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The Birth of a New Discipline?

The genomic characterization of the E. coli strain behind the outbreak in Germany led by University Münster's Helge Karch is now out in PLoS One. Karch's team used the Ion Torrent PGM platform to sequence the outbreak strain, which it then compared to historical strains. The researchers report that the outbreak strain is "unusual in several aspects" and present a model to show that two historical strains, enteroaggregative E. coli 55989 and enterohemorrhagic E. coli O104:H4, evolved from a common enterohemorrhagic E. coli O104:H4 ancestor. Then, as a result of a "stepwise gain and loss of chromosomal and plasmid-encoded virulence factors, a highly pathogenic hybrid of EAEC and EHEC emerged as the current outbreak clone," the researchers write. Study co-author Dag Harmsen tells Nature's News Blog that this work "represents the birth of a new discipline — prospective genomics epidemiology." Niyaz Ahmed, the paper's academic editor and a researcher at the University of Hyderabad in India, writes in a PLoS One blog post that the paper "has an important bearing on the new proposed field of 'epidemic forecasting.'"

However, Ahmed also notes one limitation of the study — "it is silent on the mechanistic details of 'adornment' of these bacteria with several layers of fitness," he says. "Multiple antibiotic resistance, acid tolerance, enteroaggregative capacity and shigatoxin production all bundled up in one 'naturally' chimeric strain in just 10 years is extremely dramatic! The pace of evolution of the German outbreak strains has surpassed even Helicobacter pylori."

The Scan

Gone, But Now Reconstructed SARS-CoV-2 Genomes

In a preprint, a researcher describes his recovery of viral sequences that had been removed from a common database.

Rare Heart Inflammation Warning

The Food and Drug Administration is adding a warning about links between a rare inflammatory heart condition and two SARS-CoV-2 vaccines, Reuters reports.

Sandwich Sampling

The New York Times sent tuna sandwiches for PCR analysis.

Nature Papers Describe Gut Viruses, New Format for Storing Quantitative Genomic Data, More

In Nature this week: catalog of DNA viruses of the human gut microbiome, new dense depth data dump format to store quantitative genomic data, and more.