#	Pagina
attuale pagina	/open-h2020/projects/202610/results.html

Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - HGTCODONUSE (The evolutionary significance of synonymous variations: Can codon usage preferences drive the propagation of antibiotic resistance?)

Teaser

Summary

Antibiotics have initially been seen as a remedy having the power to eradicate bacterial infectious diseases. But their intense use in human and veterinary medicine has led to the emergence and spread of numerous antibiotic resistances, which represent nowadays a real threat for our ability to cure infectious diseases. The public health problem posed by the spread of antibiotic resistances has been listed among the most worrying ones by international organisations as WHO.
Horizontal gene transfer (HGT), the capacity of bacteria cells to exchange DNA between strains or species is the main mechanism for the spread of enzymatic antibiotic resistances. Although this mechanism is extremely successful in evolutionary terms, resistance genes â€“ bacteria species associations do not seem to form randomly, meaning that antibiotic resistances do not freely diffuse among bacteria species.
The overall objective of this project is to identify factors or mechanisms that shape the routes of spread by HGT of antibiotic resistance. One particular mechanism will be studied in deep details: the mismatch in codon usage between the donor and the recipient bacteria of a horizontally transferred gene. Codon usage describes the specific way in which each bacteria species deals with the redundancy of the genetic code. The differences in codon usage lead to differences in the speed and fidelity of protein translation and can affect the functionality of the gene transferred. For this reason, (dis)similarity in codon usage might be one of the factors shaping the routes of spread of antibiotic resistance genes.

Work performed

We have undertaken experimental and comparative approaches to reach the objective of the project.
The first experimental approach is designed to get a fine scale measurement of the effect of the differences in codon usage bias and to compare them to other effects, namely differences in the amino-acid sequence of protein and in the gene regulation. This approach requires to set-up synthetic biology and deep-sequencing quantification of mutants. We are about to solve all the technical problems and to start the actual experiment.
The second experimental approach is to mimic the horizontal transfer of an antibiotic resistance gene from a high diversity of donor genomes in four different bacteria species. We have set-up the biological system that allows to mimic this transfer, both via plasmid and via chromosome integration and have designed artificial genes mimicking the codon usage of various donor species. We have also tested the experimental evolution protocol and generated knowledge on parallel evolution drivers and the role of plasmid carriage in antibiotic resistance gene evolution.
The first comparative approach is analysing the gene composition of a hundred of genomes of the pathogen Pseudomonas aeruginosa, reconstructing the phylogeny between the strains and the history of gene loss and gene acquisition by horizontal gene transfer. This will then allow us to infer evolutionary events taking place at long time scale after HGT, as for example evolution of the coding and regulatory sequences of the acquired genes or changes in the composition of the tRNA gene pool.
The second comparative approach has generated a map of presence/absence of different gentamycin resistance genes across all bacteria species, showing a diversity of situations both from the species and genes point of view. We are now testing the role of different factors in explaining the patterns described. The factors tested are for example: the carriage of the gene, the resistance spectrum of the gene, the date of first identification of the resistance or the pathogenicity of the bacteria.

Final results

We expect to generate results on the effect of differences in codon usage on the functionality of genes, to document experimentally the consequences of these differences for post-HGT evolution and to uncover the signature of this evolutionary events on the long-term. Ultimately, we hope to generate a broad picture of the current antibiotic resistance genes repartition and access the factors that shaped these patterns. Some of these factors could be targets for the design of public health policies implemented to slow down the spread of antibiotic resistance.