Enhancing Antimicrobial Resistance Detection through Genomic Surveillance

PopPIPEis a genomic-analysis pipeline that streamlines workflows and improves detection of related bacterial isolates in healthcare settings. By shortening the interval from sample receipt to actionable genomic insight, the pipeline tightens the window for targeted infection-control responses and reduces the risk of undetected spread.

Whole-genome sequencing (WGS) provides far higher resolution than culture-based typing or standard epidemiologic linkage, distinguishing near-identical strains from unrelated isolates. WGS can expose cryptic transmission chains and asymptomatic carriers missed by symptom-driven screening and improves specificity when linking cases to a common source. Together, genomic surveillance shifts detection from probabilistic, contact-tracing-dependent inference to sequence-resolved linkage for more precise outbreak delineation.

The NHS Lothian–University of St Andrews collaboration applied the pipeline on routine wards and identified transmission clusters that conventional methods missed; results were used to adjust cohorting, cleaning, and focused screening. That operational cadence demonstrates that genomic outputs can be integrated into clinical workflows and produce timely, actionable reports for infection-control teams.

Effective deployment requires on-site or rapid-access sequencing with a predictable turnaround (ideally 24–72 hours from culture-positive specimen to processed sequence), a basic bioinformatics server or cloud instance to run the pipeline, standardized sequencing workflows with QC, and formalized handoffs among laboratory, infection-control, and epidemiology teams. Training for non-bioinformaticians should prioritize cluster interpretation, SNP-thresholds for relatedness, and templated reporting; laboratory staff need competency in sequencing QC metrics and sample tracking. A concise checklist covering cluster interpretation, SNP thresholds, and templated reports supports rapid adoption and consistent readiness across sites.

Common barriers include data-sharing and governance constraints, IT integration challenges with electronic health records, a limited bioinformatics workforce, and the need to interpret low-resolution or borderline genomic signals. These challenges are tractable with standardized pipelines and SOPs, organism-specific SNP thresholds or clustering rules, routine multidisciplinary review to contextualize genomic signals, and secure minimal-data-sharing protocols that preserve privacy while enabling rapid action. With these mitigations, routine genomic surveillance becomes practical rather than ad hoc.