Bikar, S.-E. | bioRxiv Science

bioRxiv2023

Nanopore adaptive sampling of a metagenomic sample derived from a human monkeypox case

In 2022, a series of human monkeypox cases in multiple countries led to the largest and most widespread outbreak outside the known endemic areas. Genomic surveillance is of utmost importance to control such outbreaks. To this end, we performed Nanopore Whole Genome Sequencing of a local monkeypox sample on a PromethION 24. Adaptive sampling was applied for in silico depletion of the human host genome, allowing for the enrichment of low abundance viral DNA without a priori knowledge of sample composition. Nanopore sequencing allowed for high viral genome coverage, tracking of sample composition during sequencing, strain determination, and preliminary assessment of mutational pattern. Nanopore sequencing is a highly versatile method to characterize a virus in real-time without pre-sequencing target enrichment.

microbiology↗

bioRxiv2019

Identification and quantification of meat product ingredients by whole-genome metagenomics (All-Food-Seq)

Complex food matrices bear the risk of intentional or accidental admixture of non-declared species. Moreover, declared components can be present in false proportions, since expensive taxa might be exchanged for cheaper ones. We have previously reported that PCR-free metagenomic sequencing of total DNA extracted from sausage samples combined with bioinformatic analysis (termed All-Food-Seq, AFS), can be a valuable screening tool to identify the taxon composition of food ingredients. Here we illustrate this principle by analysing regional Doner kebap samples, which revealed unexpected and unlabelled poultry and plant components in three of five cases. In addition, we systematically apply AFS to a broad set of reference meat material of known composition (i.e. reference sausages) to evaluate quantification accuracy and potential limitations. We include a detailed analysis of the effect of different food matrices and the possibility of false-positive sequence read assignment to closely related species, and we compare AFS quantification results to quantitative real-time PCR (qPCR) and droplet digital PCR (ddPCR). AFS emerges as a potent PCR-free screening tool, which can detect multiple target species of different kingdoms of life within a single assay. Mathematical calibration accounting for pronounced matrix effects can significantly improves AFS quantification accuracy. In comparison, AFS performs better than classical qPCR, and is on par with ddPCR.

genomics↗