Xylella fastidiosa (Xf) is a plant pathogen causing significant losses in agriculture worldwide. Originating from America, this bacterium caused recent epidemics in southern Europe and is thus considered an emerging pathogen. As the European regulations do not authorize antibiotic treatment in plants, alternative treatments are urgently needed to control the spread of the pathogen and eventually to cure infected crops. One such alternative is the use of phage therapy, developed more than 100 years ago to cure human dysentery and nowadays adapted to agriculture. The first step towards phage therapy is the isolation of the appropriate bacteriophages. With this goal, we searched for phages able to infect Xf strains that are endemic in the Mediterranean area. However, as Xf is truly a fastidious organism, we chose the phylogenetically closest and relatively fast-growing organism X. albineans as a surrogate host for the isolation step. Our results showed the isolation from various sources and preliminary characterization of several phages active on different Xf strains, namely, from the fastidiosa (Xff), multiplex (Xfm), and pauca (Xfp) subspecies, as well as on X. albilineans. We sequenced their genomes, described their genomic features, and provided a phylogeny analysis that allowed us to propose new taxonomic elements. Among the 14 genomes sequenced, we could identify two new phage species, belonging to two new genera of the Caudoviricetes order, namely, Usmevirus (Podoviridae family) and Subavirus (Siphoviridae family). Interestingly, no specific phages could be isolated from infected plant samples, whereas one was isolated from vector insects captured in a contaminated area, and several from surface and sewage waters from the Marseille area.

Due to limitations in disease management strategies and the impact of climate change, phytopathogenic bacteria are threatening global crop production. Xanthomonas hortorum pv. vitians, the causal agent of bacterial leaf spot of lettuce, remains difficult to manage due to the lack of efficient treatment options. As an alternative, phage‐based biocontrol offers a promising solution, but its long‐term efficacy depends on a thorough understanding of phage–host interactions and the potential development of bacterial resistance. In this study, we isolated and characterised the lytic bacteriophage Φ Xhv ‐1, which defines a novel genus within the class Caudoviricetes . Using transposon insertion sequencing, we identified 36 bacterial genes essential for phage susceptibility, primarily involved in lipopolysaccharide biosynthesis and surface polysaccharide modifications. Targeted mutagenesis and fluorescence microscopy confirmed that Φ Xhv ‐1 adsorbs onto specific residues of the LPS O‐antigen side chains. Phage‐resistant mutants exhibited a decreased motility in vitro and a significant reduction in virulence in planta. These findings reveal a strong evolutionary trade‐off between phage resistance and bacterial fitness, suggesting that resistance emergence in the field may be naturally constrained. This study provides new insights into X. hortorum pv. vitians –phage interactions and supports the development of sustainable phage‐based biocontrol strategies against bacterial leaf spot of lettuce.

Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated “ Ca . Liberibacter” species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, using infected insect vectors, we assembled and characterized the accessory genome of the first circular de novo “ Candidatus Liberibacter asiaticus” (CLas) assembly (V1R1) from Réunion, one of the sparse areas worldwide hosting CLas and “ Ca . Liberibacter africanus” (CLaf). This 1.272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 has all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While P-V1R1-5-like prophages had been identified previously in CLaf genomes, our study demonstrates the first lysogenic conversion of these prophages in CLas, suggesting a positive selection of prophage-like sequences among HLB-associated “ Ca . Liberibacter” species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Réunion and all tested CLaf strains from Madagascar and Réunion harbored a Type 5-like prophage. The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Réunion but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria. IMPORTANCE: Huanglongbing (HLB) is the most severe citrus disease worldwide. The disease is associated with three “ Candidatus Liberibacter” species harboring prophage regions that have been described to play critical roles in their biology. In this study, using infected insect vectors, we assembled and characterized the accessory genome of the first circular de novo “ Ca . Liberibacter asiaticus” (CLas) assembly from Réunion, one of the very few areas in the world where both of CLas and “ Ca . Liberibacter africanus” (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity but also provides new insights into the role of the accessory genome in the evolution of these bacteria.

