Genotyping and whole genome sequencing for hospital outbreak surveillance and investigation

Rosemarie Sadsad 1,2,3, Matthew O’Sullivan 1,2,3, Vitali Sintchenko 1,2,3, Gwendolyn Gilbert 1,2,3

Centre For Infectious Diseases And Microbiology – Public Health, Westmead, NSW, Australia

Sydney Medical School, University of Sydney, Sydney, NSW, Australia

Marie Bashir Institute for Infectious Diseases and Biosecurity, Sydney, NSW, Australia


Prospective surveillance for methicillin-resistant Staphylococcus aureus (MRSA) using rapid, discriminatory binary typing is routinely conducted in a Sydney tertiary public hospital. This surveillance indicated an outbreak of the MRSA sequence type (ST) 239 in three surgical wards, spanning a one-year period. We assessed the role of whole genome sequencing (WGS) as a tool that could complement binary typing in outbreak investigations.

We retrospectively performed WGS on MRSA isolated from 48 patients from the outbreak and compared them with an Australasian ST239-MRSA-III strain. We selected patients that were admitted to surgical wards during the outbreak, who were included in MRSA colonisation point prevalence surveys, who were considered to be involved in MRSA transmission based on limited epidemiological information, and who carried a prevalent ST239 binary type.

The 48 isolates were of two binary types and differed by 384 single nucleotide polymorphisms (SNPs). Four distinct clusters or groups of isolates were identified. These clusters had formed after gaining or losing an arginine catabolic mobile element, which is considered to be a determinant for virulence or colonisation. The clusters, while genetically similar, were not always linked in time or in space. One cluster involved isolates of both binary types.

While prospective binary typing is suitable for rapidly detecting suspected nosocomial outbreaks, WGS provides richer descriptions of outbreaks and clinically relevant strains. It can identify clusters occurring within an outbreak, exclude cases from outbreaks, and link cases that differ in strain subtype or that are distant in time and space.

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