Tonight I returned from my first SABER East! It was a lot of fun! The video I watched tonight was Judith Brueur from the Great Ormond Street Hospital (GOSH) discuss the implementation of a respiratory metagenomics protocol at Guy’s and St. Thomas’ Hospital (GSTT) using Oxford Nanopore Technologies (ONT). The protocol was developed by the GSTT hospital and Brueur implemented their protocol at GOSH. The team made modifications to the reporting of bacteria and compared the GOSH and GSTT results. The output was similar between hospitals with high specificity and sensitivity. The clinical impact of the GOSH metagenomics trial was supported by high acceptability by clinicians and nurses. GOSH has experience with other metagenomic protocols, Brueur noted. The Illumina based protocol takes five days for respiratory samples. This short-read method has higher sensitivity. The research team then created mock clinical samples with viral mock communities and used untargeted Illumina and Nanopore sequencing approaches as well as capture probe enrichment with Twist and Illumina. The target enrichment metagenomics had high sensitivity and is faster! Brueur noted that there is a Twist CVRP + ONT ligation approach already. However, it is labor-intensive, noted Brueur. Torres, a member of the lab, adapted a primer set to include ONT adapters for rapid library preparation. The fast targeted ONT targeted approach is shorter and can report out preliminary results after one hour of sequencing. Longer sequencing times helped with low-copy-number pathogen detection. The team shortened other aspects of the protocol including the extraction and hybridization. Version 2 can report highly sensitive results. Brueur explained that the protocol is very robust and quick. This method can be adapted to detection of pathogens or host transcripts, for example. I wonder how I can use this method to teach principles of microbial genomics?
