Publications

4855

Abstract Since 2025, EFSA has conducted expert knowledge elicitations to estimate survey parameters for the detection of EU priority pests listed in Commission Delegated Regulation (EU) 2019/1702, in cases where pest‐specific information is lacking in the scientific literature. The design and implementation of statistically sound and risk‐based surveys require quantitative parameters such as sampling effectiveness, design prevalence and relative risk. This report presents the estimated values for Bactericera cockerelli and ‘Candidatus Liberibacter solanacearum’, together with the supporting evidence and expert rationale. These values will be integrated into the EFSA Plant Pest Survey Toolkit to guide EU Member States in designing harmonised pest surveys across the EU.

Candidatus Saccharibacteria (TM7) is an underexplored bacterial group within the human oral microbiome. These ultra-small, host-dependent organisms, despite their reduced genomes, significantly influence microbial balance and host immunity, exhibiting dual roles in oral health and disease and emerging as a key focus in microbiome research. This systematic review aimed to synthesize evidence on the prevalence, host interactions, genomic features, and ecological roles of TM7 in the oral cavity. A total of 13 peer-reviewed studies published between 2020 and 2025 were selected for detailed review based on predefined inclusion criteria, including clinical, laboratory, and metagenomic analyses focusing on TM7 detection, isolation, host specificity, and interactions with oral microbial communities. TM7 was found to be predominantly oral-adapted, exhibiting site-specific colonization with higher abundance in saliva. Coculture experiments demonstrated strict host dependence, particularly on Actinomyces, Schaalia, and Arachnia species, with strain-specific variations affecting host viability and microbial networks. TM7 genomes are highly reduced, with specialized adaptations including type IV pili and arginine deiminase pathways. Interactions with the immune system were context-dependent, with both immunomodulatory and pro-inflammatory outcomes observed. Detection methods significantly influenced TM7 prevalence and functional interpretation. Overall, TM7 represents a host-dependent, ecologically influential oral bacterium with genomic specialization, strain-level variability, and complex interactions within microbial communities. These findings highlight its potential roles in oral health and disease and emphasize the need for advanced multi-modal analytical approaches.

Lethal wilt (LW), known as “Marchitez Letal” in Colombia, is an endemic disease affecting oil palms (Elaeis guineensis Jacq.) and a leading cause of crop loss. The disease is characterized by the drying of leaflets from the tip to the base, primarily impacting the lower third of the plant and progressively moving upward. This progression leads to physiological disturbances, including necrosis at the tips of immature inflorescence bracts (spines) and the detachment of bunch fruits, ultimately causing wilting. As a phytosanitary measure, infected palms are eradicated to prevent further spread of the disease. The primary goal of this research was to identify the bacteria associated with LW and to validate a molecular detection method. A 16S amplicon-based analysis was employed to identify and compare the microbial diversity in LW-affected palm tissues with those of healthy plants. Among the 16 OTUs corresponding to different bacterial genera found in all LW samples, taxonomic classification and symptomatology suggested that the bacteria closely associated with LW belong to the genus ‘Candidatus Liberibacter’. Further phylogenetic analysis indicated that these bacteria are part of the Rhizobiaceae family, grouping closely with other species of the genus ‘Ca. Liberibacter’. The concentration of the pathogen in different oil palm tissues was determined using droplet digital PCR and quantitative PCR, expressed in copies/μl in the LW samples. This study represents the first report of ‘Ca. Liberibacter’ sp. being associated with lethal wilt in oil palms of the Arecaceae family in Colombia. The findings from this research could contribute significantly to the development of effective management strategies to prevent crop losses. [Formula: see text] Copyright © 2026 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

ABSTRACT Leptothrix mechoopdaensis BB-3 and BB-4 are metal-oxidizing, sheathed, filamentous bacteria that were isolated from a woodland iron seep near Centerville, Chico, CA, USA. Here, we report a closed circular genome sequence for each strain, assembled from reads sequenced on an Oxford Nanopore FLO-MIN114 flow cell.

Citrus greening disease, also known as huanglongbing (HLB), is caused by the gram-negative α-proteobacteria Candidatus Liberibacter species. This disease poses a significant threat to citrus production worldwide, including in Nepal. This study aimed to perform the diagnosis and phylogenetic analysis of the citrus greening pathogen in Nepal using both conventional PCR and computational methods. A total of 1,026 citrus leaf samples were collected from thirteen districts across six provinces in the country. PCR-based diagnosis was performed using the primer set Las606/LSS, which targets the 16S rRNA gene of Candidatus Liberibacter asiaticus. The reliability of the PCR was validated by including previously confirmed positive and negative controls in every run. Furthermore, each assay was performed in triplicate to ensure consistency and reproducibility of results. Additionally, 16S rRNA gene sequencing was performed using Sanger sequencing for five samples. The obtained sequences were deposited in GenBank and a phylogenetic tree was constructed based on these sequences. Among the 1,026 samples tested, 255 were positive, indicating the widespread distribution of HLB across Nepal. All consensus sequences from Nepal showed strong evolutionary relatedness within the Ca. L. asiaticus cluster, with over 99% genetic similarity to reference sequences from various parts of the world. Phylogenetic analysis revealed that the Nepalese sequences were closely related to Ca . L. asiaticus sequences from India (Punjab and Meerut) and sequences obtained from different regions of Nepal clustered closely together. The molecular findings from this study reveal a high prevalence of citrus greening disease across Nepal and underscore the urgent need for integrated management policies, including the use of certified clean planting material and vector (psyllid) control programs. The generated sequence data serves as a vital resource for developing regional diagnostic tools and guiding future surveillance strategies to mitigate HLB’s impact on the world’s citrus industry.

