Biomaterial Database

Whole Genome Sequencing Characterization of Shiga Toxin-Producing Escherichia coli Isolated from Flour from Swiss Retail Markets. 2019

Renate Boss, and Joerg Hummerjohann

1 Federal Food Safety and Veterinary Office, Schwarzenburgstrasse 155, 3003 Berne, Switzerland.

Shiga toxin-producing Escherichia coli (STEC) strains are often found in food and cause human infections. Although STEC O157:H7 is most often responsible for human disease, various non-O157 subtypes have caused individual human infections or outbreaks. The importance of STEC serogroup typing is decreasing while detection of virulence gene patterns has become more relevant. Whole genome sequencing (WGS) reveals the entire spectrum of pathogen information, such as toxin variant, serotype, sequence type, and virulence factors. Flour has not been considered as a vector for STEC; however, this product has been associated with several STEC outbreaks in the last decade. Flour is a natural product, and milling does not include a germ-reducing step. Flour is rarely eaten raw, but the risks associated with the consumption of unbaked dough are probably underestimated. The aim of this study was to determine the prevalence of STEC in flour samples (n = 93) collected from Swiss markets and to fully characterize the isolates by PCR assay and WGS. The prevalence of STEC in these flour samples was 10.8% as indicated by PCR, and a total of 10 STEC strains were isolated (two flour samples were positive for two STEC subtypes). We found one stx2-positve STEC isolate belonging to the classic serogroups frequently associated with outbreaks that could potentially cause severe disease. However, we also found several other common or less common STEC subtypes with diverse virulence patterns. Our results reveal the benefits of WGS as a characterization tool and that flour is a potentially and probably underestimated source for STEC infections in humans.

UI	MeSH Term	Description	Entries
D005433	Flour	A powdery meal obtained from ground up starchy foodstuff, such as seeds of WHEAT; RICE and other EDIBLE GRAIN; LEGUMES; and NUTS; or ground up PLANT TUBERS.	Almond Flour,Almond Meal,Corn Flour,Corn Meal,Grain Flour,Grain Meal,Nut Flour,Potato Flour,Rice Flour,Rice Meal,Soybean Flour,Soybean Meal,Wheat Flour,Wheat Meal,Semolina Flour,Almond Flours,Almond Meals,Corn Flours,Corn Meals,Flour, Almond,Flour, Corn,Flour, Grain,Flour, Nut,Flour, Potato,Flour, Rice,Flour, Semolina,Flour, Soybean,Flour, Wheat,Flours,Flours, Almond,Flours, Corn,Flours, Grain,Flours, Nut,Flours, Potato,Flours, Rice,Flours, Semolina,Flours, Soybean,Flours, Wheat,Grain Flours,Grain Meals,Meal, Almond,Meal, Corn,Meal, Grain,Meal, Rice,Meal, Soybean,Meal, Wheat,Meals, Almond,Meals, Corn,Meals, Grain,Meals, Rice,Meals, Soybean,Meals, Wheat,Nut Flours,Potato Flours,Rice Flours,Rice Meals,Semolina Flours,Soybean Flours,Soybean Meals,Wheat Flours,Wheat Meals
D000073336	Whole Genome Sequencing	Techniques to determine the entire sequence of the GENOME of an organism or individual.	Complete Genome Sequencing,Genome Sequencing, Complete,Genome Sequencing, Whole,Sequencing, Complete Genome,Sequencing, Whole Genome
D013557	Switzerland	A country in Europe. It is bordered by Austria, France, Italy, Liechtenstein, and Germany. The capital is Bern.
D016133	Polymerase Chain Reaction	In vitro method for producing large amounts of specific DNA or RNA fragments of defined length and sequence from small amounts of short oligonucleotide flanking sequences (primers). The essential steps include thermal denaturation of the double-stranded target molecules, annealing of the primers to their complementary sequences, and extension of the annealed primers by enzymatic synthesis with DNA polymerase. The reaction is efficient, specific, and extremely sensitive. Uses for the reaction include disease diagnosis, detection of difficult-to-isolate pathogens, mutation analysis, genetic testing, DNA sequencing, and analyzing evolutionary relationships.	Anchored PCR,Inverse PCR,Nested PCR,PCR,Anchored Polymerase Chain Reaction,Inverse Polymerase Chain Reaction,Nested Polymerase Chain Reaction,PCR, Anchored,PCR, Inverse,PCR, Nested,Polymerase Chain Reactions,Reaction, Polymerase Chain,Reactions, Polymerase Chain
D016680	Genome, Bacterial	The genetic complement of a BACTERIA as represented in its DNA.	Bacterial Genome,Bacterial Genomes,Genomes, Bacterial
D054323	Shiga-Toxigenic Escherichia coli	Strains of ESCHERICHIA COLI with the ability to produce at least one or more of at least two antigenically distinct, usually bacteriophage-mediated cytotoxins: SHIGA TOXIN 1 and SHIGA TOXIN 2. These bacteria can cause severe disease in humans including bloody DIARRHEA and HEMOLYTIC UREMIC SYNDROME.	E coli, Verotoxigenic,Escherichia coli, Verotoxigenic,STEC,Verotoxigenic Escherichia coli,Shiga Toxigenic E. coli,Shiga Toxigenic Escherichia coli,Shiga Toxin-Producing Escherichia coli,VTEC,Vero Cytotoxin-Producing Escherichia coli,Verotoxigenic E. coli,Verotoxin-Producing Escherichia coli
D029968	Escherichia coli Proteins	Proteins obtained from ESCHERICHIA COLI.	E coli Proteins