title: A new pyrosequencing assay for rapid detection and genotyping of Shiga toxin, intimin and O157-specific rfbE genes of Escherichia coli.
abstract: Shiga toxin (stx)-producing Escherichia coli (STEC) contamination in food and water is one of the most recognized concerns and a major financial burden in human hygiene control worldwide. Rapid and highly reliable methods of detecting and identifying STEC causing gastroenteric illnesses are crucial to prevent foodborne outbreaks. A number of tests have been developed and commercialized to detect STEC using molecular microbiology techniques. Most of these are designed to identify virulence factors such as Shiga toxin and intimin as well as E. coli O and H antigen serotype specific genes. In order to screen pathogenic STEC without relying on O:H serotyping, we developed a rapid detection and genotyping assay for STEC virulence genes using a PCR-pyrosequencing application. We adapted the PyroMark Q24 Pyrosequencing platform for subtyping 4 major virulence genes, Shiga toxin 1 and 2 (stx1 and stx2), intimin (eae) and O157-antigen gene cluster target rfbE, using Single Nucleotide Polymorphism (SNP) analysis. A total of 224 E. coli strains including isolates from Canadian environment, food and clinical cases were examined. Based on the multiple alignment analysis of 30-80 base nucleotide pyrogram reads, three alleles of the Shiga toxin 1a gene (stx1a) (stx1a-I, stx1a-II, stx1a-III) were identified. Results of the stx1, stx2, eae and rfbE genotyping revealed that each group of O:H serotype shares distinctive characteristics that could be associated with the virulence of each genotype. O157:H7/NM carries stx1a-II (94%), stx2a (82%), λ/γ1-eae (100%) and rfbE type-H7/NM (100%). Whereas isolates of the "Top-6" serotypes (O26, O45, O103, O111, O121, O145) had a high incidence of stx1a-I (90%) and stx2a (100%). stx1a-III (60%) was only observed in non Top-7 (Top-6 plus O157) STEC and Shigella spp. The entire assay, from extracting DNA from colonies on a plate to the generation of sequence information, can be completed in 5h. The method of profiling these 4 STEC pathogenic genotypes as demonstrated in this paper is rapid, easily performed, informative and cost-effective, and thus has a potential to be deployed in the food industry for the routine screening of potentially pathogenic STEC isolates.
authors.affiliation: Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, P. O. Box 640, Township Road 9-1, Lethbridge, Alberta T1J 3Z4, Canada.
authors.forename: Noriko
authors.initials: N
authors.lastname: Goji
authors.affiliation: Canadian Food Inspection Agency, Greater Toronto Area Laboratory, 2301 Midland Ave., Scarborough, Ontario M1P 4R7, Canada.
authors.forename: Amit
authors.initials: A
authors.lastname: Mathews
authors.affiliation: Canadian Food Inspection Agency, Greater Toronto Area Laboratory, 2301 Midland Ave., Scarborough, Ontario M1P 4R7, Canada.
authors.forename: George
authors.initials: G
authors.lastname: Huszczynski
authors.affiliation: Public Health Agency of Canada, Lethbridge, Laboratory for Foodborne Zoonoses, P. O. Box 640, Township Road 9-1, Lethbridge, Alberta T1J 3Z4, Canada.
authors.forename: Chad R
authors.initials: CR
authors.lastname: Laing
authors.affiliation: Public Health Agency of Canada, Lethbridge, Laboratory for Foodborne Zoonoses, P. O. Box 640, Township Road 9-1, Lethbridge, Alberta T1J 3Z4, Canada.
authors.forename: Victor P J
authors.initials: VP
authors.lastname: Gannon
authors.affiliation: Public Health Agency of Canada, National Microbiology Laboratory, 1015 Arlington St., Winnipeg, Manitoba R3E 3R2, Canada.
authors.forename: Morag R
authors.initials: MR
authors.lastname: Graham
authors.affiliation: Canadian Food Inspection Agency, National Centres for Animal Disease, Lethbridge Laboratory, P. O. Box 640, Township Road 9-1, Lethbridge, Alberta T1J 3Z4, Canada. Electronic address: kingsley.amoako@inspection.gc.ca.
authors.forename: Kingsley K
authors.initials: KK
authors.lastname: Amoako
mesh_terms: D018829:Adhesins, Bacterial / Q000235:genetics*; D001431:Bacteriological Techniques / Q000379:methods*; D002170:Canada; D002238:Carbohydrate Epimerases / Q000235:genetics*; D004926:Escherichia coli / Q000145:classification* / Q000235:genetics*; D004927:Escherichia coli Infections / Q000382:microbiology / Q000517:prevention & control; D029968:Escherichia coli Proteins / Q000235:genetics*; D005516:Food Microbiology; D005517:Foodborne Diseases / Q000382:microbiology / Q000517:prevention & control; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006801:Humans; D058889:Molecular Typing / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods; D022621:Shiga Toxin / Q000235:genetics*; D013997:Time Factors; D000637:Transaminases / Q000235:genetics*
chemical_list: D018829:Adhesins, Bacterial; D029968:Escherichia coli Proteins; C073819:eaeA protein, E coli; D022621:Shiga Toxin; D000637:Transaminases; D002238:Carbohydrate Epimerases; C061272:perosamine synthetase
keywords: Genotyping; Intimin; O157:H7/NM; Pyrosequencing; SNP; STEC