Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples.

We developed a metatranscriptomics method that can simultaneously capture the respiratory virome, microbiome, and host response directly from low biomass samples. Using nasal swab samples, we capture RNA virome with sufficient sequencing depth required to assemble complete genomes. We find a surprisingly high frequency of respiratory syncytial virus (RSV) and coronavirus (CoV) in healthy children, and a high frequency of RSV-A and RSV-B co-detections in children with symptomatic RSV. In addition, we have identified commensal and pathogenic bacteria and fungi at the species level. Functional analysis revealed that H. influenzae was highly active in symptomatic RSV subjects. The host nasal transcriptome reveled upregulation of the innate immune system, anti-viral response and inflammasome pathway, and downregulation of fatty acid pathways in children with symptomatic RSV. Overall, we demonstrate that our method is broadly applicable to infer the transcriptome landscape of an infected system, surveil respiratory infections, and to sequence RNA viruses directly from clinical samples.

A Time and Motion Analysis of Nursing Workload and Electronic Health Record Use in the Emergency Department.

INTRODUCTION: The use of an electronic health record may create unanticipated consequences for emergency care delivery. We sought to describe emergency department nursing task distribution and the use of the electronic health record. METHODS: This was a prospective observational study of nurses in the emergency department using a time-and-motion methodology. Three trained research assistants conducted 1:1 observations between March and September 2019. Nurse tasks were classified into 6 established categories: electronic health record, direct/indirect patient care, communication, personal time, and other. Nurses' perceived workload was assessed using the National Aeronautics and Space Administration (NASA) Task Load Index. RESULTS: Twenty-three observations were conducted over 46 hours. Overall, nurses spent 27% of their time on electronic health record tasks, 25% on direct patient care, 17% on personal time, 15% on indirect patient care, and 6% on communication. During morning (7 am-12 pm) and afternoon shifts (12 pm-3 pm), the use of the health record was the most commonly performed task, whereas indirect patient care was the task most performed during evening shifts (3 pm-12 pm). Using the National Aeronautics and Space Administration (NASA) Task Load Index, nurses reported an increase in mental demand and effort during afternoon shifts compared with morning shifts. DISCUSSION: We observed that emergency nurses spent more time using the electronic health record as compared to other tasks. Increased usability of the electronic health record, particularly during high occupancy periods, may be a target for improvement.