Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years
Advances in genomic technologies have revolutionised practices for hospital infection prevention and control programmes. In this Personal View, we describe a genomic epidemiology service called the Rapid Response (RR) programme at University of California, San Francisco, a large academic medical centre. In collaboration with the hospital infection-prevention team, the RR programme uses whole-genome sequencing and metagenomic next-generation sequencing for outbreak investigations, special interest analyses of emerging pathogens, and surveillance of high-priority microbes. Over 7 years (2017-24), the RR programme conducted a diversity of outbreak investigations and other analyses; most investigations ruled out transmission, and the rapid turnaround of genomic results averted further resource-intensive work. Longitudinal surveillance enabled early detection of changing incidence trends and guided timely infection-prevention responses. Our experiences with the RR programme build upon growing evidence that genomic epidemiology programmes enhance hospital infection prevention and control, augment priority pathogen surveillance, and improve patient safety.
Authors
- Charles Langelier (ORCID: https://orcid.org/0000-0002-6708-4646)
- Joanne N. Engel (ORCID: https://orcid.org/0000-0002-2168-9711)
- Angela M. Detweiler (ORCID: https://orcid.org/0000-0001-7026-5467)
- Christy Pak
- Lynn Ramírez-Àvila
- Bryan Buie
- Maíra Phelps (ORCID: https://orcid.org/0009-0001-8230-7692)
- Saba Nafees (ORCID: https://orcid.org/0000-0002-3292-7703)
- Carolyn Caughell
- Lusajo Mwakibete (ORCID: https://orcid.org/0000-0003-2762-713X)
- Rebecca T. Alvino
- Amy L. Kistler (ORCID: https://orcid.org/0000-0003-1112-719X)
- Victoria Chu (ORCID: https://orcid.org/0000-0002-7480-965X)
- Matthew K. Leroue (ORCID: https://orcid.org/0000-0001-7585-7920)
- Deborah S. Yokoe
- Charles Y. Chiu (ORCID: https://orcid.org/0000-0003-2915-2094)
- Gail Cunningham
- Christina Love
- Nicole McNeil (ORCID: https://orcid.org/0000-0002-2206-5513)
- Amy Nichols
- Norma Neff (ORCID: https://orcid.org/0000-0001-7141-5420)
- Samantha Hao (ORCID: https://orcid.org/0000-0002-4349-8131)
- Abigail Glascock (ORCID: https://orcid.org/0000-0002-6919-2632)
- Kevin Messacar (ORCID: https://orcid.org/0000-0001-5830-3491)
- Helen Reyes
- Brian C. Prince (ORCID: https://orcid.org/0000-0002-8307-9054)
- Natasha Spottiswoode (ORCID: https://orcid.org/0000-0001-6157-3716)
- Sharline Madera (ORCID: https://orcid.org/0000-0003-3658-5488)
- Katrina Kalantar (ORCID: https://orcid.org/0000-0003-0281-4625)
- Steve Miller (ORCID: https://orcid.org/0000-0002-9188-3392)
- Sarah B. Doernberg (ORCID: https://orcid.org/0000-0003-1727-6014)
- Saharai Caldera (ORCID: https://orcid.org/0000-0001-5057-9186)
- Estella Sanchez Guerrero
- Joseph L DeRisi
- Paula Hayakawa Serpa
- Emily D Crawford
- David Dynerman
- Eric Waltari
- Ryan Ward
- Jack Kamm
- Cristina M Tato
- Daniel Ivashin
- Kim Stanley
- Lucy Li
Institutions
- University of Nevada, Reno (US)
- University of California, San Francisco (US)
- Nova Southeastern University (US)
- Association for Symbolic Logic (US)
- San Francisco Department of Public Health (US)
- Delpor (United States) (US)
- Chan Zuckerberg Initiative (United States) (US)
- Faculdade São Leopoldo Mandic (BR)
- Gilead Sciences (United States) (US)
- University of Colorado Anschutz Medical Campus (US)
- University of San Francisco (US)
- University of Colorado Denver (US)
Publication Details
- Journal
- The Lancet Microbe
- Published
- 2026-01-06
- DOI
- https://doi.org/10.1016/j.lanmic.2025.101277
- Primary Topic
- Bacterial Identification and Susceptibility Testing
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- National Institutes of Health
- University of California, San Francisco
- National Heart, Lung, and Blood Institute
- National Institute of Allergy and Infectious Diseases