Implementation of microbial whole-genome sequencing for individual patient care, local outbreak recognition and national surveillance

A patient’s infection sample could reveal its entire genetic blueprint within 24 hours, telling doctors exactly which drugs will work and whether the bug is spreading through a hospital ward. Currently, identifying a pathogen, its antibiotic resistance profile, and its relatedness to other cases requires multiple separate tests that can take days or even months. These fragmented systems—one for tuberculosis, another for *E. coli*, and so on—make fast, cheap, and comprehensive characterisation impossible. Professor Derrick Crook and his team at Oxford University, working with NHS laboratories in Oxford, Brighton, Birmingham, and Leeds, aim to replace this patchwork with routine whole-genome sequencing. Within three years, they plan to show that a local network of sequencing hubs can deliver complete pathogen information within a day of culture. If successful, this would transform infection control. Hospitals could spot an outbreak in real time, rather than waiting weeks for central reference lab results. A national surveillance database would link local data, enabling faster, better-targeted treatment for individual patients and early warning of emerging resistance patterns across the UK. The system would also be cheaper and more informative than the current fragmented approach.