A neonatal MRSA outbreak investigation using rapid whole genome sequencing

Background: Isolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable using current typing techniques. Whole genome sequencing (WGS) may provide improved resolution to define transmission pathways and characterize outbreaks. Methods: We investigated a putative MRSA outbreak on a neonatal intensive care unit. Using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from 7 isolates associated with the outbreak, and another 7 MRSA isolates associated with carriage or bacteremia in the same hospital. Results: A phylogenetic tree was constructed by comparing single nucleotide polymorphisms in the core genome to a reference genome (EMRSA-15, sequence type 22). This demonstrated a distinct clustering of the outbreak isolates, and clear separation between these and the non-outbreak isolates. A previously missed transmission event was detected between two patients with bacteremia that were not part of the outbreak. We created an artificial ‘resistome’ of antibiotic resistance genes and demonstrated concordance between this and phenotypic susceptibility testing, as well as a ‘toxome’ consisting of toxin genes. One outbreak isolate was a hypermutator with a comparatively higher number of SNPs, highlighting the difficulty in imposing a simple cut-off of SNPs between isolates to decide whether they are part of a recent transmission chain. Conclusions: WGS can provide clinically relevant data within a timescale that can influence patient management. Automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation.