One of the London Calling 2023 Showcase Stage sessions was on Targeted Sequencing. Tonight, i watched the four-minute recording entitled “Rapid identification of bacterial invasion: full-length 16S or adaptive sampling?” The title intrigued me! I am waiting for the release of the updated 16S amplicon kit. There were several panelists and Thidathip Wongsurawat from the Siriraj Long-read Lab in Mahidol University in Thailand spoke about “Rapid identification of bacterial invasion in the amniotic cavity: full-length 16S or adaptive sampling?” They started with work on rapid diagnosis of intra-amniotic infection they have conducted. They are able to quickly sequence amniotic fluid and compared cultivation, Sanger sequencing, and Nanopore sequencing. The difference in turnaround varied from days, to 24 hrs, to 6 hours for cultivation, Sanger sequencing, and Nanopore sequencing. Sanger sequencing results were difficult or impossible when samples included a mix of organisms. Wongsurawat wanted to move beyond species identification and determine AMR gene information, skip the PCR step, and obtain clinically actionable data. The team obtained pus samples from intra-amniotic fluid and compared bacterial sequences with adaptive sampling and without. With adaptive sampling it took longer to obtain full genomes but the depth was greater. The team used the GridION and v14 flow cells with LSK kits. I am intrigued by adaptive sampling for metagenomics, though I haven’t used it yet!
