COVID-19 pandemic

During the pandemic, consider all patients with cough and fever or suggestive symptoms to have COVID-19 until proven otherwise. See our topic Coronavirus disease 2019 (COVID-19).

The National Institute for Health and Care Excellence (NICE) in the UK has issued new guidelines on assessment and management of suspected or confirmed CAP during the COVID-19 pandemic.1,2 It has temporarily withdrawn its pre-COVID-19 guideline on diagnosis and management of pneumonia in adults.3

The key changes are that the new guidance:1,2

  • Notes that the CRB-65 tool, recommended for severity assessment in its pre-COVID-19 guidance, is not validated in people with COVID-19, as it requires a blood pressure measurement, which may be ‘difficult or undesirable’ to obtain during the COVID-19 pandemic.1 It recommends using clinical judgement to assess severity and inform decisions on hospital admission during the pandemic.1
    Signs and symptoms of severe illness are:1
    • Severe shortness of breath at rest or difficulty breathing
    • Coughing up blood
    • Blue lips or face
    • Feeling cold and clammy with pale or mottled skin
    • Collapse or fainting (syncope)
    • New confusion
    • Becoming difficult to rouse
    • Little or no urine output.
  • Recommends considering a SARS-CoV2 polymerase chain reaction test in all patients with suspected moderate to severe CAP and in all patients who develop pneumonia while in hospital.2
  • Recommends oral doxycycline first line (in preference to oral amoxicillin) in all non-pregnant patients with suspected bacterial CAP treated in the community with oral amoxicillin as an alternative.1 It includes oral doxycycline as a recommended first-line option in patients with moderate or severe bacterial CAP treated in hospital who can tolerate oral medicines and whose condition is not severe enough to need intravenous antibiotics.2
    • Doxycycline has a broader spectrum of cover than amoxicillin, particularly against Mycoplasma pneumoniae and Staphylococcus aureus, which are more likely to be secondary bacterial causes of pneumonia during the COVID-19 pandemic.1


  1. National Institute for Health and Care Excellence. COVID-19 rapid guideline: managing suspected or confirmed pneumonia in adults in the community. April 2020 [internet publication].
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  2. National Institute for Health and Care Excellence. COVID-19 rapid guideline: antibiotics for pneumonia in adults in hospital. May 2020 [internet publication].
    Full text
  3. National Institute for Health and Care Excellence. Pneumonia in adults: diagnosis and management. Sep 2019 [internet publication]. WITHDRAWN during COVID-19 pandemic.
    Full text


Streptococcus pneumoniae (the pneumococcus) is the most common causative pathogen of CAP across a range of severities and patient ages.[15][16][17][18][19] However, other studies have found that influenza virus is the most common cause of CAP in adults.[7][13] In Europe and the US, S pneumoniae accounts for about 30% to 35% of cases.[5][16][20] Other bacterial causes include Haemophilus influenzae, Staphylococcus aureus (including MRSA), group A streptococci, and Moxarella catarrhalis

Atypical bacteria are also common causes, although they vary in frequency depending on the year and any epidemics.[19][21] The incidence of atypical pathogens in community-acquired pneumonia is approximately 22% globally, but this varies with location.[22] The most commonly reported atypical bacteria are Mycoplasma pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila. M pneumoniae accounts for up to 37% of CAP patients treated as outpatients and 10% of patients who are hospitalised.[5][16]C pneumoniae accounts for 5% to 15% of cases of CAP,[23] and L pneumophila (especially serogroup 1) accounts for 2% to 6% of CAP in immunocompetent patients.[24] A systematic review found that Chlamydia psittaci was the causative organism in 1% of patients.[25] However, a Dutch study identified C psittaci by polymerase chain reaction (PCR) of sputum (when available) as a cause of CAP in 4.8% of cases.[26]

Pseudomonas aeruginosa may also be prevalent in patients with pneumonia, depending on the region; however, it is more common in hospital-acquired and ventilator-associated pneumonia compared with CAP. It accounted for 7.7% of all isolates in CAP in a systematic review in China.[27]

Respiratory viruses are reported in about 10% to 30% of immunocompetent adults hospitalised with CAP.[16][28][29][30] Influenza virus A/B, respiratory syncytial virus, adenovirus, rhinovirus, and parainfluenza virus are the most common viral causes of CAP in immunocompetent adults. Newer pathogens reported to cause CAP include metapneumovirus and coronaviruses.[31] Detection of viral causes is increasing because of the use of PCR.

Polymicrobial aetiology in CAP varies from 5.7% to 13%, depending on the population and the microbiological diagnostic test used.[16][29][32]


Pneumonia develops subsequent to the invasion and overgrowth of a pathogenic micro-organism in the lung parenchyma, which overwhelms host defences and produces intra-alveolar exudates.[33]

The development and severity of pneumonia is a balance between pathogen factors (virulence, inoculum size) and host factors. The likely microbial causes of CAP differ according to a number of factors, including differences in local epidemiology, the setting (outpatients, hospitalised, or intensive care unit), severity of disease, and patient characteristics (e.g., sex, age, and comorbidities).[16]

Microbes that are present in the upper airways can enter the lower airways by microaspiration. Nevertheless, the defence mechanisms of the lungs (innate and acquired) keep the lower airways sterile. The development of pneumonia indicates a defect in host defences, exposure to a particularly virulent micro-organism, or a large inoculum size.

Impaired immune response (e.g., caused by HIV infection or advanced age) or dysfunction of defence mechanism (e.g., through current or passive smoking, COPD, or aspiration) leads to greater susceptibility to respiratory infections in patients.[6]

Pathogens can reach the lower respiratory tract by 4 mechanisms:

  • Inhalation, a common route of entry for viral and atypical pneumonia in younger healthy patients. Infectious aerosols are inhaled into the respiratory tract of a susceptible person to initiate infection

  • Aspiration of oropharyngeal secretions into the trachea, the primary route through which pathogens enter the lower airways

  • Haematogenous spread from a localised infected site (e.g., right-sided endocarditis)[34]

  • Direct extension from adjacent infected foci (e.g., tuberculosis can spread contiguously from the lymph nodes to the pericardium or the lung, albeit rarely).

There is a new theory that CAP may result from dysbiosis of the normal lung flora, rather than invasion of pathogenic micro-organisms in a sterile environment; however, this model requires further research.[35]

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