Dr. Ibrahim EI-Khali M. Adams

University of Khartoum, Sudan

Title: GelToWGS: Novel Algorithms and Proposed Initiative for Bridging the Gap Between PFGE and WGS Applications in Epidemiological Typing of Pathogenic Bacteria

Schedule

Abstract:

For monitoring population dynamics of pathogenic bacteria around the world, several DNA-based methods were developed during the last three decades. Pulsed-Field Gel Electrophoresis(PFGE) was the gold-standard since 1996. An international laboratory consortium (PulseNet International (PNI) have been growing ever since. PNI adopted and standardized PFGE protocols for several pathogenic bacteria. Currently 83 countries in all continents already joined PNI.

PFGE is a form of Restriction Fragment Length Polymorphism(RFLP) in which, the entire bacterial chromosome is digested using a restriction enzyme that has a rare recognition sequence across the chromosome of interest. Number and distribution of the recognition sequence of the restriction enzyme used determine the final profile. Patterns of PFGE profiles are being compared based on relative positioning of bands across Agarose gels within a range of tolerance.

But due to sophistication and cost-effective developments in DNA sequencing technology, some member states (PulseNet North America and Europe) are shifting to WGS. Whole chromosome sequences are being compared using several DNA sequence alignment methods. Although whole chromosome sequences of WGS can be digested in-silico, PFGE and WGS data are still being compared separately.

Here, the author presents three mathematical methods and their applications in bridging this gap. The first is a PFGE image analysis algorithm that is 35% more accurate than currently adopted one. The second is a bioinformatics database comparison method that allow comparing PFGE analysis results of the first algorithm to in-silico digested WGS data. The third is a simulation model that evaluates results of both; image analysis and database comparison algorithms.

Since above mentioned methods need standardization, wet-lab evaluation and implementation plan, the author will also presents a road map for achieving these goals.

Implementation of suggested bioinformatics tools is promising not only in bridging the technical gap in sharing these critical data across PNI participants, but also hundreds of thousands of PFGE data accumulated during the last 25 years will be taken into account while approaching WGS era.

Biography:

Mr. Adam was graduated from University of Khartoum, Faculty of Science in 2009. His B.Sc.(hon.) is in the subject of advanced molecular biology. He started his career as a part-time teaching assistant at the same university. Shortly after, he joined a research team who was addressing the prevalence of Rift-Valley Fever Virus(RVFV) in vector mosquito in Sudan. He focused on molecular characterization of snake venom enzymes during 2010-2016 in another project. Later, he initiated GelToWGS project based on his interest in mathematical and computational modelling of biological data. He qualified for the patency of GelToWGS in 2017.

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