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SPRING 2009
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Feature: Life Sciences

CSI: Stocking Hall Detectives Identify Lurking Killers

Food scientists at Cornell use genetic fingerprinting techniques to track incidents of food poisoning to their sources.
By Roger Segelken

CSI: Stocking Hall Detectives Identify Lurking Killers

Striking first in 1988, the killer hid in a Texas meatprocessing plant. Twelve years later, the killer struck again, and four people died—of listeriosis.

The weapon in 2000 was turkey coldcuts—in 1988 it had been hotdogs—but the killer was the same: an identical strain of Listeria monocytogenes, the food-borne pathogenic bacterium that had somehow eluded clean-up efforts after the 1988 outbreak. The strain survived a number of changes, including a change of ownership at the meat-processing plant—lurking who-knows-where in a federally inspected facility—then reemerged with a vengeance.

The fact that the exact same strain of L. monocytogenes never left the building could not have been confirmed without a recently developed, innovative approach to genomic analysis—the genetic fingerprinting work of Martin Wiedmann, PhD '97 and his partners in crime detection in Stocking Hall.

"Of course it wasn't the individual bacterial organisms that survived for 12 years—more like their great-great-greatgreat- granddaughters as direct lineal descendants. But that's the beauty of comparative genomics and rapid, sophisticated, and relatively inexpensive genome-wide analysis," explains Wiedmann, an associate professor of food science. "We are learning to distinguish the subtle changes across subsequent generations, facilitated by recombination and positive selection—and how to interpret changes when the vast majority or all core genes remain the same. We can tell whether a series of bacterial samples represents continuing evolution of the same strain—or very different strains altogether."

Genomic Analysis

Indeed, the Texas meat-plant strain of L. monocytogenes had changed a bit, as Wiedmann and colleagues report in a recently published paper, "Short-term genome evolution of Listeria monocytogenes in a non-controlled environment."

But essentially it was the same bug, bad to the bone—or rather, bad to its genomic backbone.

"Our data support the hypothesis that the 2000 human listeriosis outbreak was caused by an L. monocytogenes strain that persisted in a food-processing facility over 12 years," Wiedmann and 11 collaborators report in the journal BMC Genomics, "and show that genome sequencing is a valuable and feasible tool for retrospective epidemiological analyses."

Case closed.

Months earlier, a key paper by Wiedmann and colleagues at other institutions ("Genome-wide analyses reveal lineage-specific contributions of positive selection and recombination in the evolution of Listeria monocytogenes") laid down the principles and offered hope: "The list of genes identified as being under positive selection," they said, "can be used by the scientific community to advance the discovery of genetic factors" that allow organisms to adapt to diverse environments and hosts.

It is the kind of basic, enabling science that is best done at a place like Cornell, with its multifaceted approach to genomics and life science problems.

Wiedmann directs the Laboratory for Molecular Typing and the Laboratory of Food Microbiology and Pathogenesis of Food-borne Diseases—both based in the Department of Food Science at the Ithaca campus and occupying much of Stocking Hall's fourth floor. Beyond these particular programs, there are university-wide collaborations to develop new tools to track the source of outbreaks that threaten food safety. One is the recently established Cornell Center for Comparative and Population Genomics (3CPG, for short). Faculty members of various overlapping programs depend on an array of core facilities, such as the Cornell BioResource Center in the Biotechnology Building, for specialized equipment and techniques that individual laboratories require.

"We do the basic science and, based on our findings, also try to develop new tools and find smarter ways to use existing ones," Wiedmann says..

Searching for the $10 Test

If the holy grail of human medicine is thousand-dollar full-genome sequencing—to inform individuals of their risk for inherited disease and to customize treatment if they become sick—the microbial-pathogen detectives' goal is a relative bargain.

Martin Wiedmann, associate professor of food science, hopes to develop a $10 genomic test
to investigate foodborne-illness outbreaks.
University Photography

Martin Wiedmann, associate professor of food science, hopes to develop a $10 genomic test to investigate foodborne-illness outbreaks.

