Peanut butter was in limited supply in February 2007. Grocers began pulling popular brands off their shelves after peanut butter was linked to an outbreak of Salmonella serotype Tennessee. By the end of May 2007, more than 700 people in 47 states had been sickened in what was the first U.S. foodborne outbreak associated with peanut butter.

Erik Twait (left) and fellow clinical lab analyst Gary Moet pose in the Hygienic Laboratory’s open lab. Twait and Moet represented Iowa in a study with five other public health laboratories across the country to consider how new technologies affect the recovery of bacterial isolates from clinical specimens. The study was funded by CDC and the Association of Public Health Laboratories.

The State Hygienic Laboratory was one of the first laboratories in the nation to isolate the strain of Salmonella, which led to identification of peanut butter as the source of the illness and, as a result, its temporary removal from the marketplace.

The mystery of which food sickened people in multiple states was solved by a national surveillance system in which epidemiologists link pathogens isolated from a food product to bacteria isolated from human cases based upon the DNA fingerprint of the bacteria.

Surveillance

The key to determining the DNA fingerprint of disease causing bacteria is to obtain a bacterial isolate. If a clinical laboratory isolates certain strains of bacteria that are considered of public health significance, the isolate is sent to the state public health laboratory (SPHL) for confirmatory testing.

Food that is suspected of containing a pathogen – such as Salmonella or E.coli – follows a similar culturing process, but it is performed in a public health laboratory. When the DNA of the pathogen from the food matches the DNA of the pathogen from the patient specimen, it confirms that the suspected food made the person sick.

Multiply that process by thousands for an idea of the volume of testing at the State Hygienic Laboratory and other public health laboratories during a large-scale outbreak.

The linkage extends well beyond one state.

From isolates, laboratorians extract the DNA of a pathogen for strain characterization and send that pattern information to a surveillance system known as PulseNet. Laboratorians from other states and countries compare their DNA patterns with those from other laboratories. When there is a match, epidemiologists investigate to determine if the same food has made people sick in other locations. This information is used to determine the extent of the outbreak and ultimately to remove the contaminated food from the retail market to prevent further illness.

Changes

Things have changed.

New molecular assays that detect the DNA of various pathogens directly from patient specimens have dramatically improved diagnostic testing.

These technologies, collectively known as Culture Independent Diagnostic Testing (CIDT), allow clinical laboratories – often found in physician offices or free-standing facilities – the ability to perform molecular testing on-site without the need to culture bacteria from the specimen. However, that also leads to the lack of a bacterial isolate for DNA fingerprinting.

CIDT will inform the clinical laboratory that the specimen contains a bacterium of public health significance, but they will have no bacterial isolate to send to the state public health laboratory (SPHL). It is then up to the SPHL to culture the bacterium from the specimen for confirmatory testing and to obtain an isolate for further testing.

What difference does this make? The issue is not so much who creates isolates, although the change presents workload challenges for public health laboratories. The greater concern is maintaining surveillance systems.

“CIDTs pose a risk to the loss of the isolate for PulseNet,” said Gary Moet, one of the authors of a CIDT study with fellow Hygienic Laboratory clinical lab analyst Erik Twait. “The general scope of the study is to make sure isolates are available for surveillance systems such as PulseNet.”

The CIDT study was designed and funded by the Centers for Disease Control and Prevention (CDC) and the Association of Public Health Laboratories with the goal of determining the optimal method of recovering a bacterial isolate from a clinical specimen. The study compared different bacterial culture media and transport conditions for human stool specimens.

Multiples of thousands

The Hygienic Laboratory portion of the study focused on Shiga Toxin Producing E. coli, (STEC). Moet and Twait received specimens from the CDC that were seeded with known quantities and strains of certain STECs, which were cultured on a variety of media following various storage times and conditions. Between June and October 2015, the Hygienic Lab team compiled more than 11,000 data points that were sent to CDC.

This data will be used to write algorithms for storage and preservation methods with a focus on culture preservation methods for the foodborne pathogens Salmonella and STEC. Interim guidelines were written by the CDC, which compiled data from the six-member public health laboratory team from Iowa, Colorado, Los Angeles County, Minnesota, Tennessee and CDC.

“We also utilized a new method where Gary transferred the bacterial colonies directly from the plates they were growing on into the PCR plates without having to first extract DNA,” Twait says.

“This saved us from having to do thousands of DNA extractions, which saved us a significant amount of technician time as well as money. I’m not sure exactly how many hours it saved, but it was probably at least two hours per PCR plate run which would be at least 90 hours.”

An unexpected finding by the Hygienic Laboratory team was that using the common practice of shipping specimens at or below 40 degrees Fahrenheit did not have the best recovery rate, and that ambient transportation temperatures helped maintain their viability. This could potentially save clinics considerable transportation costs when it is necessary to forward a specimen to the SPHL.

Relevance

Each year approximately one in six Americans (or about 48 million people) get sick from foodborne diseases, 128,000 are hospitalized, and 3,000 die, according to CDC. It also announced in its 2010 FoodNet report that rates of infection in the US were at least 25 percent lower for Shigella , Yersinia , STEC (Shiga toxin–producing E. coli ) O157, Campylobacter and Listeria than they were in 2000. The rate of Salmonella was 10 percent lower.

Shoppers may only become aware of foodborne outbreaks and the efforts to solve them through announcements in the press. But behind the scenes, disease detectives are at work using surveillance and studies to respond to new tests like CIDT to keep the surveillance system intact. This helps solve the mysteries of preventable foodborne illnesses and keep favorite brands of peanut butter and other products on grocery shelves.