Bacterial genome detectives — next generation genome based, high-resolution tracing of pathogens


Extensive use of molecular typing of microbial pathogens over the last two decades has dramatically increased our understanding of the epidemiology of infectious diseases and bacterial population structures. More recently, next-generation sequencing (NGS) has fundamentally altered genomic research. The rapid development of this technology is intended to enhance performance and bring down DNA sequencing costs, thus widening the spectrum of possible applications. NGS has high potential for ultra-fast and accurate molecular typing and diagnostics, which will enable its use for medical diagnosis of pathogens and as a highly valuable tool for molecular epidemiology.
In this context, the EU research project Patho-NGen-Trace brings together an international consortium of leading experts in the field of clinical microbiology from academia, research institutes, and private enterprise. The project goals are to develop NGS, combined with whole genome mapping, into a highly efficient, next-generation DNA analysis technology that can be used for the typing and diagnostics of pathogens. Three pathogens will serve as models — Mycobacterium tuberculosis complex, methicillin-resistant Staphylococcus aureus, and Campylobacter species. This webinar describes the technical challenges of the project, including the use of whole genome amplification (WGA) to achieve reliable results from genomic DNA extracted from early culture or directly from clinical samples. WGA methods were assessed on 6 key parameters: DNA enrichment rate, amplification reproducibility, minimal locus bias, sequence error rate, compatibility with subsequent WGS analysis, and price per test.

Caroline Allix-Béguec, Ph.D.

Caroline Allix-Béguec Webinar image
Caroline Allix-Béguec is a Research Development and Innovation Manager at Genoscreen, France. She leads research projects, provides training, and manages services in molecular microbiology. Her experience in mycobacterial typing acquired during her Ph.D. at Brussels Pasteur Institute in Belgium led to the development and commercialization of a leading typing solution for Mycobacterium tuberculosis, used throughout the world by reference centers and hospitals. She also works on typing scheme development and validation for other pathogens and microorganisms of interest. Her research interests include moving from classical genetic typing methods toward next-generation sequencing tools for microorganism tracing and she is currently involved in a European consortium aiming to establish these methods and make them accessible to biologists.