"We'd like to be able to do a rapid full-genome screen on each and every microorganism of interest, to investigate outbreaks of foodborne illness, for ten dollars apiece," Wiedmann says.

He notes that the first attempts to sequence the human genome took years and cost more than a billion dollars. Now automated sequencing technologies and sophisticated methodologies are lowering the cost of genome-wide screens for individual humans. Likewise, the cost is coming down for sequencing the much smaller genomes of microbes. The tab for something like Listeria is now around $1,000. Next it will be $100 apiece, then $50, until the $10 goal is in sight, he predicts.

The quick-and-affordable aspect is critical, considering that listeriosis patients in the year 2000 turkey coldcut outbreak were scattered across 11 different states.

Various forms of Listeria are found almost everywhere (see the sidebar article, "Listeriosis and Listeria"), and some nonpathogenic species are innocuous, like the aptly named L. innocua. One Wiedmann survey of urban environments found potentially pathogenic L. monocytogenes in 2.9 to 12.6 percent of the samples taken from sidewalks, leaves, and trash cans in four different cities in New York State.

So, in the unlikely event that listeriosis were to be blamed on the hot dogs at your favorite sports venue, rapid, inexpensive, genome-wide screens could finger the bad bug's accomplice: Was it the hotdog vendor? The hotdog factory? Or even the third guy from the aisle who passed the dog to the unwitting consumer?

Being able to track food-safety outbreaks quickly can save thousands of lives—and Weidmann's team is frequently asked to help.

The Floor-Mat Problem

As to precisely where the Texas Listeria hid for 12 years, that's still something of a mystery, Wiedmann acknowledges. Food-processing plants—including the cleanest ones—are very complex places.

Andrea Moreno Switt, a post-doctoral fellow in Professor Wiedmann's laboratory, prepares
samples for subtype analysis.
 

Andrea Moreno Switt, a post-doctoral fellow in Professor Wiedmann’s laboratory, prepares samples for subtype analysis.

The best-intentioned attempts at sanitation sometimes cannot reach a Listeria hiding in a plant—Wiedmann says, explaining the "floor-mat problem."

Resilient floor mats are a workplace requirement of OSHA, the federal Occupational Safety and Health Administration, to relieve stress when workers stand on hard (but more easily cleaned) floors all day long. Chemical sanitizers can kill pathogens on the surface of the mats, which are many layers thick. But the next time a worker steps on a "clean" mat, belowsurface pathogens squish to the surface. One solution to the floor-mat problem is to substitute shoes with extra cushioning in the soles, Wiedmann adds, crossing one more hiding place off the worry list.

Careers for Food Detectives

Besides, if there were no places for pathogenic organisms to hide, there would be less work for graduates of Wiedmann's food science programs.

Cornell food science graduates who know killer bugs when they see them are much in demand at major food-processing companies (Kraft and General Mills, to name two), at federal agencies (the Centers for Disease Control and Prevention, in particular), and testing labs (such as Silliker Inc.). Alumni connections to Silliker and to Colorado State University fostered a newly developed workshop series, "Molecular Methods in Food Microbiology"—one way that Cornell's Department of Food Science reaches out to food industry professionals, scientists from government and public health laboratories, representatives from industry trade organizations, and other academic researchers. A similar workshop will be held each year in Thailand, also in cooperation with graduates of Cornell's food science program.

As a way of further ensuring the safety of the world's food supply, Cornell now also offers a dual-degree program in food science with Tamil Nadu Agricultural University in India.

"Global trends in the food industry demand that we train food scientists and food engineers transnationally and transculturally to ensure that food systems worldwide are sustainable, safe, and nutritious," says Wiedmann.

When Wiedmann's classes and workshops reconvene this year, students and food-industry insiders will hear about the Texas turkey case. And they'll be learning how to genetically "fingerprint" killers that don't have fingers—only evolving flagella—to their name.


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