Implementing portable, real-time 16S rRNA sequencing in the healthcare sector enhances antimicrobial stewardship

BackgroundAntimicrobial resistance (AMR) poses a significant global health challenge, resulting in over 1.27 million deaths in 2019 and projected to cause up to 10 million deaths annually in the future. To address this issue, the healthcare sector requires rapid and accurate bacterial identification, which is currently not readily available for effective antimicrobial stewardship. In a UK national first, we implemented 16S ribosomal RNA (rRNA) sequencing using Oxford Nanopore Technology (ONT) in an NHS setting to enhance diagnostic capabilities, aiming to reduce antibiotic misuse and improve patient outcomes. MethodsWe implemented 16S rRNA sequencing via ONT, running samples from seven NHS hospitals across Cheshire and Merseyside. We focused on samples from sterile sites, such as "pus", "fluid", and "tissue", typically collected from critical care units. The assay was validated against traditional methods including Sanger sequencing and MALDI-TOF, with a turnaround time of 24-72 hours. Clinical impact was measured by analysing changes in antibiotic regimens and patient outcomes based on 16S assay results over a period of several months post-launch. FindingsONT 16S rRNA sequencing significantly impacted antibiotic treatment in 34.2% of cases, reducing patient stays and outperforming traditional methods by detecting additional bacterial organisms and identifying bacteria missed by reference labs. It provided species-level identification and confirmed non-infectious conditions in 5.4% of cases, aiding alternative treatment decisions. Its speed, cost-effectiveness, and minimal training requirements contributed to its successful integration into clinical practice. InterpretationThe integration of ONT 16S sequencing into routine NHS diagnostics has significantly improved antimicrobial stewardship by offering a faster, more sensitive, and accurate bacterial identification method. Earlier use of this assay in cases where routine cultures are likely to fail could enhance patient outcomes further by enabling timely, targeted antibiotic therapies, reducing hospital stays, and curbing unnecessary antibiotic use.