In the case of bacterial samples, WGS enables the sequencing of an entire pathogen genome including plasmids. This broad sequencing allows for the identification of antibiotic resistance profiles, which can be used to inform first-line drug use decisions [171]. The drawback of WGS for bacterial samples is that it usually requires a separate culture step to ensure the sample is free of contaminant or commensal bacteria; however, sequencing directly from a host isolate and skipping culture has been performed with targeted enrichment [172]. Furthermore, while WGS datasets accurately define known drug resistance markers, the discovery of novel mutations and their effects on phenotype bring added uncertainty to the test [173, 174].
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