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

  25 August 2022

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 differences in software performance were observed. As a consequence, efforts to harmonise AMR predictions from sequence data should focus on: (1) establishing universal minimum to assess performance thresholds (e.g. a control isolate panel, minimum sensitivity/specificity thresholds); (2) standardising AMR gene identifiers in reference databases and gene nomenclature; (3) producing consistent genotype/phenotype correlations.

Further reading: Nature Scientific Reports
Author(s): J. Nunez-Garcia, M. AbuOun, N. Storey, M. S. Brouwer, J. F. Delgado-Blas, S. S. Mo, N. Ellaby, K. T. Veldman, M. Haenni, P. Châtre, J. Y. Madec, J. A. Hammerl, C. Serna, M. Getino, R. La Ragione, T. Naas, A. A. Telke, P. Glaser, M. Sunde, B. Gonzalez-Zorn, M. J. Ellington & M. F. Anjum
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