E. coli

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Mixup of drinking and irrigation water sparks dangerous outbreak in children

CDC, children, E. coli, hemolytic uremic syndrome, irrigation water, outbreak, Science, Shiga toxin–producing Escherichia coli (STEC) O157:H7, Utah / /

fearsome faucets —

Of 13 children sickened, 7 hospitalized and 2 had life-threatening complications.

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A child cools off under a water sprinkler.

Enlarge / A child cools off under a water sprinkler.

In 1989, a city in Utah upgraded its drinking water system, putting in a whole new system and repurposing the old one to supply cheap untreated water for irrigating lawns and putting out fires. That meant that the treated water suitable for drinking flowed from new spigots, while untreated water gushed from the old ones. Decades went by with no apparent confusion; residents seemed clear on the two different water sources. But, according to an investigation report published recently by state and county health officials, that local knowledge got diluted as new residents moved into the area. And last summer, the confusion over the conduits led to an outbreak of life-threatening illnesses among children.

In July and August of 2023, state and local health officials identified 13 children infected with Shiga toxin-producing Escherichia coli (STEC) O157:H7. The children ranged in age from 1 to 15, with a median age of 4. Children are generally at high risk of severe infections with this pathogen, along with older people and those with compromised immune systems. Of the 13 infected children, seven were hospitalized and two developed hemolytic uremic syndrome, a life-threatening complication that can lead to kidney failure.

Preliminary genetic analyses of STEC O157:H7 from two of the children suggested that the children’s infections were linked to a common source. So, health officials quickly developed a questionnaire to narrow down the potential source. It soon became clear that the irrigation water—aka untreated, pressurized, municipal irrigation water (UPMIW)—was a commonality among the children. Twelve of 13 infected children reported exposure to it in some form: Two said they drank it; five played with UPMIW hoses; three used the water for inflatable water toys; two used it for a water table; and one ran through sprinklers. None reported eating fruits or vegetables from home (noncommercial) gardens irrigated with the UPMIW.

The report on the investigation, published in the Centers for Disease Control and Prevention’s Morbidity and Mortality Weekly Report, did not name the city in Utah. But press releases from a county health department identified the affected city as Lehi, about 30 minutes south of Salt Lake City.

Further genetic testing of STEC O157:H7 isolates linked all of the children’s infections together, as well as to water from five of nine UPMIW exposure sites and samples from the reservoir where the irrigation water is sourced. Microbial source tracking indicated that the contamination could have come from the feces of birds or ruminants.

The county health department and the city put out press releases and informational mailers. They warned residents about the risks of UPMIW, telling them not to drink it or let children play in it. “Do not use irrigation water for bounce houses, pools, slip-n-slides, or any other recreational activities. It is common for children to swallow or get water in their mouths while playing.”

The notices also said that the CDC recommended against watering lawns with the water, though the county advised residents to merely “use caution” when allowing children to play on grass irrigated with UPMIW. “Keep an eye on them,” the advisers warned, and try to prevent them from putting their hands or anything from the lawn in their mouths. “E. coli is hardy and can stick.”

This is not the first time that irrigation water has been linked to outbreaks. In 2010 and 2015, two other Utah cities reported campylobacteriosis outbreaks linked to cross-connections between UPMIW and drinking water lines.

The researchers say such outbreaks can be avoided by efforts to prevent contamination in irrigation water, such as treating water, cleaning reservoirs, and covering them. And, of course, clearly labeling irrigation water and keeping residents informed about its dangers are key to preventing infections.

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New E. coli strain will accelerate evolution of the genes of your choice

biochemistry, Biology, E. coli, evolution, mutation rate, mutations, Science / /

Making mutants —

Strain eliminates the trade-offs of a high mutation rate.

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Woman holding a plate of bacteria with clusters of bacteria on it.

Genetic mutations are essential for innovation and evolution, yet too many—or the wrong ones—can be fatal. So researchers at Cambridge established a synthetic “orthogonal” DNA replication system in E. coli that they can use as a risk-free way to generate and study such mutations. It is orthogonal because it is completely separate from the system that E. coli uses to copy its actual genome, which contains the genes E. coli needs to survive.

The genes in the orthogonal system are copied with an extraordinarily error-prone DNA replication enzyme, which spurs rapid evolution by generating many random mutations. This goes on while E. coli’s genes are replicated by its normal high-fidelity DNA copying enzyme. The two enzymes work alongside each other, each doing their own thing but not interfering with the other’s genes.

Engineering rapid mutation

Such a cool idea, right? The scientists stole it from nature. Yeast already has a system like this, with a set of genes copied by a dedicated enzyme that doesn’t replicate the rest of the genome. But E. coli is much easier to work with than yeast, and its population can double in 20 minutes, so you can get a lot of rounds of replication and evolution done fast.

The researchers generated the system by pillaging a phage—a virus that infects E. coli. They took out all of the phage genes that allow the phage to grow uncontrollably until it bursts the E. coli cell it infected open. The engineering left only a cassette containing the genes responsible for copying the phage genome. Once this cassette was inserted into the E. coli genome, it could simultaneously replicate at least three different strings of genes placed next to it in the DNA, maintaining them for over a hundred generations—all while leaving the rest of the E. coli genome to be copied by other enzymes.

The scientists then tweaked the mutation rate of the orthogonal DNA-replicating enzyme, eventually enhancing it 1,000-fold. To test if the system could be used to evolve new functions, they inserted a gene for resistance to one antibiotic and saw how long it took for that gene to mutate into one conferring resistance to a different antibiotic. Within twelve days, they got 150 times more resistance to the new antibiotic. They also inserted the gene encoding green fluorescent protein and increased its fluorescence over 1,000-fold in five days.

Evolving detoxification

Not 20 pages later, in the same issue of Science, Frances Arnold’s lab has a paper that provides evidence of how powerful this approach could be. This team directed the evolution of an enzyme the old-fashioned way: through sequential rounds of random mutagenesis and selection for the desired trait. Arnold won The Nobel Prize in Chemistry 2018 for the directed evolution of enzymes, so she knows what she’s about. In this recent work, her lab generated an enzyme that can biodegrade volatile methyl siloxanes. We make megatons of these compounds every year to stick in cleaning products, shampoos and lotions, and industrial products, but they linger in the environment. They contain carbon-silicon bonds, which were never a thing until humans made them about 80 years ago; since nature never made these bonds, there is no natural way to break them, either.

“Directed evolution with siloxane was particularly challenging,” the authors note in their introduction, for various technical reasons. “We started from an enzyme we had previously engineered for other chemistry on siloxanes—that enzyme, unlike the natural enzyme, showed a tiny bit of activity for siloxane Si-C bond cleavage. The overall project, however, from initial discovery to figuring out how to measure what we wanted, took several years,” Arnold said. And it is only the first step in possibly rendering siloxanes biodegradable. The accelerated continuous evolution that the new orthologous system allows will hopefully greatly facilitate the development of enzymes and other proteins like this that will have applications in research, medicine, and industry.

We do not (yet) have machines that can efficiently assemble long stretches of DNA or make proteins. But cells do these things extremely efficiently, and E. coli cells have long been the ones used in the lab as little factories, churning out whatever genes or proteins researchers program into them. Now E. coli can be used for one more molecular task—they can be little hotbeds of evolution.

Science, 2024.  DOI: 10.1126/science.adi5554, 10.1126/science.adk1281

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