Novel Virulent Bacteriophages Infecting Mediterranean Isolates of the Plant Pest Xylella fastidiosa and Xanthomonas albilineans

Abstract

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.

Characterization of Stenotrophomonas maltophilia phage AXL1 as a member of the genus Pamexvirus encoding resistance to trimethoprim–sulfamethoxazole

“…5 ) with a GC content of 67.3% that is similar to the host S. maltophilia GC content. BLASTn analysis of AXL1 showed high relatedness to phages in the genus Pamexvirus , most closely aligning to Xanthomonas phage Bosa 20 with 91.01% identity over 97% of the genome. Among this genus, in order of percent identity to AXL1, are Xanthomonas phage Xp12 21 , Stenotrophomonas phage DLP4 7 , Xanthomonas phage Xoo-sp2 22 , and the Pseudomonas phages AAT-1 23 , PaMx28, and PaMx74 24 .…”

Isolation and characterization of vB_XciM_LucasX, a new jumbo phage that infects Xanthomonas citri and Xanthomonas fuscans

“…Di Lallo et al (2014) [ 42 ] isolated phage ΦPSA2, whose bacterial host is the causal agent of kiwifruit bacterial canker, from a municipal sewage sample. Clavijo-Coppens et al (2021) [ 43 ] have reported that phages able to infect the plant pathogens Xylella fastidiosa and Xanthomonas albilineans were isolated from surface and sewage waters, but not from infected plants.…”

Exploring Active Peptides with Antimicrobial Activity In Planta against Xylella fastidiosa

“…Xanthomonas albilineans ( Xa ), strain CFBP2523 (GenBank accession number, MDCB00000000), was purchased from the “French Collection of Plant-associated Bacteria” (Angers, France) and was grown on LPGA for 2 days at 28 °C [ 26 ]. Xylella fastidiosa subsp.…”

“…Due to the particular nature of Xf, and to establish an approximate starting concentration of peptides with which Xf cells could be afterward challenged, prior screening was performed using the surrogate Xa , a phylogenetically close and relatively swift-growing organism [ 26 ].…”