The use of multiplex PCR for the detection of respiratory pathogens in hospitalised adults with community-acquired pneumonia during the pre-COVID era in South Africa: A retrospective cohort

Background Community-acquired pneumonia (CAP) is a major cause of hospitalisation. In South Africa 74% of adults hospitalised with CAP are patients living with HIV (PLWH). Streptococcus(S) pneumoniae remains a leading cause of CAP in PLWH. Rapid and accurate pathogen identification has significant management implications. The objectives of the study is to: describe respiratory pathogens detected by the BioFire® FilmArray® multiplex PCR pneumonia panels (MPPP) and compare S. pneumoniae detection with standard diagnostics in adults admitted with CAP. Secondary objectives were to stratify pathogens by HIV status and assess length of stay (LOS) and mortality risk. Methods Stored sputum specimens from the PotPrev trial collected between August to December 2019, pre-covid era, were analysed using MPPP. S. pneumoniae identification was made by three separate methods: multiplex PCR (mPCR) on sputum, single-plex PCR on nasopharyngeal swab (NPS) and blood. Results In 146 samples analysed, MPPP detected 275 pathogens in 119 patients (81.5%). Seven organisms accounted for 80% of pathogens: Streptococcus pneumoniae (24.7%), Haemophilus influenzae (17.8%), Staphylococcus aureus (9.1%), Mycobacterium tuberculosis (9.1%), Moraxella catarrhalis (8.4%), Rhinovirus (5.5%) and Influenza virus (4.4%). Among 68 S. pneumoniae cases, NPS lytA PCR had the highest sensitivity (91.2%), followed by mPCR (67.6%) and blood lytA PCR (27.9%). Of note, mPCR detected 7.4% additional cases. Concordance between NPS lytA PCR and mPCR was 61.3%, and blood lytA PCR 24.6%. Among PLWH, a wider spectrum of pathogens was observed, with Pneumocystis jirovecii pneumonia accounting for a high proportion of cases (8.7%). There were no differences in bacterial (p = 0.37), viral (p = 0.5), mortality (p = 0.6), or length of stay (median six days, p = 0.96) in PLWH. Survivors and non-survivors had similar LOS (p = 0.68). Low oxygen saturation was associated with reduced survival (p = 0.039). Conclusion MPPP in addition to standard diagnostics increases pathogen detection in hospitalized CAP. PLWH had distinct aetiology with a higher pathogen burden. These findings support the value of molecular diagnostics and context-specific approaches in high HIV-burden settings.