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
Smart Innovations  


Unrestricted financial support by:

Antimicrobial Resistance Fighter Coalition


JSS University


Technology Database

Display your AMR Technology, Product and Service

Suppliers and Users of Technologies, Products and Services benefit from CAPI.
CAPI (Continuous AMR Partnering Initiative) unites Suppliers and Users worldwide with the aim to add to the curbing of AMR.

Read more and make your own Technology Page >>
What is going on with AMR?
Stay tuned with remarkable global AMR news and developments!