Assessing the genome level diversity of Listeria monocytogenes from contaminated ice cream and environmental samples linked to a listeriosis outbreak in the United States.
A listeriosis outbreak in the United States implicated contaminated ice cream produced by one company, which operated 3 facilities. We performed single nucleotide polymorphism (SNP)-based whole genome sequencing (WGS) analysis on Listeria monocytogenes from food, environmental and clinical sources, identifying two clusters and a single branch, belonging to PCR serogroup IIb and genetic lineage I. WGS Cluster I, representing one outbreak strain, contained 82 food and environmental isolates from Facility I and 4 clinical isolates. These isolates differed by up to 29 SNPs, exhibited 9 pulsed-field gel electrophoresis (PFGE) profiles and multilocus sequence typing (MLST) sequence type (ST) 5 of clonal complex 5 (CC5). WGS Cluster II contained 51 food and environmental isolates from Facility II, 4 food isolates from Facility I and 5 clinical isolates. Among them the isolates from Facility II and clinical isolates formed a clade and represented another outbreak strain. Isolates in this clade differed by up to 29 SNPs, exhibited 3 PFGE profiles and ST5. The only isolate collected from Facility III belonged to singleton ST489, which was in a single branch separate from Clusters I and II, and was not associated with the outbreak. WGS analyses clustered together outbreak-associated isolates exhibiting multiple PFGE profiles, while differentiating them from epidemiologically unrelated isolates that exhibited outbreak PFGE profiles. The complete genome of a Cluster I isolate allowed the identification and analyses of putative prophages, revealing that Cluster I isolates differed by the gain or loss of three putative prophages, causing the banding pattern differences among all 3 AscI-PFGE profiles observed in Cluster I isolates. WGS data suggested that certain ice cream varieties and/or production lines might have contamination sources unique to them. The SNP-based analysis was able to distinguish CC5 as a group from non-CC5 isolates and differentiate among CC5 isolates from different outbreaks/incidents.
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Yi
Y
Chen
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Yan
Y
Luo
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Phillip
P
Curry
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Ruth
R
Timme
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
David
D
Melka
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Matthew
M
Doyle
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Mickey
M
Parish
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Thomas S
TS
Hammack
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Marc W
MW
Allard
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Eric W
EW
Brown
Center for Food Safety and Applied Nutrition, Food and Drug Administration College Park, MD, United States of America.
Errol A
EA
Strain
D004196:Disease Outbreaks; D005516:Food Microbiology; D005517:Foodborne Diseases / Q000453:epidemiology / Q000382:microbiology; D014644:Genetic Variation; D016680:Genome, Bacterial; D006801:Humans; D007054:Ice Cream / Q000382:microbiology*; D008089:Listeria monocytogenes / Q000145:classification / Q000235:genetics* / Q000821:virology; D008088:Listeriosis / Q000453:epidemiology* / Q000382:microbiology* / Q000635:transmission; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D039002:Prophages / Q000235:genetics; D017422:Sequence Analysis, DNA; D012703:Serotyping; D014481:United States / Q000453:epidemiology