Using WGS, CDC Identifies Source of Outbreaks of One Persistent E. Coli Strain

romaine lettuce, whole and chopped on a plate — Credit: Karolina Grabowska via Pexels

Using whole genome sequencing (WGS), the U.S. Centers for Disease Control and Prevention (CDC) was able to link a persistent, drug-resistant strain of Escherichia coli O157:H7 to multiple sources for various foodborne illness outbreaks.

The strain—REPEXH01—is identified as “persistent” as it has previously caused various instances of foodborne illness and outbreaks in the U.S. In 2017, the first illness caused by E. coli O157:H7 REPEXH01 was reported to CDC’s PulseNet. Since then, there have been 634 reported REPEXH01 infections, and 14 foodborne illness outbreak investigations related to the strain have taken place.

Using WGS, CDC was able to identify two confirmed sources and three suspected sources of the foodborne illness outbreaks. Confirmed sources were implicated by epidemiologic and traceback or laboratory data, and include recreational water and romaine lettuce. Suspected sources were implicated by epidemiologic data only, and include ground beef in two instances and leafy greens in a third instance.

REPEXH01 is genetically diverse, as bacteria in this strain are within 21 allele differences of one another by WGS. This makes REPEXH01 more diverse than typical multistate foodborne outbreaks, where bacteria generally fall within 10 allele differences of one another.

WGS also revealed that the strain includes two major genetic subclusters, each the cause of at least two outbreaks linked to different sources and geographic regions. Possible reasons for the differences among genetic subclusters are still being investigated. More research is needed to determine if any genetic subclusters are associated with specific foods, animal populations, or geographic regions.

Finally, the National Antimicrobial Resistance Monitoring System (NARMS) surveillance system provides data on the antimicrobial resistance (AMR) of E. coli O157:H7 REPEXH01. Bacteria isolated from most samples isolated from sickened people showed resistance to the antibiotics chloramphenicol, streptomycin, sulfisoxazole, tetracycline, and trimethoprim-sulfamethoxazole.