Amplicon-based sequencing as a diagnostic tool for severe pneumonia in the ICU

The microbiological diagnosis of severe pneumonia in intensive care unit (ICU) patients remains challenging. We investigated whether amplicon-based sequencing (ABS) could provide additional value in this setting. Bacterial 16S rRNA coupled with fungal internal transcribed spacer (ITS) ABS was compared with standard of care (SOC) comprising cultures, PCR and galactomannan on bronchoalveolar lavages of immunosuppressed and immunocompetent ICU patients presenting severe pneumonia (n = 24) and noninfected lung-transplanted patients (n = 12). The ABS-matched SOC results were complete for 20/36 (55.5%) samples. Regarding 16S rRNA, ten samples showed partial agreement, whereas five others were fully discordant. Discordances were observed mainly for gram-negative organisms, either for quantification (Enterobacteria) or identification (Enterobacter sp., Haemophilus sp.). Only 1 of the 36 ITS results were discordant with the SOC results. The ABS has proven to be more valuable in immunosuppressed patients. Despite limitations in bacterial identification, pathogens not reported by SOC were detected in 8 samples (coinfections, bacterial superinfections from viral pneumonia). ITS identification was reliable, and semiquantification helped distinguish P. jirovecii infection and colonization. The correlation between galactomannan and ITS was good. While 16S rRNA sequencing is interesting for severe pneumonia of undefined aetiology in IS patients, ITS could provide additional diagnostic value for severe fungal pneumonia.