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Whole-genome sequencing data-based modeling for the investigation of an outbreak of community-associated methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit in Hong Kong

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Abstract

We describe a nosocomial outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) ST59-SCCmec type V in a neonatal intensive care unit (NICU) in Hong Kong. In-depth epidemiological analysis was performed by whole-genome sequencing (WGS) of the CA-MRSA isolates collected from patients and environment during weekly surveillance and healthcare workers from the later phase of the outbreak. Case–control analysis was performed to analyze potential risk factors for the outbreak. The outbreak occurred from September 2017 to February 2018 involving 15 neonates and one healthcare worker. WGS analysis revealed complicated transmission dynamics between patients, healthcare worker, and environment, from an unrecognized source introduced into the NICU within 6 months before the outbreak. In addition to enforcement of directly observed hand hygiene, environmental disinfection, cohort nursing of colonized and infected patients, together with contact tracing for secondary patients, medical, nursing, and supporting staff were segregated where one team would care for CA-MRSA-confirmed/CA-MRSA-exposed patients and the other for newly admitted patients in the NICU only. Case–control analysis revealed use of cephalosporins [odds ratio 49.84 (3.10–801.46), p = 0.006] and length of hospitalization [odds ratio 1.02 (1.00–1.04), p = 0.013] as significant risk factors for nosocomial acquisition of CA-MRSA in NICU using multivariate analysis. WGS facilitates the understanding of transmission dynamics of an outbreak, providing insights for outbreak prevention.

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Acknowledgements

Genomic sequences of the CA-MRSA isolates in this work have been deposited in the GenBank under BioProject number PRJNA493547.

Funding

This study was partially supported by grants from the Health and Medical Research Fund (HMRF), Food and Health Bureau, Hong Kong SAR Government (HKM-15-M10 and HKM-15-M12), and Seed Fund for Basic Research, University Research Committee, University of Hong Kong.

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Authors and Affiliations

  1. Department of Microbiology, Queen Mary Hospital, Hong Kong, Special Administrative Region, China

    Vincent C. C. Cheng, Jonathan H. K. Chen, Simon Y. C. So & Sally C. Y. Wong

  2. Infection Control Team, Queen Mary Hospital, Hong Kong West Cluster, Hong Kong, Special Administrative Region, China

    Vincent C. C. Cheng & Shuk-Ching Wong

  3. Department of Microbiology and Carol Yu Centre for Infection, Queen Mary Hospital, The University of Hong Kong, Hong Kong, Special Administrative Region, China

    Huiluo Cao, Siddharth Sridhar, Kwok-Yung Yuen & Pak-Leung Ho

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  1. Vincent C. C. Cheng
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Correspondence to Pak-Leung Ho.

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Ethical approval was not required because the infection control measures are the standard patient care to control and prevent hospital outbreak.

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Cheng, V.C.C., Wong, SC., Cao, H. et al. Whole-genome sequencing data-based modeling for the investigation of an outbreak of community-associated methicillin-resistant Staphylococcus aureus in a neonatal intensive care unit in Hong Kong. Eur J Clin Microbiol Infect Dis 38, 563–573 (2019). https://doi.org/10.1007/s10096-018-03458-y

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