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Strain-level characterization without culture enrichment? Easing and accelerating outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling
adaptive sampling, following whole genome amplification to increase the amount of genetic material to meet sequencing standards. The strain-level data analysis was performed as previously described (Buytaers ...
Development of strain-level shotgun metagenomics approaches to detect and characterize microbiological contaminants in the context of food safety
contaminant present in the sample at once, possibly also at the SNP level. At the time this study started, shotgun metagenomics for the study of food contaminants was in its infancy. Moreover, strain-level ...
Shotgun metagenomics as a ONE Health tool for better protecting human health
laboratories, however without isolation and in a shorter time-frame. This could be achieved to the strain level even in samples with several E. coli strains. The method was also used to solve a Salmonella ...
Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak
Salmonella SNP analysis strain-level Abstract: Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to ...
Development of a genoserotyping system for the identification of Salmonella serotypes
of the results in a database to improve the Salmonella surveillance in Belgium. The 4 modules and the DSS were validated by comparison with the classical method, including more than 1300 strains and ...