6 Identifying and managing co-infections

6.1 Managing viral or fungal pneumonia


Do not offer an antibiotic for preventing or treating pneumonia if SARS-CoV-2, another virus, or a fungal infection, is likely to be the cause.
Antibiotics do not work on viruses, and inappropriate antibiotic use may reduce availability. Also, inappropriate use may lead to Clostridioides difficile infection and antimicrobial resistance, particularly with broad-spectrum antibiotics. [23 March 2021]

Evidence as of March 2021 suggests that bacterial co-infection occurs in less than about 8% of people with COVID-19, and could be as low as 0.1% in people in hospital with COVID-19. Viral and fungal co-infections occur at lower rates than bacterial co-infections.

Secondary infection or co-infection (bacterial, viral or fungal) is more likely the longer a person is in hospital and the more they are immunosuppressed (for example, because of certain types of treatment).

The type and number of secondary infections or co-infections will vary depending on the season and any restrictions in place (for example, lockdowns).

6.2 Other causes of pneumonia

Identifying other causes of pneumonia


To help identify other causes of pneumonia and to inform decision making about using antibiotics, consider the following tests:

  • a full blood count

  • chest imaging (X-ray, CT or ultrasound)

  • respiratory and blood samples (for example, sputum or a tracheal aspirate sample, blood culture)

  • urine samples for legionella and pneumococcal antigen testing

  • throat, nasopharyngeal or sputum samples for respiratory viral (and atypical pathogen) polymerase chain reaction testing; for more information, see Public Health England's COVID-19 guidance for sampling and for diagnostic laboratories. [23 March 2021, amended 27 July 2022]

High C-reactive protein levels do not necessarily indicate whether pneumonia is due to bacteria or SARS‑COV‑2.

Low C-reactive protein level indicates that a secondary bacterial infection is less likely.


Do not use C-reactive protein to assess whether a person has a secondary bacterial infection if they have been having immunosuppressant treatment. [23 March 2021]

There is insufficient evidence to recommend routine procalcitonin testing to guide decisions about antibiotics. Centres already using procalcitonin tests are encouraged to participate in research and data collection.

Procalcitonin tests could be useful in identifying whether there is a bacterial infection. However, it is not clear whether they add benefit beyond what is suggested in recommendation 6.2.1 on tests to help differentiate between viral and bacterial pneumonia to guide decisions about antibiotics. The most appropriate threshold for procalcitonin is also uncertain.

Antibiotic treatment in the community


Do not offer an antibiotic for preventing secondary bacterial pneumonia in people with COVID-19. [23 March 2021]


If a person has suspected or confirmed secondary bacterial pneumonia, start antibiotic treatment as soon as possible. Take into account any different methods needed to deliver medicines during the COVID-19 pandemic (see recommendation 3.1.1 on minimising face-to-face contact).[23 March 2021]

For antibiotic choices to treat community-acquired pneumonia caused by a secondary bacterial infection, see the recommendations on choice of antibiotic in NICE's guideline on pneumonia (community-acquired): antimicrobial prescribing.


Advise people to seek medical help without delay if their symptoms do not improve as expected, or worsen rapidly or significantly, whether they are taking an antibiotic or not. [23 March 2021]

Starting antibiotics in hospital


Start empirical antibiotics if there is clinical suspicion of a secondary bacterial infection in people with COVID-19. When a decision to start antibiotics has been made:

  • Start empirical antibiotic treatment as soon as possible after establishing a diagnosis of secondary bacterial pneumonia, and certainly within 4 hours.

  • Start treatment within 1 hour if the person has suspected sepsis and meets any of the high-risk criteria for this outlined in NICE's guideline on sepsis. [23 March 2021]

Choice of antibiotics in hospital


When choosing antibiotics, take account of:

  • local antimicrobial resistance data and

  • other factors such as their availability. [23 March 2021]


Give oral antibiotics if the person can take oral medicines and their condition is not severe enough to need intravenous antibiotics. [23 March 2021]


Consider seeking specialist advice on antibiotic treatment for people who:

  • are immunocompromised

  • have a history of infection with resistant organisms

  • have a history of repeated infective exacerbations of lung disease

  • are pregnant

  • are receiving advanced respiratory support or organ support. [23 March 2021]


Seek specialist advice if:

  • there is a suspicion that the person has an infection with multidrug-resistant bacteria and may need a different antibiotic or

  • there is clinical or microbiological evidence of infection and the person's condition does not improve as expected after 48 to 72 hours of antibiotic treatment. [23 March 2021]

Reviewing antibiotic treatment in hospital


Review all antibiotics at 24 to 48 hours, or as soon as test results are available. If appropriate, switch to a narrower-spectrum antibiotic, based on microbiological results. [23 March 2021]


Reassess people if their symptoms do not improve as expected, or worsen rapidly or significantly. [23 March 2021]

6.3 COVID-19-associated pulmonary aspergillosis (CAPA)

For people who are critically ill and have, or have had, COVID-19 as part of their acute illness:

  • COVID-19-associated pulmonary aspergillosis (CAPA) is a recognised cause of someone's condition not improving despite treatment (for example, antibiotic therapy, ventilatory support)

  • there are no specific combinations of signs or symptoms for diagnosing CAPA

  • the risk of having CAPA may increase with age and chronic lung disease.

Diagnosing CAPA


When deciding whether to suspect CAPA in someone who is critically ill and has, or has had, COVID-19 as part of their acute illness:

  • base your decisions on individual risk factors and the person's clinical condition

  • involve a multidisciplinary team, including infection specialists

  • refer to local protocols on diagnosing and managing CAPA.

    Local protocols for diagnosing and managing CAPA should be developed with a multidisciplinary team and based on knowledge of local prevalence. [16 December 2021]


Do not do diagnostic tests for CAPA if there is low clinical suspicion of the condition. [16 December 2021]


When investigating suspected CAPA:

  • use a range of tests to increase the likelihood of making a confident diagnosis

  • if possible, include bronchoalveolar lavage (BAL) as part of diagnostic testing, taking into account the risks of BAL in relation to the person's clinical condition

  • discuss the diagnostic testing strategy and final diagnosis with a multidisciplinary team that includes infection specialists. [16 December 2021]


Test for antifungal resistance if an Aspergillus isolate is cultured from a CAPA test sample. [16 December 2021]


Commissioners and local trusts should ensure that results of diagnostic tests for CAPA are available in a timeframe that informs and supports clinical decision making. [16 December 2021]


Monitor and report testing for, and diagnosis and management of, CAPA in line with local protocols.

Local protocols for diagnosing and managing CAPA should be developed with a multidisciplinary team and based on knowledge of local prevalence. [16 December 2021]

For a short explanation of why the panel made these recommendations, see the rationale section on diagnosing CAPA.

Full details of the evidence and the panel's discussion are in:

Treating CAPA


Only use antifungal treatments to treat CAPA if:

  • diagnostic investigations support a diagnosis of CAPA or

  • the results of diagnostic investigations are not available yet, but CAPA is suspected, and a multidisciplinary team or local protocols support starting treatment. [16 December 2021]


When considering antifungal treatment for CAPA:

  • discuss treatment options with a multidisciplinary team that includes infection specialists

  • follow local protocols that include best practice guidance on treating invasive aspergillosis. [16 December 2021]


For people having antifungal treatment for suspected CAPA, stop treatment if the results of investigations do not support a diagnosis of CAPA and a multidisciplinary team agrees. [16 December 2021]

For a short explanation of why the panel made these recommendations, see the rationale section on treating CAPA.

Full details of the evidence and the panel's discussion are in evidence review K: CAPA – effectiveness and safety of treatments.