A systematic outbreak investigation of SARS-CoV-2 transmission clusters in a tertiary academic care center.

Humans SARS-CoV-2 / genetics COVID-19 / epidemiology Phylogeny Disease Outbreaks Cross Infection / epidemiology Tertiary Care Centers
COVID-19 Epidemiologic cluster Nosocomial outbreaks Outbreak investigation SARS-CoV-2 cluster Whole genome sequencing

Journal

Antimicrobial resistance and infection control
ISSN: 2047-2994
Titre abrégé: Antimicrob Resist Infect Control
Pays: England
ID NLM: 101585411

Informations de publication

Date de publication:
21 04 2023
Historique:
received: 15 01 2023
accepted: 12 04 2023
medline: 25 4 2023
pubmed: 22 4 2023
entrez: 21 04 2023
Statut: epublish

Résumé

We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020. At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains. The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7%), more commonly affecting HCWs (16/24, 66.7%) than patients (8/24, 33.3%), followed by transmission between patients (6/33, 18.2%), and among HCWs and patients (3/33, 9.1%, respectively two HCWs and one patient). Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.

Sections du résumé

BACKGROUND
We sought to decipher transmission pathways in healthcare-associated infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within our hospital by epidemiological work-up and complementary whole genome sequencing (WGS). We report the findings of the four largest epidemiologic clusters of SARS-CoV-2 transmission occurring during the second wave of the pandemic from 11/2020 to 12/2020.
METHODS
At the University Hospital Basel, Switzerland, systematic outbreak investigation is initiated at detection of any nosocomial case of SARS-CoV-2 infection, as confirmed by polymerase chain reaction, occurring more than five days after admission. Clusters of nosocomial infections, defined as the detection of at least two positive patients and/or healthcare workers (HCWs) within one week with an epidemiological link, were further investigated by WGS on respective strains.
RESULTS
The four epidemiologic clusters included 40 patients and 60 HCWs. Sequencing data was available for 70% of all involved cases (28 patients and 42 HCWs), confirmed epidemiologically suspected in house transmission in 33 cases (47.1% of sequenced cases) and excluded transmission in the remaining 37 cases (52.9%). Among cases with identical strains, epidemiologic work-up suggested transmission mainly through a ward-based exposure (24/33, 72.7%), more commonly affecting HCWs (16/24, 66.7%) than patients (8/24, 33.3%), followed by transmission between patients (6/33, 18.2%), and among HCWs and patients (3/33, 9.1%, respectively two HCWs and one patient).
CONCLUSIONS
Phylogenetic analyses revealed important insights into transmission pathways supporting less than 50% of epidemiologically suspected SARS-CoV-2 transmissions. The remainder of cases most likely reflect community-acquired infection randomly detected by outbreak investigation. Notably, most transmissions occurred between HCWs, possibly indicating lower perception of the risk of infection during contacts among HCWs.

Identifiants

DOI: 10.1186/s13756-023-01242-y PMID: 37085891 PMC: PMC10119817
pubmed: 37085891
doi: 10.1186/s13756-023-01242-y
pii: 10.1186/s13756-023-01242-y
pmc: PMC10119817
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Pagination

38

Informations de copyright

© 2023. The Author(s).

Références

PLoS Pathog. 2021 Mar 19;17(3):e1009374
pubmed: 33740028
Crit Care Med. 2021 Mar 1;49(3):428-436
pubmed: 33512941
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Emerg Infect Dis. 2020 Oct;26(10):2489-2491
pubmed: 32758345
Microbiol Res. 2022 Oct;263:127133
pubmed: 35901580
Bioinformatics. 2019 Feb 1;35(3):526-528
pubmed: 30016406
Nat Commun. 2021 Feb 10;12(1):905
pubmed: 33568663
Infect Control Hosp Epidemiol. 2022 Apr;43(4):474-480
pubmed: 33823950
Nat Commun. 2022 Feb 3;13(1):671
pubmed: 35115517
Clin Infect Dis. 2021 Jun 1;72(11):e727-e735
pubmed: 32954414
Clin Infect Dis. 2022 May 3;74(9):1579-1585
pubmed: 34329418
J Infect. 2020 Oct;81(4):621-624
pubmed: 32735893
Int J Nurs Stud. 2021 Feb;114:103811
pubmed: 33352440
Virulence. 2021 Dec;12(1):1209-1226
pubmed: 34030593
PLoS Med. 2021 Oct 12;18(10):e1003816
pubmed: 34637439
J Hosp Infect. 2020 Oct;106(2):325-329
pubmed: 32730771
Lancet. 2020 May 23;395(10237):1608-1610
pubmed: 32401714
Mol Biol Evol. 2020 May 1;37(5):1530-1534
pubmed: 32011700
Lancet Infect Dis. 2020 Oct;20(10):e261-e267
pubmed: 32711692
Bioinformatics. 2008 Jun 1;24(11):1403-5
pubmed: 18397895
Clin Microbiol Infect. 2022 Jan;28(1):93-100
pubmed: 34400345
J Infect Dis. 2020 Sep 14;222(8):1270-1279
pubmed: 32726441
Antimicrob Resist Infect Control. 2022 Mar 18;11(1):51
pubmed: 35303939

