Dr. Gabriel E. Wagner from the Medical University of Graz presented on “Reliable whole-genome genotyping for bacterial surveillance using nanopore sequencing data” as part of the Oxford Nanopore Technologies (ONT) YouTube series. Wagner spoke about the importance of genomic surveillance for both known pathogens and surveillance of variants, including antimicrobial and vaccine resistance. This topic, Wagner noted, is connected to animal health. Whole genome sequencing provides high resolution, and now can be done for hundreds of isolates in parallel. Wagner and team wanted to try to use long-read sequencing. They used core genome MLST that uses hundreds of genes. The first study wanted to benchmark for pertussis isolates short and long read sequencing. The analysis of isolates seemed to suggest identification of more targets was possible with long-read sequencing. However, they were concerned about DNA modifications causing misidentifications. DNA modifications for some isolates affected identification. Basecalling updates and bacterial methylation helped. For Wagner’s study, 80 multi-drug resistant organisms were sequenced with short and long reads. Assembly with Flye and Medaka polishing with methylation and polishing improved identification of alleles. The Medaka v2 bacterial methylation model improved assembly and identification of targets and decreased misplacement of antimicrobial resistance targets on plasmids and chromosomes. cgMLST Polisher and updated basecaller improved identification when samples were sent out to five labs for testing. Wagner concluded that SUP 5.0 basecalled data show minimal models, Medaka 2.x with bacterial methylation model significantly reduces errors, and ONT cgMLST Polisher was highly effective for m4.3 data. Wagner noted that the latest ONT tools and models with the cgMLST Polisher improve ONT sequencing accuracy and make it reliable and reproducible for genomic surveillance of bacterial pathogens. I will now check out cgMLST Polisher and for updated Dorado models!
