Rapid identification of pathogens, antibiotic resistance genes and plasmids in blood cultures by nanopore sequencing
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A long time (~2-3 days) is needed for pathogen identification and its AMR resistance characterization in blood stream infections after blood culture is flagged positive. To reduce time (<24 hours) for blood culture diagnostics in clinic using real-time nanopore sequencing and sequence analysis. Here we address the questions: What is the least time in order to get the information on: a) taxonomy; b) antibiotic resistance genes; c) plasmids? and How fast can we get the whole genome covered and do MinION sequence data allow AMR gene variant identification?