Because the diagnosis of co/superinfection in COVID-19 patients is challenging, empirical antibiotic therapy is frequently initiated until microbiological analysis results. We evaluated the performance and the impact of the BioFire® FilmArray® Pneumonia plus Panel on 112 respiratory samples from 67 COVID-19 ICU patients suspected of co/superinfections. Globally, the sensitivity and specificity of the test were 89.3% and 99.1%, respectively. Positive tests led to antibiotic initiation or adaptation in 15% of episodes and de-escalation in 4%. When negative, 28% of episodes remained antibiotic-free (14% no initiation, 14% withdrawal). Rapid multiplex PCRs can help to improve antibiotic stewardship by administering appropriate antibiotics earlier and avoiding unnecessary prescriptions.
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http://dx.doi.org/10.1007/s10096-021-04213-6 | DOI Listing |
Microbiol Spectr
January 2025
Department of Laboratory Medicine, Korea University Anam Hospital, Korea University College of Medicine, Seoul, South Korea.
Unlabelled: Respiratory tract infections are major global health issues that require rapid and accurate diagnostic methods. Multiplex quantitative PCR (qPCR) is commonly used for pathogen detection in respiratory samples. However, the optimal specimen selection for detecting bacterial pathogens is not well-explored.
View Article and Find Full Text PDFGenome Res
January 2025
Center for Genomic Research (CRG), Universitat Pompeu Fabra (UPF), ICREA
Nanopore direct RNA sequencing (DRS) enables direct measurement of RNA molecules, including their native RNA modifications, without prior conversion to cDNA. However, commercial methods for molecular barcoding of multiple DRS samples are lacking, and community-driven efforts, such as DeePlexiCon, are not compatible with newer RNA chemistry flowcells and the latest-generation GPU cards. To overcome these limitations, we introduce SeqTagger, a rapid and robust method that can demultiplex direct RNA sequencing datasets with 99% precision and 95% recall.
View Article and Find Full Text PDFAnal Chem
January 2025
Nanophotonic Systems Laboratory, Department of Mechanical and Process Engineering, ETH Zurich, 8092 Zurich, Switzerland.
Droplet-based microfluidics is a powerful tool for high-throughput analysis of liquid samples with significant applications in biomedicine and biochemistry. Nevertheless, extracting content-rich information from single picolitre-sized droplets at high throughputs remains challenging due to the weak signals associated with these small volumes. Overcoming this limitation would be transformative for fields that rely on high-throughput screening, enabling broader multiparametric analysis.
View Article and Find Full Text PDFWe propose and demonstrate, for the first time to the best of our knowledge, an all-polarization-maintaining (all-PM) dual-comb Er-fiber laser based on combined figure-8 and figure-9 architectures. The opposite signs of the non-reciprocal phase shifts required for figure-8 and figure-9 architectures in the shared nonlinear amplifying loop mirror (NALM) are achieved using a single non-reciprocal phase shifter (NRPS) that operates in two orthogonal polarizations. The capability of common mode noise cancellation, environmental stability, long-term reliability, and the tunable range of the repetition rate difference Δ between two combs has been investigated and characterized.
View Article and Find Full Text PDFSci Rep
January 2025
Institute of Emerging Infectious Diseases, Korea University, Seoul, Republic of Korea.
This study aimed to evaluate the usefulness of amplicon-based real-time metagenomic sequencing applied to cerebrospinal fluid (CSF) for identifying the causative agents of bacterial meningitis. We conducted a 16S rRNA amplicon sequencing using a nanopore-based platform, alongside routine polymerase chain reaction (PCR) testing or bacterial culture, to compare its clinical performance in pathogen detection on CSF samples. Among 17 patients, nanopore-based sequencing, multiplex PCR, and bacterial culture detected potential bacterial pathogens in 47.
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