A proportion of pneumonia cases are due to bacteria which can be difficult to detect using Gram stain and standard culture methods. The most common of these atypical pathogens include M. pneumoniae, Chlamydophila pneumoniae, and Legionella pneumophila.¹²

Atypical pneumonia symptoms can include headache, low-grade fever, cough, and malaise, and tend to be on the milder side of CAP which is why cases can be referred to as ‘walking’ pneumonia. However, the pathogens can cause severe pneumonia requiring admission to the intensive care unit.^12,13

M. pneumoniae can cause up to 20% of CAP cases and can be the source of some hospital-based epidemics. It is a likely cause of outbreaks in close community settings such as boarding schools, universities, and military bases.¹²

Legionnaire’s disease is a pneumonia subtype caused mainly by L. pneumophila. From 2017 to 2023, the number of reported cases in England and Wales ranged between 337 and 604, with an average of 29 deaths or 3.1% of cases, annually. More than half of cases are due to community exposure and about a third due to travel abroad, with seasonal peaks occurring in late summer.¹⁴

Less common are other Chlamydophila and Legionella species, Coxiella burnetii (causing Q fever, usually being sourced from farm animals) and Chlamydia psittaci (from infected birds, typically kept as pets, such as parrots, parakeets, cockatiels and budgerigars, causing psittacosis). Respiratory viral causes can also be behind atypical pneumonia.^12,15,16

The fungus Pneumocystis jirovecii (formerly P. carinii) causes pneumocystis pneumonia (PCP), traditionally associated with acquired immunodeficiency syndrome (AIDS), with 100% mortality if untreated. However, it can occur in immunosuppressed patients without the human immunodeficiency virus (HIV) and has been increasing in the wider population.^17,18