Periodic Reporting for period 4 - HGTCODONUSE (The evolutionary significance of synonymous variations: Can codon usage preferences drive the propagation of antibiotic resistance?)
Berichtszeitraum: 2020-12-01 bis 2022-05-31
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 – 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 was 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.
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 – 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 was 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.
We have implemented a combination of experimental microbiology, experimental evolution, deep-sequencing based technique, comparative approaches and modelling and the main results are:
The main results of the action are:
- when antibiotic resistance genes move by horizontal transfer fom one species to another, the level of resistance they confer vary strongly. The factors determining the resistance levles are manyfold and include the carriage by mobile genetic elements, the adequation between the gene transferred and the expression machinery of the receiving genome (promoter strength, synonymous variation,...). This implies that horizontal transfer is not a mechanism providing excatly the same function to all potential receiver genomes and that the circulation of resistance genes is strongly dependent on a gene * genome * environment interaction.
- receiving one or several genes by horizontal transfer is not only providing new pieces and new function but also genertaing selection pressures which trigger genetic changes elsewhere in the genome. We have shown this at two very difference time scales by experimental evolution and by a comparative pan-genome approach.
- the propagation dynamics of hypermutators and their role in the evolution of antibiotic resistance is more complex than predicted by theoretical models and result from an interplay between the intensity of the stress generated by antibiotics, the rate of mutations producing hypermutators (with a role of transposable elements) and the clonal interference in the hypermutator fraction of the populations.
- at the european scale, dynamics of the prevalence of aminoglycoside resistance genes are explained more by international trade and migrations and by exchanges within ecosystems than by antibiotic consumption. This prompts for taking measures beyond the reduction of antibiotic consumption reduction, which is necessary but not sufficient to start finding solution to this world-wide public health problem.
- at the world-wide level, the circulation of aminoglycoside resistance genes by horizontal transfer are mainly driven by the ecological distance, the phylogenetic distance and the (dis)similarity in codon usage between donors and receivers. These traffic rules can however be strongly changed when the gene is carried by mobile genetic elements and in particular nested ones which seem to allow high distance transfers. We have also shwon on the aminoglycoside resistance model, that frequent donors of these resistance genes are soil bacteria (including aminoglycoside producers) and that pathogens are overrepresented in the frequent receivers.
These results have been presented in various conferences and workshops including the SMBE conference and the Evolutionary Medecine and Public Health conference. They have been published in five published papers and an online prepints and eight more papers are in preparation.
The main results of the action are:
- when antibiotic resistance genes move by horizontal transfer fom one species to another, the level of resistance they confer vary strongly. The factors determining the resistance levles are manyfold and include the carriage by mobile genetic elements, the adequation between the gene transferred and the expression machinery of the receiving genome (promoter strength, synonymous variation,...). This implies that horizontal transfer is not a mechanism providing excatly the same function to all potential receiver genomes and that the circulation of resistance genes is strongly dependent on a gene * genome * environment interaction.
- receiving one or several genes by horizontal transfer is not only providing new pieces and new function but also genertaing selection pressures which trigger genetic changes elsewhere in the genome. We have shown this at two very difference time scales by experimental evolution and by a comparative pan-genome approach.
- the propagation dynamics of hypermutators and their role in the evolution of antibiotic resistance is more complex than predicted by theoretical models and result from an interplay between the intensity of the stress generated by antibiotics, the rate of mutations producing hypermutators (with a role of transposable elements) and the clonal interference in the hypermutator fraction of the populations.
- at the european scale, dynamics of the prevalence of aminoglycoside resistance genes are explained more by international trade and migrations and by exchanges within ecosystems than by antibiotic consumption. This prompts for taking measures beyond the reduction of antibiotic consumption reduction, which is necessary but not sufficient to start finding solution to this world-wide public health problem.
- at the world-wide level, the circulation of aminoglycoside resistance genes by horizontal transfer are mainly driven by the ecological distance, the phylogenetic distance and the (dis)similarity in codon usage between donors and receivers. These traffic rules can however be strongly changed when the gene is carried by mobile genetic elements and in particular nested ones which seem to allow high distance transfers. We have also shwon on the aminoglycoside resistance model, that frequent donors of these resistance genes are soil bacteria (including aminoglycoside producers) and that pathogens are overrepresented in the frequent receivers.
These results have been presented in various conferences and workshops including the SMBE conference and the Evolutionary Medecine and Public Health conference. They have been published in five published papers and an online prepints and eight more papers are in preparation.
(1) The strong synonymous variant-by-species interaction in determining the level of resistance conferred is an experimental result with a strong impact at least at two different levels: (1) it is adding a strong point on the growing list of experimental results showing that synonymous variation is not neutral. Despite this accumulation of findings, synonymous differences are still considered as neutral (or silent) in many fields and still extensively used as a neutral reference in molecular evolution models, in particular in methods identifying loci under selection. The results already obtained are calling for a methodological rethinking in molecular evolution and the distribution of fitness effects we will obtain when the data of task 1.1 will be analysed will be key in this reflexion as they will provide the effect of individual synonymous and non-synonymous mutations on the same codons.
(2) The results of our integrative study on the propagation of aminoglycoside resistance genes is establishing at the world-wide scale what had been found through studies at more local scales and examples: the quantity of antibiotics used in human and veterinary medicine explains only a small part of the prevalence dynamics of these resistance genes and global trade and migration explain more. This means that the measures of antibiotic consumption reduction currently taken to limit the prevalence and propagation of antibiotic resistances cannot won’t be sufficient and that limiting the constant importation and spread through different ecosystems of resistant bacteria is also necessary.
(2) The results of our integrative study on the propagation of aminoglycoside resistance genes is establishing at the world-wide scale what had been found through studies at more local scales and examples: the quantity of antibiotics used in human and veterinary medicine explains only a small part of the prevalence dynamics of these resistance genes and global trade and migration explain more. This means that the measures of antibiotic consumption reduction currently taken to limit the prevalence and propagation of antibiotic resistances cannot won’t be sufficient and that limiting the constant importation and spread through different ecosystems of resistant bacteria is also necessary.