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'An Explosion of Evidence'

In a paper published online in advance in the New England Journal of Medicine, a public-private team led by investigators at the University of Cambridge shows that whole-genome sequencing can provide clinically relevant data on bacterial transmission in real time, such that it can influence infection control and patient management. Using the Illumina MiSeq platform, the team investigated a putative methicillin-resistant Staphylococcus aureus — MRSA — outbreak in a Cambridge University Hospitals National Health Service Foundation Trust neonatal intensive care unit. They sequenced DNA from seven isolates associated with that outbreak and another seven MRSA isolates associated with carriage of the bug or bacteremia in that same hospital. First, by comparing SNPs in the core genome to a reference, EMRSA-15, the team constructed a phylogenetic tree that "revealed a distinct cluster of outbreak isolates and clear separation between these and the non-outbreak isolates," it writes. From this, the team detected a previously missed transmission event between two patients with bacteremia who were not part of the outbreak. Then the group went on to create what it calls an "artificial resistome" of antibiotic-resistance genes, and a "toxome" of toxin genes.

Overall, as team writes in NEJM, this study shows that "whole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care."

Cambridge's Sharon Peacock, lead author on the study, tells Reuters: "I think we are at the very beginning of an explosion of evidence to support the use of whole-genome sequencing in public health."

Daily Scan's sister publication GenomeWeb Daily News has more on this study.

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