Harmonisation of in-silico next-generation sequencing based methods for diagnostics and surveillance.

ABSTRACT: Improvements in cost and speed of next generation sequencing (NGS) have provided a new pathway for delivering disease diagnosis, molecular typing, and detection of antimicrobial resistance (AMR). Numerous published methods and protocols exist, but a lack of harmonisation has hampered meaningful comparisons between results produced by different methods/protocols vital for global genomic diagnostics and surveillance. As an exemplar, this study evaluated the sensitivity and specificity of five well-established in-silico AMR detection software where the genotype results produced from running a panel of 436 Escherichia coli were compared to their AMR phenotypes, with the latter used as gold-standard. The pipelines exploited previously known genotype-phenotype associations. No significant differ

SUBMITTER: Nunez-Garcia J 

PROVIDER: S-EPMC9396611 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature