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Reconstructing the co-evolution of genes in bacterial genomes to unravel the hidden ecology of mobile genetic elements

Thursday 7 June 2018, 1.00PM

Speaker(s): Florent Lassalle, Imperial College London, Department of Infectious Disease and Epidemiology, London, United Kingdom.

Improving our understanding of bacterial ecology is key to the adequate handling of contemporary challenges such as curbing antibiotic resistance in human pathogens or using biological agents for stimulation or protection of crops. Most organisms are best adapted to a narrow set of environmental conditions in which they compete and strive, their ecological niche. As the means of adaptation of an organism to its ecological niche are coded in its genome, the nature of this niche should therefore be attainable via the study and comparisons of genomes. In Bacteria, however, genes of adaptive value are frequently exchanged between genomes, notably through horizontal gene transfer of mobile genetic elements (MGEs), challenging the concept of bacterial taxa (and their whole genome) to be adapted to a unique, well-defined ecological niche.

I here investigate how genetic units, of sizes ranging from an operon to a species’ core genome, can be mapped to stable ecological adaptations, and how their pattern of assembly into genomes and fluid association within pangenomes, can help us understand the nature of bacterial ecology. For this, I developed an innovative phylogenetic method to study the structure of bacterial pangenomes based on patterns of long-term co-evolution between genes. This method can recognize co-selected groups of genes based on conserved associations through their complicated history of vertical and horizontal transmission.

I applied this approach to the family Enterobacteriaceae, a group of mostly commensal bacteria from which highly-virulent and multi-drug resistant opportunistic pathogens regularly emerge. Pathogenic and non-pathogenic strains alike often carry MGEs that encode multiple virulence and antimicrobial resistance (AMR) genes, causing a growing threat to public health. From a diverse collection of 880 publicly available genomes, I reconstructed the set of gene-level evolutionary events (duplication, transfer, loss) that occurred within this vast pangenome. The identification of conserved associations between backbones of MGEs and cargo accessory genes suggest cryptic co-selection mechanisms can promote the maintenance and spread of these elements out of clinical selective pressure.

Location: TBC