Canadian Food Inspection Agency Canada
Title: Strategy for developing a molecular sub typing tool for a food borne bacterial pathogen using a whole genome analysis approach: the case of Salmonella Enteritidis
Dele Ogunremi is a research scientist at the Canadian Food Inspection Agency, Ottawa Laboratory Fallow field, and is a trained veterinarian with doctoral and postdoctoral training in Molecular Biology and Immunology. He graduated with DVM (1984) and MVSc (1986) from the University of Ibadan, Nigeria and PhD from the University of Saskatchewan, Canada (1993), where he also completed a postdoctoral training (1996). His research interests include the application of genomics sequencing technology to detect, identify and characterize food borne microbial pathogens. He has generated, assembled and characterize Salmonella and Listeria genomes. Recently he completed the development of genomics based single nucleotide polymorphism genotyping test for Salmonella Enteritidis. He played a lead role in the establishment of the Pulse Field Gel Electrophoresis at the Canadian Food Inspection Agency. His research work has been protected by patents granted in Canada, United States and New Zealand.
Differentiating between outbreaks of food borne infections and sporadic occurrences requires a highly discriminatory laboratory tool for pathogen subtyping which has remained a difficult goal for a highly clonal organism such as Salmonella Enteritidis (SE). Because of the high degree of similarities among isolates of SE, developing a reliable and informative sub typing tool requires the availability of comprehensive information on the organism such as that provided only by whole genome analysis. By examining core and accessory genome compartments of SE for genetic diversities, markers and traits that distinguish related strains from unrelated strains can be defined. The proportion of SE genome constituting the core compartment is large, i.e., >95% of the entire chromosome, and diversity among isolates are limited to an average of 600 single nucleotide polymorphisms (SNPs) between two apparently, unrelated strains. The accessory genome include mobile genetic elements especially prophages, which are made of remnants or full sequences of infecting bacteriophages that have since integrated into the SE genome. It was found six prophages to be present consistently and showing little or negligible diversity among 12 SE genomes including the reference Salmonella Enteritidis P125109 phage type. The presence and composition of another eight prophages or remnants provided considerable diversity for delineating isolates into groups of SE subtypes. The use of SNPs in SE genomes assembled with the aid of the reference P125109 genome and the composition of prophages could provide a complementary and synergistic framework for differentiating SE subtypes for the purpose of regulatory intervention during food borne outbreaks.
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