Epidemiology and aetiology of severe community acquired pneumonia at Royal Darwin Hospital Intensive Care Unit

The aetiology of severe community acquired pneumonia (CAP) differs between tropical Australia and temperate parts of the country. We undertook an audit to describe the implementation of a new testing algorithm to determine the additional diagnostic yield, if any, of a newly-introduced rapid diagnostic test in severe CAP in an Intensive Care Unit (ICU) in a tertiary facility in Australia’s Northern Territory. All adult patients with severe CAP admitted during a 12-month period were included. A diagnostic algorithm was implemented whereby patients in whom the microbiological diagnosis remained uncertain at 48 hours of intubation were eligible to have an endotracheal tube aspirate tested using a multiplex real-time polymerase chain reaction (RT-PCR) (BioFire Diagnostics, Salt Lake City, UT). This detects Adenovirus, Coronaviruses, Human metapneumovirus, Rhinovirus, Enterovirus, Influenza A and B, Parainfluenza 1-4, Respiratory syncytial virus (RSV), Bordetella pertussis, Chlamydophila pneumoniae and Mycoplasma pneumoniae.

There were 86 eligible CAP diagnoses during the study period. We found that a microbiological aetiology was detected using standard diagnostics in 50/86 (58%). Most common pathogens were: Streptococcus pneumoniae (10), Burkholderia pseudomallei (9), Influenza (9), Staphylococcus aureus (8), Acinetobacter baumannii (3), Pseudomonas aeruginosa (3), Myocbacterium tuberculosis (2) and Nocardia sp (1). Eight patients were eligible for testing using the RT-PCR according to the algorithm; 5 tests were performed showing Rhinovirus/ Enterovirus (1), Parainfluenza-3 (1) and Respiratory Syncytial Virus (1) or no pathogens (2). Therefore, the additional diagnostic yield using the algorithm in this patient subset was low.

Multiplex testing for respiratory infections may have an important place, but few patients were eligible using a strict algorithm, and clinician uptake was low. Implementation of a new test requires careful consideration about strategies for targeted use and clinician education. Current local guidelines on empirical CAP antimicrobial therapy are appropriate for the range of pathogens which predominate in this tropical environment.