Sugar beet cultivation in Europe is threatened by two vector-borne diseases: syndrome “basses richesses”, caused by the phloem-limited pathogen ‘Candidatus Arsenophonus phytopathogenicus’, and phytoplasmoses associated with ‘Ca. Phytoplasma solani’ subgroup 16SrXII-A and the related subgroup 16SrXII-P. Infections lead to reduced sugar yield, biomass and growth abnormalities. In Germany, Pentastiridius leporinus represents the main vector. Despite their importance, genetic diversity remains poorly understood. During a two-year survey, barcoded amplicons were generated from infected sugar beet samples from Germany and neighbouring countries using the phytoplasma markers 16S rRNA-ITS-23S rRNA, tuf, and groEL-stamp-nadE, as well as rplO-secY-rpmJ and groEL for ‘Ca. A. phytopathogenicus’. Amplicon pools underwent single-molecule real-time sequencing and amplicon-sequence-variant inference. Additionally, planthopper samples from sugar beet in Germany were analysed and compared to sugar beet data for ‘Ca. A. phytopathogenicus’. No genetic diversity of ‘Ca. A. phytopathogenicus’ was detected, whereas 16SrXII-A and -P showed variation below the subgroup level. 16SrXII-A exhibited higher diversity than 16SrXII-P. In Germany, 16SrXII-A formed a single cluster, while 16SrXII-P comprised two clusters based on 16S rRNA-ITS-23S rRNA. In neighbouring countries, only 16SrXII-A showed diversity, resolving up to four clusters by groEL-stamp-nadE. These results provide a basis for the identification of dominant strains supporting comparative variety evaluation for tolerance.

Citrus huanglongbing (HLB) is recognized as the most destructive bacterial disease affecting citrus. Among the causal agents, Candidatus Liberibacter asiaticus (Las) is the predominant species causing HLB epidemics worldwide. Detecting this phloem limited bacterium at early or low titer stages and assessing its cellular activity remain major challenges for HLB research and management. To address these limitations, we developed a one step reverse transcription quantitative PCR (RT qPCR) assay for highly sensitive Las detection using total nucleic acids and the established Li 16S rRNA/rDNA primer–probe set. This method simultaneously amplifies both Las 16S rRNA and rDNA in a single reaction, increasing sensitivity by up to 500 fold compared with qPCR, which targets only 16S rDNA. The improved sensitivity reduced false negatives, expanded sampling capacity, and enabled detection of low titer infections previously undetectable. In addition, the higher abundance of 16S rRNA generated a consistent Ct gap between RT qPCR and qPCR, which we used to estimate relative Las cell activity in vivo in host insects and plants and to identify the most effective inoculum sources. This comparative detection strategy was further applied to evaluate inoculum potential, monitor changes in relative cell activity during in vitro cultures, and assess antimicrobial treatments targeting Las. The persistent detection of long lasting, low titer Las infections underscores the complex biology of the HLB causal agent and highlights ongoing challenges for effective disease management.

Abstract Mauritius is one of the two countries where two huanglongbing (HLB)-associated bacteria, ‘ Candidatus Liberibacter asiaticus’ (CLas) and ‘ Ca . Liberibacter africanus’ (CLaf), have coexisted since at least the 1990s, offering insights into their interactions, particularly given their divergent thermal tolerances. The objective of the study was to revisit the unique HLB epidemiological situation in Mauritius using modern diagnostic and genotyping techniques in the broader context of global warming. Using multiple-locus variable number tandem repeat analysis (MLVA), multilocus sequence analysis (MLSA), a real-time PCR assay, and a loop-mediated isothermal amplification (LAMP) assay, we detected both species. While CLas was commonly detected from sea level up to 580 m above sea level (masl), CLaf was commonly detected between 300 and 600 masl, where temperatures appear higher than in African regions where CLaf has been reported, suggesting putative adaptation to warmer temperatures of Mauritian CLaf. LAMP data also identified some limitations in inclusivity in Keremane’s system. Based on tandem-repeat (TR) data, a single population of CLas was identified whose level of diversity did not differ statistically from that of Réunion, a geographically proximate island with a similar epidemiological situation. These two populations were only weakly differentiated, consistent with the detection of very few private alleles in Mauritius. Prophage- and miniature inverted-repeat transposable element (MITE)-based genotyping confirmed the high genetic relatedness between samples from these islands. Altogether, our results suggest a putative identical source for CLas and/or epidemiological links between these islands. We discuss the implications of our results for surveillance and management of HLB.