This meeting report summarizes the scientific activities of the ninth annual conference of Phages.fr, organized by the French Phages network. This year, the conference took place from 12 to 14 November 2024, in Sète, in the south of France. The conference hosted 136 participants from both the public and private sectors, representing 63 French groups and 16 international ones from Austria, Belgium, Finland, Germany, Guinea, Sweden, the UK, and the USA. The meeting brought together both young and senior scientists, offering them the opportunity to share their findings and ideas across four main topics: Ecology and Evolution, Phage-Host Interaction, Structure and Assembly, and Applications in Therapy and Biotechnology. For the first time, Phages.fr also offered a special session dedicated to the social and human sciences applied to microbiology. Over the 3 days, a total of 62 presentations were given (20 oral presentations and 42 posters), and five invited speakers delivered exceptional lectures introducing each session. The ninth annual symposium concluded with a public lecture titled “Viruses of Bacteria: New Allies in Human and Agricultural Health.” The lecture aimed to raise public awareness about the therapeutic potential of phages in combating harmful bacteria that affect human and plant health, as well as their role in food safety.

Xylella fastidiosa (Xf) est une bactérie à Gram négatif à croissance lente qui appartient à la grande famille des Xanthomonadacées. Transmise par des insectes vecteurs, Xf se développe uniquement dans les vaisseaux du xylème des plantes infectées. Touchant plus de 560 espèces de plantes Xf a été identifiée d’abord sur le continent américain. Xf a été détectée dans le bassin méditerranéen et provoque diverses maladies dont le syndrome de dépérissement rapide de l'olivier en Italie, elle est listée dans les organismes de quarantaine en Europe. En l'absence de méthodes efficaces contre Xf, nous proposons l'utilisation de bactériophages pour le biocontrôle de cette bactérie.Afin d’isoler des bactériophages spécifiques de Xf j’ai dû m’adapter à sa croissance lente en utilisant un hôte alternatif à croissance plus rapide. J’ai ainsi isolé et caractérisé différents bactériophages à partir d’insectes vecteurs et de sources plus généralistes comme des eaux usées. In vitro, l'activité lytique de deux phages (FC03 et FC12) a été confirmée sur trois souches de Xf présentes en Europe. Des plants de vigne infectés artificiellement par Xf ont été traités par FC03 et FC12. Le traitement montre un retard du développement de symptômes et une altération nette de la croissance de bactérienne au cours du temps. Finalement, le contenu en prophages de 56 génomes de Xf a été évalué afin d’anticiper la résistance liée aux prophages. Une forte variation et une divergence importante du contenu en prophages dans les génomes de Xf ont ainsi été mises en évidence.L’ensemble de ces résultats ouvre des perspectives encourageantes pour l’utilisation des phages comme agent de biocontrôle en agriculture.

Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated ‘ Ca. Liberibacter’ species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, we assembled and characterized the accessory genome of the first circular de novo ‘ Candidatus Liberibacter asiaticus’ (CLas) assembly (V1R1) from Réunion, one of the sparse areas worldwide hosting CLas and ‘ Ca. Liberibacter africanus’ (CLaf). This 1,272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 have all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While being reported for the first time in a CLas strain, P-V1R1-5-like prophages were previously identified in CLaf genomes, making it the first evidence of shared prophage-like sequence among HLB-associated ‘ Ca , Liberibacter’ species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Réunion and all tested CLaf strains from Madagascar and Réunion harbored a Type 5-like prophage. The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Réunion, but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria. IMPORTANCE: Huanglongbing (HLB) is the most severe citrus disease worldwide. The disease is associated with three ‘ Candidatus Liberibacter’ species harboring prophage regions that have been described to play critical roles in their biology. In this study, we assembled and characterized the accessory genome of the first circular de novo ‘ Ca. Liberibacter asiaticus’ (CLas) assembly from Réunion, one of the very few areas in the world where both of CLas and ‘ Ca. Liberibacter africanus’ (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity, but also provides new insights into the role of the accessory genome in the evolution of these bacteria.