Biology subjects

Rieux, A.

Publications and source records attributed to Rieux, A..

9 recordsLinked to original sources

bioRxiv2026

Ecology, genomics and biocontrol potential of bacteriophages infecting the bacterial wilt pathogen Ralstonia solanacearum species complex in Reunion Island

The Ralstonia solanacearum species complex (RSSC), the causal agent of bacterial wilt, is among the most destructive soil-borne plant pathogens worldwide, yet effective and sustainable control strategies remain limited. Bacteriophages represent promising biocontrol agents, but their efficacy depends on ecological compatibility with local pathogen populations. Here, we combined ecological sampling, comparative genomics, phenotypic characterization and plant assays to investigate RSSC-infecting phages in Reunion Island and evaluate their biocontrol potential. We isolated 45 phages from diverse agricultural matrices and obtained complete genome sequences for 35 novel isolates. Phylogenomic analyses revealed a locally diversified assemblage comprising multiple known taxa and several putative new genera, forming clusters largely distinct from global reference phages. Phage diversity and antibacterial activity were structured primarily by bacterial phylogeny rather than plant host or geographic origin, indicating that plants act mainly as ecological interfaces while environmental bacterial populations shape phage specialization. The community displayed two contrasting evolutionary strategies: expanding virulent lineages associated with strong antibacterial activity and persistent temperate lineages carrying integration and host-interaction functions. Host-range assays confirmed phylotype-dependent susceptibility, and strictly lytic phages showed consistently higher inhibitory activity. Guided by combined genomic and phenotypic screening, we designed a multi-family phage cocktail targeting dominant local RSSC lineages. The cocktail exhibited strong in vitro suppression of bacterial growth and significantly reduced disease severity in tomato plants. Together, our results demonstrate that effective phage biocontrol depends on evolutionary matching between phages and regional pathogen populations. Integrating ecological, genomic and functional characterization provides a robust framework for selecting locally adapted phages and developing durable phage-based strategies for managing bacterial wilt.

microbiology↗

bioRxiv2026

Distribution of antibiotic resistance genes across contrasted tropical agroecosystems in Reunion Island

This study presents the first exploratory assessment of antibiotic resistance genes (ARGs) and antibiotic residues in agricultural environments on Reunion Island, a French tropical territory in the south-western Indian Ocean. Sixteen samples from diverse matrices (manure, soil, water, and vegetables) across different agroecosystems were analyzed using high-throughput qPCR targeting 332 ARGs and chemical methods targeting 58 antibiotic compounds and trace elements. ARGs were widely detected across all matrices, with highest abundance observed in amended soils and manure. Surprisingly, ARG profiles, in terms of both abundance and average number, were comparable between unamended soils and natural soils. Antibiotic residues were found in only five manure and soil samples, with no clear correlation between the presence of these residues, trace elements and ARG abundance. Organic amendments significantly increased ARG levels in soils and non-metric multidimensional scaling revealed that ARG profiles clustered primarily by matrix type rather than by location. High-risk ARGs were widely prevalent, with 86% detected and 23% ubiquitous across all samples, and their occurrence in water and raw vegetables suggests potential human exposure through the food chain. This study highlights the influence of agricultural practices on environmental antimicrobial resistance in tropical island contexts and supports the need for expanded One Health surveillance integrating the environmental, animal and human compartments. SynopsisThis study shows that agricultural practices can shape the environmental spread of antibiotic resistance in tropical island ecosystems, highlighting potential risks for ecosystems, food safety, and human health. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/702181v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1d07b87org.highwire.dtl.DTLVardef@5e1150org.highwire.dtl.DTLVardef@1c2afe4org.highwire.dtl.DTLVardef@a9be55_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2022

Herbarium Specimen Sequencing Allows Precise Datation of Xanthomonas citri pv. citri Diversification History

