Gaia Nebbia from the Guy’s and St. Thomas’ NHS Foundation Trust in the UK presented at London Calling 2024. The session focused on respiratory metagenomics in clinical service. This study explored metagenomic sequencing for respiratory infection control and diagnostics. The team identified areas of improvement for the identification of viral sequences. The aim of the pilot study was the feasibility of implementing the assay in a diagnostic setting with a quick turnaround. Samples were taken from ICU patients. The sample was split. A part went to the clinical microbiology lab. Another portion went to sequencing with a quick seven-hour turnaround. Nebbia noted that the respiratory clinical microbiology workflow is complex, with many branching points. The respiratory metagenomics workflow took samples for DNA and RNA extraction. Human DNA depletion increased the sensitivity of microbial reads. Performance characteristics-ROC curve thresholds were obtained for virus sensitivity. Hours of sequencing and quality control standards were considered. For example, spike-in respiratory panel controls were incorporated. The results over sixteen weeks, December 2023-April 2024, included 113 samples from 73 patients. The failure rate was just 6% (seven samples). Sensitivity was 98%: one missed E. coli in the otherwise negative sample. The specificity was 95%: three detected oral flora in no growth samples. For fungi, sensitivity was 93%, missing one Candida. Specificity was 99%: one Candida was detected in no growth culture. For viruses, the sensitivity was 88%. It missed three viruses (Rhinovirus, Influenza A, and Influenza A) with high Ct values at the detection limit. Viral genome recovery was good. Nebbia then shared a couple of case studies. They concluded that there is a low failure rate in the feasibility study. Quality control is “very good” with their workflow. The bioinformatics pipeline could be improved. Nebbia noted that wider multi-site implementation is needed. This session provided a comparison of clinical microbiology approaches to a fast-turnaround metagenomics sequencing workflow with several extraction methods and host depletion.
