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The rise of antibiotic resistance threatens modern medicine; to combat it new diagnostic methods are required. Sequencing the whole genome of a pathogen offers the potential to accurately determine which antibiotics will be effective to treat a patient. A key limitation of this approach is that it cannot classify rare or previously unseen mutations.
The objectives of this study were: All data sets used are described in Supplementary Fig. 2 and Supplementary Table 1 with full sample information in Supplementary Data 1–11.
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