Rapid genomic characterization of high-risk pathogens using long-read sequencing to identify nosocomial outbreaks
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Typically, Illumina based sequencing has been necessary to achieve sufficient confidence to identify two or more bacterial strains causing infections as being genetically related, suggestive of healthcare transmission.
The Oxford Nanopore Technologies new chemistries (V14) and improving basecalling algorithms hold promise to improve long-read based methods to measure genetic relatedness with similar sensitivity/specificity to short-read methods.
We sought to develop an Oxford Nanopore Technologies sequencing pipeline capable of rapid outbreak detection in healthcare settings