Erin C. Ho

Plasma microbial cell-free DNA (mcfDNA) sequencing is a novel diagnostic tool for pediatric complicated community-acquired pneumonia (cCAP). However, rigorous evaluation of real-world mcfDNA performance is lacking. We compared mcfDNA sequencing to a composite reference standard consisting of blood cultures, pleural fluid (PF) cultures, and targeted PF PCRs in children with cCAP requiring pleural effusion or empyema drainage at Children’s Hospital Colorado from 2022 to 2024. We calculated positive/negative percent agreement (PPA/NPA), Jaccard similarity index, and theoretical time to pathogen detection. We investigated mcfDNA positivity in pediatric controls without bacterial infections. Receiver operating characteristic (ROC) analysis explored potential mcfDNA detection cutoff values to define “true clinical positivity.” Across 45 cCAP cases, mcfDNA sequencing detected a probable pathogen in 86.7% versus 8.9% by blood culture, 20.0% by PF culture, and 71.1% by PF PCRs ( P < 0.001). Against the culture+PCR composite reference standard, mcfDNA had a PPA of 91.9% (83.1%–100.0%), NPA of 35.7% (10.6%–60.8%), and a Jaccard index of 0.74. Bacterial cfDNA was detected in 52% of controls. ROC analysis yielded an area under the curve of 0.9, with potential optimal detection cutoffs ranging between 158 and 491 mcfDNA molecules per microliter. Theoretical median time to pathogen detection was 3.0 days with mcfDNA versus 4.5 days for pleural fluid PCRs, driven primarily by PF sampling time. Plasma mcfDNA sequencing had a significantly higher diagnostic yield than cultures and a similar yield to PF PCRs; however, over half of non-bacterial controls had low-level mcfDNA detected, potentially complicating interpretation. mcfDNA detection level cutoffs may help elucidate the clinical significance of detected pathogens. IMPORTANCE: More sensitive diagnostic tests, particularly non-invasive options, are needed to better identify the causative organism(s) in children with complicated community-acquired pneumonia and help inform pathogen-directed therapy. A novel, potentially powerful diagnostic tool for pneumonia is plasma microbial cell-free DNA sequencing, available commercially as Karius Spectrum. However, unknowns regarding its real-world performance and proper role in clinical practice remain. This study aims to address two ongoing concerns: first, the lack of robust comparisons of microbial cell-free DNA (mcfDNA) sequencing performance against validated conventional and state-of-the-art diagnostic modalities (i.e., pleural fluid testing and blood cultures); and second, the unknown baseline positivity rates of mcfDNA in children without bacterial infections. Results from this study may help inform clinical practice decisions and testing implementation strategies.

While Streptococcus pneumoniae (Spn) is the leading cause of pediatric complicated community acquired pneumonia (cCAP), it is infrequently recovered by culture-based methods. We studied the real-world clinical impact of an Spn PCR assay for pleural fluid. This pre-post quasi-experimental cohort study compared pathogen detection, antibiotic usage, and outcomes in children hospitalized with cCAP requiring pleural effusion or empyema drainage at Children’s Hospital Colorado between 2016 and 2023. Patients were compared across two diagnostic periods: pre-Spn PCR and post-Spn PCR. Cox proportional hazard models compared time from admission to pathogen detection, optimal therapy (narrowest pathogen-directed or guideline-recommended empiric therapy), and MRSA therapy discontinuation between periods. Compared to the pre-Spn PCR cohort (N=149), the post-Spn PCR cohort (N=79) was more likely to have a pathogen detected (73.4% post-PCR vs. 38.9% pre-PCR, p < 0.001), driven by more Spn detections (45.6% vs. 14.1%, p < 0.001). Time to pathogen detection during hospitalization was shorter in the post-Spn PCR period (p < 0.001). The post-PCR cohort was more likely to receive optimal therapy (84.8% vs. 53.0%, p < 0.001), with shorter median times to optimal antibiotics (4.9 vs. 10.0 days, p < 0.001) and MRSA therapy discontinuation (1.5 vs. 2.5 days, p = 0.03). There were no differences in hospital length of stay or readmissions. Spn molecular testing of pleural fluid in children with cCAP resulted in significantly more microbiologic diagnoses and was associated with the optimization of antibiotics and decreased exposure to MRSA therapy, suggesting its clinical impact for pediatric complicated pneumonia. This graphical abstract is also available at Tidbit: https://tidbitapp.io/tidbits/clinical-impact-of-pleural-fluid-streptococcus-pneumoniae-pcr-testing-in-children-with-complicated-pneumonia?utm_campaign=tidbitlinkshare&utm_source=ITP

There is uncertainty regarding which hospitalized patients with acute gastroenteritis (AGE) benefit from gastrointestinal panel (GIP) testing. Unnecessary testing may lead to increased costs, overdiagnosis, and overtreatment. In general, AGE management and outcomes are most impacted if an actionable (bacterial or parasitic) result is obtained. We aimed to assess which clinical reasons for ordering GIP testing (“order indications”) and patient factors were associated with actionable results. This is a cross-sectional study of pediatric patients hospitalized between 2015 and 2018 at a large pediatric health care system with diarrhea and a GIP performed. Multivariable regression analysis was used to determine associations between actionable GIP results and order indication, stool frequency, and demographics. Findings were evaluated in patients with complex chronic conditions (CCC) and non-CCC patients. There were 1124 GIPs performed in 967 encounters. Non-CCC patients had more actionable results than CCC patients, and reasons for testing differed. Across both cohorts, age ≥1 year old was positively associated with actionable results. For non-CCC patients, actionable results were associated with “diarrhea with blood or pus” order indication and nonwinter season; international travel was associated with non-Clostridioides difficile bacteria and parasites. No order indications were associated with actionable results for CCC patients. Patient factors and order indications that may help identify children hospitalized for AGE with actionable GIP results include older age (regardless of CCC status), as well as bloody stools and international travel in previously healthy children. Prospective validation of these findings could help improve diagnostic stewardship and decrease unnecessary testing.

In the fall of 2022, we observed a sharp rise in pediatric invasive group A Streptococcus (iGAS) hospitalizations in Colorado. We compared the epidemiology, clinical features, and patient outcomes in this outbreak to prior years. Between October 2022 and April 2023, we prospectively identified and reviewed iGAS cases in hospitalized pediatric patients at Children’s Hospital Colorado. Using laboratory specimen records, we also retrospectively compared the number of patients with sterile site GAS-positive cultures across three time periods: pre-COVID-19 (January 2015 – March 2020), height of COVID-19 pandemic (April 2020 – September 2022), and outbreak (October 2022 – April 2023). Among 96 prospectively identified iGAS cases, median age was 5.7 years old; 66% were male, 70% previously healthy, 39% required critical care, and four patients died. Almost 60% had associated respiratory viral symptoms, 10% had toxic shock syndrome, and 4% had necrotizing fasciitis. Leukopenia, bandemia, and higher C-reactive protein values were laboratory findings associated with need for critical care. There were significantly more cases during the outbreak (9.9/month outbreak vs. 3.9/month pre-pandemic vs. 1.3/month pandemic), including more cases with pneumonia (28% outbreak vs. 15% pre-pandemic vs. 0% pandemic) and multifocal disease (17% outbreak vs. 3% pre-pandemic vs. 0% pandemic), p <0.001 for all. Outbreak case numbers were almost triple the pre-pandemic baseline. The high percentage of cases with associated viral symptoms suggests a link to coinciding surges in respiratory viruses during this time. Invasive GAS can be severe and evolve rapidly; clinical and laboratory features may help in earlier identification of critically ill children.