Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting-Reference-Cited by-同舟云学术

Integrated Genomic and Social Network Analyses of Severe Acute Respiratory Syndrome Coronavirus 2 Transmission in the Healthcare Setting

Published:2024-01-16 Issue: Volume: Page:
ISSN:1058-4838
Container-title:Clinical Infectious Diseases
language:en
Short-container-title:

Author:

Keehner Jocelyn¹²,Abeles Shira R²³,Longhurst Christopher A⁴⁵,Horton Lucy E²³⁶,Myers Frank E³,Riggs-Rodriguez Lindsay⁷,Ahmad Mohammed⁸,Baxter Sally⁹,Boussina Aaron¹⁰,Cantrell Kalen¹¹,Cardenas Priscilla¹²,De Hoff Peter¹³¹⁴¹⁵,El-Kareh Robert⁴¹⁶,Holland Jennifer¹⁷,Ikeda Daryn¹²,Kurashige Kirk¹⁷,Laurent Louise C¹³¹⁴¹⁵,Aigner Stefan,Andersen Kristian G,Anderson Catelyn,Baer Nathan A,Barber Tom,Bauk Marco,Beck Jennifer N,Belda-Ferre Pedro,Betty Maryann,Birmingham Amanda,Castro-Martinez Anelizze,Cheung Willi,De Hoff Peter,Fisch Kathleen M,Gangavarapu Karthik,Gargano Isabella,Hakim Abbas,Harsono Shania,Henson Benjamin,Hobbs Charlotte,Holmes Jacqueline,Jepsen Kristen,Knight Rob,Kurzban Ezra,Laurent Louise C,Marotz Clarisse A,Matteson Nathaniel L,Moshiri Niema,Ngo Toan T,Ostrander Tyler R,Perkins Sarah,Plascencia Ashley,Rivera Andrea,Rivera Ariana,Salido Rodolfo A,Sathe Shashank,Seaver Phoebe,Schwab Madison,Veder Anthony,Yeo Gene W,Zeller Mark,Lucas Andrew⁸,Pride David²¹⁸,Sathe Shashank¹³¹⁹¹⁴,Tran Allen R⁸,Vasylyeva Tetyana I²^ORCID,Yeo Gene¹³¹⁹¹⁴^ORCID,Knight Rob⁵²⁰²¹¹⁴²²^ORCID,Wertheim Joel O²,Torriani Francesca J²³^ORCID,

Affiliation:

1. Division of Infectious Diseases, Department of Medicine, University of California–SanFrancisco , San Francisco, California , USA

2. Division of Infectious Diseases and Global Public Health, Department of Medicine, UC San Diego Health , San Diego, California , USA

3. Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health , San Diego, California , USA

4. Division of Biomedical Informatics, Department of Medicine, UC San Diego Health , La Jolla, California , USA

5. Department of Pediatrics, University of California–San Diego , La Jolla, California , USA

6. Vaccine Research and Development Unit, Pfizer Inc , San Diego, California , USA

7. Population Health Services Organization—Programs and Strategy, UC San Diego Health , San Diego, California , USA

8. Information Services EMR, UC San Diego Health , San Diego, California , USA

9. Division of Biomedical Informatics at the University of California–San Diego , San Diego, California , USA

10. Division of Biomedical Informatics, University of California–San Diego , La Jolla, California , USA

11. Department of Computer Science & Engineering, Jacobs School of Engineering, University of California , San Diego, California , USA

12. UC San Diego Health's Contact Tracing Team, Infection Prevention and Clinical Epidemiology Unit, UC San Diego Health , San Diego, California , USA

13. Sanford Consortium of Regenerative Medicine, University of California–San Diego , La Jolla, California , USA

14. Expedited COVID Identification Environment Laboratory, Department of Pediatrics, University of California–San Diego , La Jolla, California , USA

15. Division of Maternal Fetal Medicine, Department of Obstetrics, Gynecology, and Reproductive Sciences, UC San Diego Health , San Diego, California , USA

16. Division of Hospital Medicine, Department of Medicine, UC San Diego Health , La Jolla, California , USA

17. Analytics and Population Health Department, UC San Diego Health , San Diego, California , USA

18. Department of Pathology, UC San Diego Health , La Jolla, California , USA

19. Department of Cellular and Molecular Medicine, University of California–San Diego , La Jolla, California , USA

20. Department of Bioengineering, University of California–San Diego , La Jolla, California , USA

21. Department of Computer Science and Engineering, University of California–San Diego , La Jolla, California , USA

22. Center for Microbiome Innovation, University of California–San Diego , La Jolla, California , USA

Abstract

Abstract Background Infection prevention (IP) measures are designed to mitigate the transmission of pathogens in healthcare. Using large-scale viral genomic and social network analyses, we determined if IP measures used during the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic were adequate in protecting healthcare workers (HCWs) and patients from acquiring SARS-CoV-2. Methods We performed retrospective cross-sectional analyses of viral genomics from all available SARS-CoV-2 viral samples collected at UC San Diego Health and social network analysis using the electronic medical record to derive temporospatial overlap of infections among related viromes and supplemented with contact tracing data. The outcome measure was any instance of healthcare transmission, defined as cases with closely related viral genomes and epidemiological connection within the healthcare setting during the infection window. Between November 2020 through January 2022, 12 933 viral genomes were obtained from 35 666 patients and HCWs. Results Among 5112 SARS-CoV-2 viral samples sequenced from the second and third waves of SARS-CoV-2 (pre-Omicron), 291 pairs were derived from persons with a plausible healthcare overlap. Of these, 34 pairs (12%) were phylogenetically linked: 19 attributable to household and 14 to healthcare transmission. During the Omicron wave, 2106 contact pairs among 7821 sequences resulted in 120 (6%) related pairs among 32 clusters, of which 10 were consistent with healthcare transmission. Transmission was more likely to occur in shared spaces in the older hospital compared with the newer hospital (2.54 vs 0.63 transmission events per 1000 admissions, P < .001). Conclusions IP strategies were effective at identifying and preventing healthcare SARS-CoV-2 transmission.

Funder

CDC

NIH–NIAID

Expedited COVID Identification Environment

COVID-19 qPCR

Publisher

Oxford University Press (OUP)

Subject

Infectious Diseases,Microbiology (medical)

Link

https://academic.oup.com/cid/advance-article-pdf/doi/10.1093/cid/ciad738/55566545/ciad738.pdf

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