To sprout shoots, seeds need a warm, moist environment.
Problem is, bacteria like E. coli and salmonella also happen to love that kind of setting.
Add to the fact that some seeds, particularly alfalfa, have lots of nooks and crannies on their surface for bacteria to hide and some chlorine baths used to disinfect seeds don't always eliminate E. coli, and you have one formidable challenge for sprout growers, according to a University of Illinois researcher.
In food-related E. coli and salmonella outbreaks in the U.S. and Europe, it's not uncommon for sprouts to be the culprit. Most recently the German government traced the strain of E. coli that caused 39 deaths and more than 3,400 illnesses in Europe to vegetable sprouts grown in Germany.
In the U.S., there have been at least 30 foodborne illness outbreaks since 1996 linked to raw or lightly cooked sprouts, according to the Centers for Disease Control and Prevention. Most of the outbreaks were related to salmonella and E. coli.
One of the most recent sprout-related outbreaks occurred between November 2010 and February 2011, when 140 people from 26 states fell ill with a particular strain of salmonella. Investigators with the Food and Drug Administration fingered the outbreak to eating alfalfa sprouts from Tiny Greens Farm of Urbana or spicy sprouts at Jimmy John's restaurants.
A sample of compost runoff from outside the Urbana farm turned up a salmonella strain "indistinguishable" from the one responsible for the outbreak, according to the FDA.
Last month, the FDA's district director sent a warning letter  to Tiny Greens outlining its findings and called on owner Bill Bagby Jr. to "investigate and determine the causes of the violations and take prompt actions to correct them to bring your products into compliance" with food safety laws.
Investigators inspected the facility seven times between Dec. 20, 2010, and Jan. 28, 2011, and "documented conditions and practices that are likely to have contaminated your product with the salmonella outbreak strain."
Among other findings, those conditions included:
— runoff water from the compost pile pooling into a drain along the walkway near the entrance to the greenhouse;
— an employee entering the compost area to dump production waste and walking through the compost pile and the pooled water, then returning to the production area wearing the same clothing and boots worn outside;
— employees pushing a cart containing trays of alfalfa sprouts from the sprouting area through the greenhouse exit, including wheeling it through the compost pile and wearing the same clothing and boots worn outside; and
— germination drum doors stored on drum frames less than 12 inches from the floor and the investigator noting water and debris from the floor splashing onto the doors.
Tiny Greens, according to the FDA letter, agreed to prohibit boots worn in the production facility to be worn outside the building. But in its May letter, the FDA asked for additional information and requests of the farm, including that the carts wheeled through the outdoor compost area be cleaned prior to entering the production area.
Last week, the FDA confirmed Tiny Greens provided a written response to the warning letter, but the agency would not imme- diately release a copy of that letter. A Freedom of Information Act request for a copy is pending.
An agency spokeswoman said the case is considered to be an open investigation and under review by the FDA, and she was unable to share further details.
Messages left for Bagby at the farm were not returned.
In many of the sprout-related foodborne outbreaks, sprout seeds have been the culprit.
And that is because "when we look at the surface under a microscope there are valleys and mountains. ... Those mountains are huge compared to the size of E. coli so they can hide," said Hao Feng, associate professor in the University of Illinois Department of Agricultural and Biological Engineering.
Another problem: Chlorine baths, which some growers use to disinfect seeds before growing them, are not always effective at eliminating dangerous bacteria. And if you make the bath stronger chemically, you risk damaging or killing the seeds, he said.
"And that is only effective for alfalfa seeds. For broccoli or radish sprouts, (a chlorine bath) is not very effective," Feng said.
Chlorine also can form harmful byproducts, he said.
In his lab, Feng and his students have been studying the effect of soaking radish seeds, pre-germination, in a chlorine solution followed by a calcinated calcium spray during sprouting.
They've also looked at different solutions, including a combination of malic acid and thiamine dodecylsulfate on alfalfa seeds.
"I think currently irradiation is the best way to do it. (Radiation) can penetrate the seeds. That's probably the more effective method, but people may not like irradiation, so consumer acceptance is an issue," Feng said.
Also, small growers probably cannot afford to have radiation machines, he added.
"People try to use a combination of sanitizer with surfactant," said Brian Gorman, president of Chicago Indoor Garden, which grows sprouts in a facility off Division Avenue. Indoor Garden supplies restaurants and grocery stores like Whole Foods.
"It's unfortunate Tiny Greens had an issue, and we don't wish that upon anyone," Gorman said.
The sprouts industry has been "on the forefront for testing within the whole food industry," he said. Growers have independent labs test water and water runoff for bacteria like E. coli and salmonella and about 98 percent of the time the results are negative.
But when results come back positive, growers put everything on hold, he said.
"If I had stuff for next-day delivery, it wouldn't go out the door," Gorman said.
The FDA has recommendations for treating seeds, but those are recommendations, Gorman said, and processes may vary by grower.
"Not everybody adheres to this type of (seed) soaking, and what they might do instead is do double or triple their testing in their own facility or send out for backup testing," he said.
At his facility, the sprouts are grown hydroponically and water samples are collected from where the seeds are growing and from the water runoff. He is planning to add an in-house lab to do additional testing, a step he said more growers have considered taking.
Some growers will use compost for growing greens, others will use only organic soil for microgreens like wheatgrass, according to Gorman.
Duane Friend, a University of Illinois Extension educator who recently organized a composting workshop, said bacteria like salmonella can be present in the raw material, such as manure, that is added to composts.
When the material in the compost heats up and if it's maintained at a temperature of 131 degrees Fahrenheit for a certain number of days (usually five to 14), the pathogens will be killed, he said.
"If you maintain those temperatures those type of bacteria are killed effectively," Friend said. Even in the winter, a compost pile can heat up to those temperatures, he said.
Still, E. coli can be found on any type of raw food product. One of the concerns with backyard composting is, it's probably not a good idea to put it around edible crops or even use compost tea off of it, he said.
Instead, use it for your flowers or work it into your soil in the fall prior to a spring planting, Friend said.