Art and Science of Laboratory Medicine

Art and Science of Laboratory Medicine

Friday, December 9, 2016

Whole genome sequencing cannot yet be used to determine antimicrobial susceptibility

EUCAST experts publish report where they show that whole genome sequencing (WGS) cannot yet be used to determine antimicrobial susceptibility of many important bacterial species.

Whole genome sequencing (WGS) offers the potential to predict antimicrobial susceptibility from a single assay. The European Committee on Antimicrobial Susceptibility Testing (EUCAST) established a subcommittee to review the current development status of WGS for bacterial antimicrobial susceptibility testing (AST).

The published evidence for using WGS as a tool to infer antimicrobial susceptibility accurately is currently either poor or non-existent and the evidence / knowledge base requires significant expansion. The primary comparators for assessing genotypic-phenotypic concordance from WGS data should be changed to epidemiological cut-off values (ECOFFs) in order to improve differentiation of wild type from non-wild type isolates (harbouring an acquired resistance). Clinical breakpoints should be a secondary comparator. This assessment will reveal whether genetic predictions could also be used to guide clinical decision making. Internationally agreed principles and quality control (QC) metrics will facilitate early harmonization of analytical approaches and interpretative criteria for WGS-based predictive AST. Only datasets that pass agreed QC metrics should be used in AST predictions. Minimum performance standards should exist and comparative accuracies across different WGS laboratories and processes should be measured. In order to facilitate comparisons, a single public database of all known resistance loci should be established, regularly updated and strictly curated using minimum standards for the inclusion of resistance loci. For most bacterial species the major limitations to widespread adoption for WGS-based AST in clinical labs remain the current high-cost and limited speed of inferring antimicrobial susceptibility from WGS data as well as the dependency on prior culture since analysis directly on specimens remains challenging.

For most bacterial species there is currently insufficient evidence to support the use of WGS-inferred AST to guide clinical decision making. WGS-AST should be a funding priority if it is to become a rival to phenotypic AST. This report will be updated as the available evidence increases.

Read the report:

CMI, Clinical Microbiology and Infection

1 comment:

JVKohl said...

Perhaps the focus should be on what can be done with WGS. It can be used to link energy-dependent bioluminescence from bacteria in the light organ of bobtail squid to the nutrient energy-dependent pheromone controlled weekend resurrection of the bacterial flagellum in Pseudomonas fluorescens via the conserved molecular mechanisms of cell type differentiation in all living genera.

Examining that fact in the context of what is currently known about autophagy (Yoshinori Ohsumi)links everything known about biophysically constrained protein folding chemistry (Ben Feringa) to energy-dependent fixation of RNA-mediated amino acid substitutions in supercoiled DNA, which protect all organized genomes from virus-driven energy theft and genomic entropy (Gunter Witzany).

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