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

  • Vincent C. C. Cheng
  • Shuk-Ching Wong
  • Huiluo Cao
  • Jonathan H. K. Chen
  • Simon Y. C. So
  • Sally C. Y. Wong
  • Siddharth Sridhar
  • Kwok-Yung Yuen
  • Pak-Leung HoEmail author
Original Article


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.


Whole-genome sequencing Outbreak Community-associated methicillin-resistant Staphylococcus aureus Neonatal intensive care unit 



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


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.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

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

Informed consent

No informed consent was required since this was a retrospective analysis of data.

Supplementary material

10096_2018_3458_MOESM1_ESM.docx (855 kb)
ESM 1 (DOCX 854 kb)
10096_2018_3458_MOESM2_ESM.xlsx (15 kb)
ESM 2 (XLSX 15 kb)


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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Vincent C. C. Cheng
    • 1
    • 2
  • Shuk-Ching Wong
    • 2
  • Huiluo Cao
    • 3
  • Jonathan H. K. Chen
    • 1
  • Simon Y. C. So
    • 1
  • Sally C. Y. Wong
    • 1
  • Siddharth Sridhar
    • 3
  • Kwok-Yung Yuen
    • 3
  • Pak-Leung Ho
    • 3
    Email author
  1. 1.Department of MicrobiologyQueen Mary HospitalHong KongChina
  2. 2.Infection Control Team, Queen Mary HospitalHong Kong West ClusterHong KongChina
  3. 3.Department of Microbiology and Carol Yu Centre for Infection, Queen Mary HospitalThe University of Hong KongHong KongChina

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