It can also identify outbreak-associated cases originally believed to be sporadic ones, said the researchers.
The Rhode Island Department of Health (RIDOH) investigated a cluster of three listeriosis cases in November 2014.
Listeriosis has a long incubation period (3–70 days), making exposure recall difficult but it has a small genome that is relatively easy to analyze.
WGS to support investigation
Using WGS to support epidemiologic, laboratory and environmental investigations, the department identified one restaurant as the likely source and also linked it to a listeriosis case in 2013.
Interviews by the Center for Acute Infectious Disease Epidemiology identified a single common restaurant visited by the three patients.
RIDOH’s Center for Food Protection inspected and collected food and environmental samples at the establishment.
Pulsed field gel electrophoresis (PFGE) analysis showed that clinical L. monocytogenes isolates from the case-patients shared an identical, common pattern.
Results of whole genome multilocus sequence typing (wgMLST) showed the isolates were closely related (0–5 allelic differences) and a close genetic match to a clinical isolate from a 2013 patient, who was re-interviewed and reported eating at the same restaurant.
The allelic differences are consistent with slow, spontaneous mutation occurring over a long period due to persistent contamination, said the researchers.
“There is no set number of allelic differences used to determine whether clusters of cases are part of actual outbreaks. Thus, WGS is not sufficient by itself to identify outbreaks and must be performed in conjunction with epidemiologic, laboratory, and environmental investigations. In the investigation we describe, WGS was used in this supporting role.”
Collected samples
To start 10 food and environmental food samples were collected from the restaurant. Swab samples were from the food slicer, preparation tables, and walk-in cooler.
Environmental investigation of the restaurant identified issues related to control of L. monocytogenes: the temperature of the refrigerated unit that held sliced meat and other food items was elevated (52°F [11°C]), and cleanliness issues with the preparation tables and slicer.
An additional 19 environmental samples were later collected; however, the refrigerated unit and preparation tables had been replaced, so additional swabs could not be collected from those surfaces.
The sample of sliced prosciutto was the only L. monocytogenes–positive sample; however, just one of the 2014 case-patients reported eating prosciutto (in an antipasto salad) at the restaurant. Other foods reported included green salad and coleslaw.
RIDOH tested a sample of prosciutto from an unopened package from the establishment but the sample tested negative and no positive tests had been reported at the plant in at least one year.
Since September 2013, WGS has been performed on all clinical L. monocytogenes isolates identified in the US by the Centers for Disease Control and Prevention and several state public health laboratories.
Researchers said investigation results implicated a restaurant with sanitation issues and improper sliced meat storage as the likely source of the multiyear listeriosis outbreak.
“Our findings support the need to control L. monocytogenes at retail food establishments. Storing meat at <41°F (5°C) can prevent ≈9% of listeriosis cases.
“In addition, retail delicatessens and food establishments can prevent L. monocytogenes–associated illnesses among customers by controlling cross-contamination, cleaning and sanitizing food contact surfaces, and eliminating environmental niches.”
Source: Emerg Infect Dis. 2016 Aug
“Whole genome sequencing detection of ongoing Listeria contamination at a restaurant, Rhode Island, USA, 2014”
Authors: Barkley JS, Gosciminski M, Miller A.