NEXT-generation sequencing (NGS) for antimicrobial resistance (AMR) could revolutionize hospital infection control, according to a newly proposed global framework from a team of international infection prevention experts. With antimicrobial-resistant pathogens accounting for a significant share of healthcare-associated infections (HAIs), the need for precision surveillance and rapid response is more urgent than ever.
The framework, developed during the 3rd Geneva Infection Prevention and Control Think Tank, outlines a structured approach to implementing pathogen sequencing in healthcare settings. It specifically targets pathogens carrying AMR mechanisms, offering practical guidance on how NGS can be used to inform public health and infection prevention strategies.
The proposal identifies key pillars for successful implementation: maintaining high standards in laboratory processes, ensuring quality sequence data, selecting reliable databases and bioinformatics tools, analyzing genomic data effectively, and enabling secure, actionable data sharing. The integration of NGS into broader healthcare systems is also a central recommendation, with a particular focus on tailoring strategies for low- and middle-income countries where resources may be limited but the burden of AMR is high.
The authors emphasize that while NGS offers transformative potential in identifying and tracking resistant organisms, its widespread adoption requires more than just technology. Building infrastructure, fostering cross-disciplinary collaboration, and establishing robust data-sharing practices are essential for success.
This framework comes at a critical time, as healthcare systems globally grapple with rising AMR rates and complex hospital outbreaks. By creating a roadmap for real-world integration of genomic surveillance, the group hopes to shift the conversation from theoretical promise to practical application.
For clinicians, microbiologists, infection control teams, and public health leaders in the U.S. and beyond, the message is clear: sequencing is no longer just a research tool, it’s a frontline defense against one of the greatest challenges in modern medicine.
Reference: Laufer Halpin A et al. A framework towards implementation of sequencing for antimicrobial-resistant and other health-care-associated pathogens. Lancet Infect Dis The. 2025;25(4):e235-e244.