Over the past decade, the field of ancient genomics has triggered considerable progress in the study of various pathogens, including those affecting crops. In this context, herbarium collections have been an important source of dated, identified and preserved DNA, whose use in comparative genomics and phylogeography may shed light into the emergence and evolutionary history of plant pathogens. In this study, we reconstructed 13 historical genomes of the bacterial crop pathogen Xanthomonas citri pv. citri (Xci) from infected citrus herbarium specimens using a shotgun-based deep sequencing strategy. Following authentication of the historical genomes based on ancient DNA damage patterns, we compared them to a large set of modern genomes to reconstruct their phylogenetic relationships, pathogeny-associated genes content and estimate several evolutionary parameters, using Bayesian tip-dating calibration and phylogeography inferences. Our results reveal that Xci originated in Southern Asia ~11,500 years ago and diversified during the beginning of the 13th century, after Citrus diversification and before spreading to the rest of the world. This updated scenario links Xci specialization to Neolithic climatic change and the development of agriculture, and its diversification to the human-driven expansion of citriculture through the early East-West trade and later colonization. The analysis of data obtained from such historical specimens is challenging and must undergo adapted treatment before being compared to modern samples. Nevertheless, we confirm here that herbarium collections are a precious tool to improve the knowledge of the evolutionary history of plant pathogens.

evolutionary biology↗

bioRxiv2022

Two bridgehead invasions of Xylella fastidiosa subsp. multiplex in France

Of American origin, a wide diversity of Xylella fastidiosa strains belonging to different subspecies have been reported in Europe since 2013 and its discovery in Italian olive groves. Strains from the subspecies multiplex (ST6 and ST7) were first identified in France in 2015 in urban and natural areas. To trace back the most probable scenario of introduction in France, the molecular evolution rate of this subspecies was estimated at 3.2165 x 10-7 substitutions per site per year, based on heterochronous genome sequences collected worldwide. This rate allowed the dating of the divergence between French and American strains in 1987 for ST6 and in 1971 for ST7. The development of a new VNTR-13 scheme allowed tracing the spread of the bacterium in France, hypothesizing an American origin. Our results suggest that both sequence types were initially introduced and spread in Provence-Alpes-Cote dAzur (PACA); then they were introduced in Corsica in two waves from the PACA bridgehead populations.

microbiology↗

bioRxiv2020

Discriminating lineages of Batrachochytrium dendrobatidis using quantitative PCR

The ability to detect and monitor infectious disease in a phylogenetically informative manner is critical for their management. Phylogenetically informative diagnostic tests enable patterns of pathogen introduction or changes in the distribution of genotypes to be measured, enabling research into the ecology of the pathogen. Batrachochytrium dendrobatidis (Bd), a causative agent of chytridiomycosis in amphibian populations, emerged worldwide in the 21st century and is composed of six lineages which are display varying levels of virulence in their hosts. Research into the distribution, ecology and pathogenicity of these lineages has been hampered by an inability to type lineage efficiently. Here, we describe a lineage-specific TaqMan qPCR assay that differentiates the two lineages of Bd most commonly associated with chytridiomycosis: BdGPL and BdCAPE. We demonstrate how this assay can be used for the surveillance of wild populations of amphibians in Southern Africa using skin swabs, tissue samples and cultured isolates.

ecology↗

bioRxiv2020

Time-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen

The reconstruction of the evolutionary histories of pathogen populations in space and time has greatly improved our understanding of their epidemiology. However, analyses are usually restricted to the non-recombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome. Yet, horizontal gene transfer is of striking importance to the evolution of bacteria as it can redistribute phenotypically important genes. For bacterial pathogens, those include resistance to antimicrobial compounds and virulence factors. Understanding the gene turnover in genomes at microevolutionary scales is key to apprehend the pace of this evolutionary process. Here we addressed this question for the epidemic lineage of a major bacterial plant pathogen, relying on a dense geographic sampling spanning 39 years of evolution. Gene turnover rate exceeded SNP mutation rates by three orders of magnitude. Accessory genes were preferentially plasmid-encoded, but we evidenced a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. We argue that turnover of accessory genes provides a potent evolutionary force in monomorphic bacteria, and exemplify this statement retracing the history of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens.

