After a good vacation in San Miguel de Allende, Mexico, I am back! Tonight I watched Michael Wiley from the University of Nebraska Medical Center in the USA present at London Calling 2025 on “Automated sample-to-answer workflows for whole genome sequencing to investigate hospital-acquired infections.” The public health labs are embedded in the medical center and are next to Nebraska Medicine, the largest health center in the state. Wiley spoke about CDC PulseNet starting in 1996 with pulse-field gel electrophoresis and moving to Illumina WGS in 2013-2016. Wiley’s institution has had the ClearDX system with a GridION on a Hamilton liquid handler. The setup tie is 30 mins and the run time is 27 hrs for the ClearDX. The cost per run of the ClearDX with the Illumina 2 Seq100s is about $2000. The ElysION from Oxford Nanopore Technologies (ONT) was purchased by Wiley’s institution and does take longer to setup. It has one device and runs a Tecan liquid handler. The system takes about two hours to set up with bead bashing included and can process up to 24 samples. With the NO-MISS protocol, the cost per run is $1100-1200. Wiley’s team obtains samples from hospital acquired infections as part of a national program. The team is using BugSeq for data analysis. The comparison of Illumina and ONT showed similar trees. Wiley mentioned that the ElysION was hardcoded to run in High Accuracy basecalling and not super accurate (SUP). The CDC recommends >30X coverage for Illumina and the team strives fro 50-60X for ONT. The pangenome analysis was robust and along with plasmid analysis, the both platforms were very similar. Plasmid replicon types agreed but there was better resolution of plasmid sequences with ONT reads. Evidence of horizontal gene transmission and clonal transmission could be inferred. This work by the Nebraska Public Health Laboratory has helped benchmark automated analysis with ONT.