Auteurs

Matthias von Rotz (M)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.

Richard Kuehl (R)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.

Ana Durovic (A)

Swiss Tropical and Public Health Institute, Basel, Switzerland.

Sandra Zingg (S)

Intensive Care Unit, University Hospital Basel, University of Basel, Basel, Switzerland.

Anett Apitz (A)

Employee Health Service, University Hospital Basel, Basel, Switzerland.

Fanny Wegner (F)

Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Helena M B Seth-Smith (HMB)

Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Tim Roloff (T)

Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Karoline Leuzinger (K)

Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.

Hans H Hirsch (HH)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.
Clinical Virology, Laboratory Medicine, University Hospital Basel, University of Basel, Basel, Switzerland.
Transplantation and Clinical Virology, Department Biomedicine, University of Basel, Basel, Switzerland.

Sabine Kuster (S)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.

Manuel Battegay (M)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland.

Luigi Mariani (L)

Department of Neurosurgery, University Hospital Basel, University of Basel, Basel, Switzerland.

Stefan Schaeren (S)

Department of Traumatology and Orthopedics, University Hospital Basel, University of Basel, Basel, Switzerland.

Stefano Bassetti (S)

Division of Internal Medicine, University Hospital Basel, University of Basel, Basel, Switzerland.

Florian Banderet-Uglioni (F)

Employee Health Service, University Hospital Basel, Basel, Switzerland.

Adrian Egli (A)

Division of Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland.
Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland.
Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.

Sarah Tschudin-Sutter (S)

Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Petersgraben 4, 4031, Basel, Switzerland. sarah.tschudin@usb.ch.

Articles similaires

Comprehensive comparative analysis and development of molecular markers for Lasianthus species based on complete chloroplast genome sequences.

Yue Zhang, Meifang Song, Deying Tang et al.
1.00
Genome, Chloroplast Phylogeny Genetic Markers Base Composition High-Throughput Nucleotide Sequencing

[Redispensing of expensive oral anticancer medicines: a practical application].

Lisanne N van Merendonk, Kübra Akgöl, Bastiaan Nuijen
1.00
Humans Antineoplastic Agents Administration, Oral Drug Costs Counterfeit Drugs

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female

Evaluation of Low-Value Services Across Major Medicare Advantage Insurers and Traditional Medicare.

Ciara Duggan, Adam L Beckman, Ishani Ganguli et al.
1.00
Humans United States Aged Cross-Sectional Studies Medicare Part C

Classifications MeSH

questionsmedicales.fr › Eucaryotes › Animaux › Chordés › Vertébrés › Mammifères › Eutheria › Primates › Haplorhini › Catarrhini › Hominidae › Humains › A systematic outbreak investigation of...
questionsmedicales.fr › Virus › Virus à ARN › Virus à ARN à brin positif › Nidovirales › Coronaviridae › Coronavirus › Betacoronavirus › Virus du SRAS › SARS-CoV-2 › A systematic outbreak investigation of...
questionsmedicales.fr › Maladies de l'appareil respiratoire › Infections de l'appareil respiratoire › Pneumopathie infectieuse › Pneumopathie virale › COVID-19 › A systematic outbreak investigation of...
questionsmedicales.fr › Sciences de l'information › Phylogenèse › A systematic outbreak investigation of...
questionsmedicales.fr › Environnement et santé publique › Santé publique › Épidémies de maladies › A systematic outbreak investigation of...
questionsmedicales.fr › États, signes et symptômes pathologiques › Processus pathologiques › Caractéristiques de la maladie › Maladie iatrogène › Infection croisée › A systematic outbreak investigation of...
questionsmedicales.fr › Établissements, main d'oeuvre et services de soins de santé › Établissements de santé › Hôpitaux › Centres de soins tertiaires › A systematic outbreak investigation of...