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Hospitals worldwide are facing an increasing incidence of hard-to-treat infections. Limiting infections and providing patients with optimal drug regimens require timely strain identification as well as virulence and drug-resistance profiling. Additionally, prophylactic interventions based on the identification of environmental sources of recurrent infections (e.g., contaminated sinks) and reconstruction of transmission chains (i.e., who infected whom) could help to reduce the incidence of nosocomial infections. WGS could hold the key to solving these issues. However, uptake in the clinic has been slow. Some major scientific and logistical challenges need to be solved before WGS fulfils its potential in clinical microbial diagnostics. In this review we identify major bottlenecks that need to be resolved for WGS to routinely inform clinical intervention and discuss possible solutions.

Original publication




Journal article


Trends in microbiology

Publication Date





1035 - 1048


UCL Genetics Institute, University College London, Gower Street, London WC1E 6BT, UK; These authors made equal contributions. Electronic address:


Humans, Bacteria, Cross Infection, Virulence Factors, Diagnostic Tests, Routine, Sequence Analysis, DNA, Drug Resistance, Bacterial, Virulence, Base Sequence, Phenotype, Genes, Bacterial, Genome, Bacterial, Multilocus Sequence Typing, Whole Genome Sequencing