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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.

The Scan

Tens of Millions Saved

The Associated Press writes that vaccines against COVID-19 saved an estimated 20 million lives in their first year.

Supersized Bacterium

NPR reports that researchers have found and characterized a bacterium that is visible to the naked eye.

Also Subvariants

Moderna says its bivalent SARS-CoV-2 vaccine leads to a strong immune response against Omicron subvariants, the Wall Street Journal reports.

Science Papers Present Gene-Edited Mouse Models of Liver Cancer, Hürthle Cell Carcinoma Analysis

In Science this week: a collection of mouse models of primary liver cancer, and more.