• Viruses (the good news)

  • Typically acquired through close contact
  • Typically acquired during childhood
  • Typically often virtually asymptomatic
  • Typically transient
  • Typically leading to sustained protective immune responses
  • Typically have low survival in the environment
  • There is a few vaccines available
• Viruses (the bad news)

  • Normally diagnosed on clinical presentation (serology and PCR becoming more common)
  • Generic early symptoms (fever, malaise, rash)
  • Some viruses are immediately life-threatening (e.g., SARS - severe acute respiratory syndrome)
  • Only a few vaccines available
  • Antiherpetic/antiretrovial drugs can be effective but problems with efficacy and treatment resistance (e.g., aciclovir)
  • Few other treatments are available
  • Clinical presentations in immunocompromised patients are extreme
  • Potential for persistence, virus reactivation, oncogenesis (i.e., tumours, e.g., HBV, HCV)
  • They survive for longer than one may expect
  • Multiple varieties for every virus
  • Often airborne or present in bodily fluids
• Common cold


  Nasopharyngitis = rhinitis + pharyngitis + fever
• Rhinovirus


  • Common cold, aerosol; contact everyone; 1 bill. / yr in the US
  • Inflammation of the nose mucous membrane
  • Diagnosis: clinical
  • Rhinovirus, replication 33oC
  • Mainly viruses: Rhinoviruses (2/3rd of cases), Coronaviruses (CoV), Influenza (flu) virus, Parainfluenza virus, Respiratory Syncytial Virus (RSV), HSV, Coxsackie Virus A
  • Inflammation pharynx mucous membrane & lymphoid tissue
• Causes of Pharyngitis/Tonsilitis


  • Common cold viruses and Coxsackie virus A (Herpangina), EBV, HSV
  • Streptococcus pyogenes, Corynebacterium diphteriae, Neisseria gonorrhoea, Mycoplasma pneumoniae
• Pharyngitis / Tonsilitis


  • Sore throat, headache, patchy exudates, cervical lymphadenopathy, chills
  • Orally: mucositis & gingivitis, erythema & discomfort, petechiae on soft palate
  • Generic features: malaise, fever
• HCoV infections (UK) are not that rare
• Group A Streptococci


  • Streptococcus pyogenes
• Group B Streptococci


  • Streptococcus agalactiae
• Streptococcus pyogenes


  Group A Streptococcus (GAS)
• Streptococcus agalactiae


  Group B Streptococcus
• Microorganisms that can cause pneumonia

  • Streptococcus pneumoniae
  • Haemophilus influenzae
  • Mycoplasma pneumoniae
  • Legionella pneumophila
  • Staphylococcus aureus
  • Chlamydophilia pneumoniae
  • Coxiella burnetii
  • Moraxella catharralis
  • Mycobacterium tuberculosis
  • Klebsiella pneumoniae
  • Respiratory Syncytial Virus (RSV)
  • Influenza virus
  • Mumps virus
  • Varicella Zoster Virus (VZV)
  • Candida
  • Histoplasma
  • Coccidium
  • Pneumocystis
  • Toxoplasma
• Streptococcus pneumoniae is a common cause of bacterial pneumonia
• Legionella pneumophila causes pneumonia with no sputum production and gastrointestinal symptoms
• Staphylococcus aureus can cause pneumonia after influenza infection
• Mycobacterium tuberculosis can directly cross the lung fissures, as can some fungal infections like actinomycosis, blastomycosis, and mucormycosis
• Viruses or Mycoplasma pneumoniae typically have normal or lower white blood cell counts
• Without a chest X-ray, pneumonia can be difficult to distinguish from other common respiratory infections, posing a challenge for GPs in primary care
• 1. Reactive Protein (CRP) testing, along with signs and symptoms, can help diagnose pneumonia when chest X-rays are not readily available
• Pneumoniae


  Inflammation of the lungs
• Bronchitis


  Inflammatory condition of the tracheobronchial tree
• Typical symptoms of bronchitis

  • Nagging cough (most common)
  • No fever or chills (typically)
  • Yellow/green sputum (approx. 50% patients)
  • Shortness of breath
  • Sore throat
  • Runny or stuffy nose
  • Headaches
  • Muscle aches
  • Extreme fatigue
• Bronchitis is typically self-limiting (3 weeks)