It’s not every day that you see an outbreak of foodborne illness spanning five years. But that’s what happened with a Listeria outbreak first announced 10 days ago by the Centers for Disease Control and Prevention (CDC).
Just last month, it was whole-genome sequencing that connected together the 24 illnesses reaching back to 2010. But good old-fashioned epidemiology is what tracked down the source — soft cheeses produced by Karoun Dairies of San Fernando, CA.
Soft cheeses are not an unexpected source of Listeria infections, but some of the specific types linked to this outbreak weren’t familiar to investigators.
Eighteen victims said they ate Middle Eastern, Eastern European, Mediterranean or Mexican-style cheeses, and Ani, Bulgarian feta, Middle Eastern-style string cheese and nabulsi were some of the cheeses not specifically on the radar before.
“We saw there was a Middle East connection back then, but there was just too little information,” says medical epidemiologist Brendan Jackson. “Nothing was really standing out back then, so we stopped following that cluster at that point.”
Then, in August 2015, PulseNet — the national network of public health and food regulatory agency laboratories that tracks foodborne illnesses — flagged some Listeria cases. After consulting their database of whole-genome sequencing for the pathogen, CDC identified more historic cases. These were caused by four additional Listeria pulsed-field gel electrophoresis (PFGE) patterns, also known as DNA fingerprints, which were closely related to the first.
“Suddenly, we went from just a few cases … to upwards of 20,” Jackson says. “Once we had those numbers, it was fairly easy to see that there was a signal for soft cheese.”
Thanks to the Listeria Initiative, which began in 2004, all Listeria patients were interviewed using a standardized questionnaire that asks about the same foods.
“That way, even with patients that got sick a couple years ago, we have some information on what they ate,” Jackson says.
The questionnaire does ask about some specific cheeses, such as Mexican-style cheese (e.g., queso fresco), feta, and “other soft white cheese.”
Even though CDC couldn’t go back to the victims in the older cases for more details, at least they had some general ideas.
Fifteen patients were of Middle Eastern or Eastern European descent, or shopped at Middle Eastern-style markets. With the help of California’s health department, CDC researched those cultures so they could include a list of pertinent cheeses in their supplemental questionnaire for more recently infected patients.
So, while “Have you eaten queso fresco?,” may not have registered with the victims of this outbreak, “Have you eaten nabulsi?,” may have.
The follow-up questions also included other foods, just to be sure that cheese wasn’t appearing as a marker for something else.
“We’re planning on eventually having questions on Middle Eastern-style cheeses” in the standardized survey, Jackson says. This investigation “was really relying on very detailed interviews by state and local health departments.”
In those follow-up conversations with epidemiologists, a couple of the people sickened were able to specifically name the brand of cheese they’d eaten. Looking at the types of cheese Karoun produces, they seemed to fit with the pattern, and the company voluntarily recalled and ceased production of certain of its cheeses.
Memory is a huge limitation for foodborne illness investigations, especially for Listeria, which has an incubation period of up to 70 days. Can you remember everything you ate between two and three months ago, or between five and six months ago? It’s pretty difficult.
One thing that does help investigations is that people often have fairly regular diets and eat certain foods on an ongoing basis. But it’s still a limitation and the reason why investigators react even to small signals.
“We tried to do as many open-ended interviews as possible,” Jackson says of that outbreak. “It requires some very patient patients and their families willing to sit and answer questions for hours or more.”
It also helps to have the same person conducting multiple interviews because they can make connections between patients that other people can’t.
Caramel apples still hadn’t come up after about 20 patients had been interviewed — many of them twice.
Jackson says there was “a really astute epidemiologist in Texas” who, at the end of a long interview with a patient’s wife, thought to ask about caramel apples after it had been mentioned by a different patient.
“To us, who hadn’t heard that other interview, it didn’t really mean much, but to him, he had heard that before,” Jackson notes.
He compares tricky outbreak investigations to “a giant knot that you can’t possibly untangle.” When epidemiologists “pull the right string in the right place,” it just unravels.
There’s no doubt that the Listeria Whole Genome Sequencing Project has had an impact on illness investigations.
In the year before the project got started, PulseNet detected 14 clusters of Listeria and solved one outbreak. In the first year of whole-genome sequencing, 19 clusters were detected and four outbreaks solved. It also reduced the average cluster size.
“This year is shaping up to be better still,” Jackson says.
But don’t forget about the epidemiology. It’s still important to interpreting the sequencing results and to cracking outbreak investigations, as the soft cheese-linked outbreak shows.
When a food isolate is almost identical to a patient isolate in whole-genome sequencing, that’s a good lead that will probably pan out. But, in many cases, investigators just don’t know the food source.
“There is a perception among some people out there that whole-genome sequencing will make epidemiology obsolete,” Jackson says. “Investigation after investigation shows that’s just not the case. They have to be used together to be the most effective.”
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