Evidence map›Paper›PMID 41512899›Full record

ReviewThe Lancet. Microbe2026

Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.

Victoria T Chu, Natasha Spottiswoode, Ryan Ward, Deborah S Yokoe, Lynn Ramirez-Avila, Maira S Phelps, Abigail Glascock, Emily D Crawford, Jack Kamm, Samantha Hao and 34 more

Abstract readReview
PubMed Full text at PMC Publisher
In one paragraph

Review in The Lancet. Microbe, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

44 authors.

Victoria T ChuDepartment of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
Natasha SpottiswoodeDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Ryan WardDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Deborah S YokoeDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Lynn Ramirez-AvilaDepartment of Pediatrics, University of California, San Francisco, San Francisco, CA, USA.
Maira S PhelpsChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Abigail GlascockChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Emily D CrawfordDelve Inc, San Francisco, CA, USA.
Jack KammGenentech Inc, San Francisco, CA, USA.
Samantha HaoDepartment of Neurology, University of California, San Francisco, San Francisco, CA, USA.
Lucy LiFeature Health Inc, San Francisco, CA, USA.
David DynermanSymbolica AI Inc, Stanford, CA, USA.
Eric WaltariChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Saba NafeesChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Katrina L KalantarChan Zuckerberg Initiative, Redwood City, CA, USA.
Saharai CalderaDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Sharline MaderaGilead Inc, Foster City, CA, USA.
Estella Sanchez GuerreroNova Southeastern University, Fort Lauderdale, FL, USA.
Daniel IvashinDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Paula Hayakawa SerpaFaculdade São Leopoldo Mandic, São Paulo, Brazil.
Christina LoveDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Lusajo L MwakibeteChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Sarah B DoernbergDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Amy KistlerChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Rebecca AlvinoUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Joanne EngelDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Charles Y ChiuDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA.
Christy PakUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Gail CunninghamUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Helen ReyesUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Bryan BuieUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Kevin MessacarDepartment of Pediatrics, University of Colorado, Aurora, CO, USA.
Matthew LeroueDepartment of Pediatrics, University of Colorado, Aurora, CO, USA.
Brian C PrinceDepartment of Biochemistry, Molecular Biology and Biotechnology, University of Nevada, Reno, NV, USA.
Angela M DetweilerChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Kim StanleyUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Carolyn CaughellUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Nicole McNeilUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Norma NeffChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Amy NicholsUCSF Health, University of California, San Francisco, San Francisco, CA, USA.
Steve MillerDelve Inc, San Francisco, CA, USA.
Joseph L DeRisiDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Cristina M TatoChan Zuckerberg Biohub San Francisco, San Francisco, CA, USA.
Charles R LangelierDepartment of Medicine, University of California, San Francisco, San Francisco, CA, USA; Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA. Electronic address: chaz.langelier@ucsf.edu.

Funding

CTSA K12 Program at University of Colorado DenverK12TR004412 · NCATS · UNIVERSITY OF COLORADO DENVER · PI ELLEN L BURNHAM · 2024 to 2026
$3.2M
Integrated Host/Microbe Metagenomics to Improve Lower Respiratory Tract Infection Diagnosis in Critically Ill ChildrenR01HL155418 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LANGELIER, CHARLES · 2021 to 2024
$1.6M
Metagenomic surveillance of pathogen and antimicrobial resistance gene transmission in hospitalized neonatesK23AI185326 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI CHU, VICTORIA TIEN-YU · 2024 to 2025
$395k
NCATS NIH HHS K12 TR004412NHLBI NIH HHS R01 HL155418NIAID NIH HHS K23 AI185326
6 · The paper itself

Abstract

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.

Indexed as

Cross InfectionGenomicsInfection ControlMolecular EpidemiologyAcademic Medical CentersDisease OutbreaksHigh-Throughput Nucleotide SequencingHumansSan FranciscoWhole Genome Sequencing

Identifiers

PMID41512899
PMCPMC13108401

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.