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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

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.

Family Genetic Risk Score Linked to Diagnostic Trajectory in Psychiatric Disorders

Researchers in JAMA Psychiatry find ties between high or low family genetic risk scores and diagnostic stability or change in four major psychiatric disorders over time.

Study Questions Existence of Fetal Microbiome

A study appearing in Nature this week suggests that the reported fetal microbiome might be the result of sample contamination.

Fruit Fly Study Explores Gut Microbiome Effects on Circadian Rhythm

With gut microbiome and gene expression experiments, researchers in PNAS see signs that the microbiome contributes to circadian rhythm synchronicity and stability in fruit flies.