genomics↗

bioRxiv2019

Plasmodium vivax Malaria viewed through the lens of an eradicated European strain

The protozoan Plasmodium vivax is responsible for 42% of all cases of malaria outside Africa. The parasite is currently largely restricted to tropical and subtropical latitudes in Asia, Oceania and the Americas. Though, it was historically present in most of Europe before being finally eradicated during the second half of the 20th century. The lack of genomic information on the extinct European lineage has prevented a clear understanding of historical population structuring and past migrations of P. vivax. We used medical microscope slides prepared in 1944 from malaria-affected patients from the Ebro Delta in Spain, one of the last footholds of malaria in Europe, to generate a genome of a European P. vivax strain. Population genetics and phylogenetic analyses placed this strain basal to a cluster including samples from the Americas. This genome allowed us to calibrate a genomic mutation rate for P. vivax, and to estimate the mean age of the last common ancestor between European and American strains to the 15th century. This date points to an introduction of the parasite during the European colonisation of the Americas. In addition, we found that some known variants for resistance to anti-malarial drugs, including Chloroquine and Sulfadoxine, were already present in this European strain, predating their use. Our results shed light on the evolution of an important human pathogen and illustrate the value of antique medical collections as a resource for retrieving genomic information on pathogens from the past.

genetics↗

bioRxiv2017

The global distribution and spread of the mobilized colistin resistance gene mcr-1

Colistin represents one of the very few available drugs for treating infections caused by carbapenem resistant Enterobacteriaceae (CRE). As such, the recent plasmid-mediated spread of the mobilized colistin resistance gene mcr-1 poses a significant public health threat requiring global monitoring and surveillance. In this work, we characterize the global distribution of mcr-1 using a dataset of 457 mcr-1 positive sequenced isolates consisting of currently publicly available mcr-1 carrying sequences combined with an additional 110 newly sequenced mcr-1 positive isolates from China. We find mcr-1 in a diversity of plasmid backgrounds but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% higher posterior density), followed by a dramatic demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of mobile elements carrying antibiotic resistance genes across multiple levels of genomic organization.

microbiology↗

bioRxiv2017

Coexistence of multiple endemic and pandemic lineages of the rice blast pathogen

The rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is both a threat to global food security and a model for plant pathology. Molecular pathologists need an accurate understanding of the origins and line of descent of M. oryzae populations, to identify the genetic and functional bases of pathogen adaptation, and to guide the development of more effective control strategies. We used a whole-genome sequence analysis of samples from different times and places to infer details about the genetic makeup of M. oryzae from a global collection of isolates. Analyses of population structure identified six lineages within M. oryzae, including two pandemic on japonica and indica rice, respectively, and four lineages with more restricted distributions. Tip-dating calibration indicated that M. oryzae lineages separated about a millenium ago, long after the initial domestication of rice. The major lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and evidence of DNA acquisition from multiple lineages. Tests for weak natural selection revealed that the pandemic spread of clonal lineages entailed an evolutionary cost, in terms of the accumulation of deleterious mutations. Our findings reveal the coexistence of multiple endemic and pandemic lineages with contrasting population and genetic characteristics within a widely distributed pathogen.\n\nImportanceThe rice blast fungus Magnaporthe oryzae (syn. Pyricularia oryzae) is a textbook example of a rapidly adapting pathogen, and is responsible for one of the most damaging diseases of rice. Improvements in our understanding of Magnaporthe oryzae diversity and evolution are required, to guide the development of more effective control strategies. We used genome sequencing data for samples from around the world to infer the evolutionary history of M. oryzae. We found that M. oryzae diversified about a thousand years ago ago, separating into six main lineages: two pandemic on japonica and indica rice, respectively, and four with more restricted distributions. We also found that a lineage endemic to continental Southeast Asia displayed signatures of sexual recombination and the acquisition of genetic material from multiple lineages. This work provides a population-level genomic framework for defining molecular markers for the control of rice blast and investigations of the molecular basis of differences in pathogenicity between M. oryzae lineages.

evolutionary biology↗