Parapneumonic effusion in children: Rapid pathogen detection in pleural fluid using multiplex bacterial PCR.

Abstract

Parapneumonic effusion is a complication of severe pneumonia. In children,. it is usually caused by Streptococcus pneumoniae and Staphylococcus aureus. However, group A Streptococcus (GAS) has emerged in 2022–2023, causing an increase in severe pneumonia, a common manifestation of invasive GAS.1 Early targeted antibiotic treatment is crucial in pneumonia complicated by parapneumonic effusion. However, identification of the causative bacteria can be difficult as cultures of upper respiratory tract specimens often reflect asymptomatic colonisation. Further, the diagnostic yield is less than 30% from blood and pleural fluid cultures, and from 16S rRNA polymerase chain reaction (PCR) on pleural fluid.2 Multiplex PCR assays with specific bacterial DNA primers allow rapid identification of numerous pathogens within hours despite preceding antibiotic treatment. https://www.biofiredx.com/products/the-filmarray-panels/filmarray-pneumonia/ However, this method has not been approved for pleural fluid. In 2021, we introduced multiplex PCR as a diagnostic test on pleural fluid in children with complicated pneumonia. The aim of this study was to investigate the diagnostic yield of multiplex PCR on pleural fluid. We enrolled all patients aged 0–17 years with community-acquired parapneumonic effusion investigated with multiplex PCR at Copenhagen University Hospital, Rigshospitalet, from 1 January 2021, to 8 March 2023. The hospital is a tertiary care referral centre for chest tube drainage for eight paediatric departments (2.6 million inhabitants), the Faroe Islands and Greenland. Patients were identified through a dedicated database and retrospectively validated through the hospital's electronic medical system by retrieving patients admitted with diagnosis codes of pleural effusion and pleural empyema. Medical records were retrospectively reviewed for clinical and laboratory data, including microbiological results. The study was approved by the Danish Patient Safety Authority (3–3013-1774/1) and Data Protection Agency (P-2019-05). Twenty-one patients with parapneumonic effusion investigated with multiplex PCR (BioFire FilmArray Pneumonia Panel; BioMérieux) were enrolled (Table 1). A bacterium was identified in 20 of 21 (95%) samples; 13 GAS, four S. pneumoniae, two S. aureus and one Haemophilus influenzae (Table 1). Culture of pleural fluid and/or blood was positive in seven of 21 (33%) patients. In patients with positive cultures, the pathogens were identical to those found by multiplex PCR. All received antibiotics before pleural fluid investigation (median: 59 h, range: 2–240). The median duration of pleural drainage was 7 days (range: 2–17), 12 (57%) received intrapleural fibrinolytics and the median length of hospitalisation was 12 days (range: 1–35). Four patients received mechanical ventilation including three with GAS and one with MRSA. One patient died due to GAS toxic shock syndrome. In children with community-acquired pneumonia needing chest tube drainage, multiplex PCR identified a bacterium in pleural fluid in 95% of cases. This high diagnostic yield contrasted with the low yield from pleural fluid cultures of 33%, which could be because most patients received antibiotics prior to culture. Further, multiplex PCR identified methicillin resistance genes in samples with MRSA, confirmed by conventional cultures. Multiplex PCR assays have not been approved for pleural fluid. Until now, few small studies have investigated the clinical use of multiplex PCR in children with parapneumonic effusions.3, 4 Their findings showed sensitivities of 72–100%, in line with our results. Thus, multiplex PCR appears to identify microorganisms in pleural fluid with high sensitivity and has the advantage of delivering a test result within a few hours. High pathogen detection impacts antibiotic stewardship, allowing for early targeted therapy. This is particularly valuable for children with parapneumonic effusions requiring prolonged antibiotics. Further, multiplex PCR detects antimicrobial resistance genes, which shortens the time to effective therapy and, thus, may be life-saving in settings with low antimicrobial resistance where empirical therapy does not cover resistant pathogens, such as MRSA. The multiplex PCR was negative in one case, which may reflect that the causative pathogen was not included in the PCR panel, for example, Fusobacterium, Streptococcus anginosus and Mycobacterium tuberculosis. Thus, it is important to acknowledge that multiplex PCR assays have DNA primers for selected pathogens only. In cases with no pathogen detection on PCR or culture, we recommend proceeding with broad-range 16S rRNA PCR and/or metagenomic sequencing. Community-acquired pneumonia needing chest tube drainage was caused by GAS in most cases since 1 October 2022, which is compatible with the worldwide emergence of invasive GAS in 2022–2023. The reason for the emergence of GAS is yet unknown but does not seem to be due to new or more virulent strains.1 The emergence may reflect a population with ‘GAS immunity debt’ following a period of reduced circulation during the COVID-19 lockdown.1 Prior to the resurgence of GAS, S. aureus and S. pneumonia were most common. The main limitation of this study was the small number of included cases. Thus, larger studies are needed to validate our findings. Second, although the pathogens identified by multiplex PCR were equal to all culture-positive cases, we only had few cases confirmed by culture. In conclusion, a shift in bacteria causing parapneumonic effusion was observed since October 2022, when most cases were caused by GAS, an otherwise rare cause of severe pneumonia. Multiplex PCR on pleural fluid had rapid and high pathogen identification compared to conventional culture and may direct early targeted antibiotic treatment. This study was funded by Innovation Fund Denmark (0176-00020B). The authors have no conflicts of interests.