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

Antimicrobial resistance (AMR) poses a significant global health challenge, resulting in over 1.27 million deaths in 2019 and is projected to cause up to 10 million deaths annually in the future. To address this issue, the healthcare sector requires rapid (24-72 h) and accurate (to genus or species-level) bacterial identification. We implemented 16S ribosomal RNA (rRNA) sequencing using Oxford Nanopore Technology (ONT) in an NHS setting to enhance diagnostic capabilities, reduce antibiotic misuse and improve patient outcomes.

We used ONT-based 16S rRNA sequencing on sterile site samples (pus, fluid, tissue) from seven NHS hospitals in Cheshire and Merseyside, England. The assay, validated against Sanger sequencing and MALDI-TOF, had a 24-72 h turnaround. Clinical impact was assessed by tracking antibiotic changes and patient outcomes over several months.

ONT 16S sequencing informed antimicrobial stewardship in 56.9% of cases (124/218). It was mainly used when cultures failed (32.1%) or when patients were already on antibiotics (32.6%). Results often confirmed existing therapy (26.6%) or led to no change (28%) but still supported targeted prescribing. Streptococcus and Staphylococcus were most frequently detected genera, with Streptococcus common in ICU samples. The assay had the highest clinical impact in patients who are immunosuppressed, improving treatment precision.

The integration of ONT 16S sequencing into routine NHS diagnostics has enabled antimicrobial stewardship by offering a faster method with improved taxonomic resolution. Its earlier use in cases where routine cultures are likely to fail may contribute additional microbiological information for antimicrobial decision-making and may reduce diagnostic uncertainty.

Liverpool Clinical Laboratories (LCL) funded this work.