Development and comparative validation of genomic-driven PCR-based assays to detect Xanthomonas citri pv. citri in citrus plants

• DOI: 10.1186/s12866-020-01972-8
• Publication Date: 2020-10-01T08:03:52Z
• Authors: Isabelle Robène; Véronique Maillot...; Aude Chabirand; Aurélie Moreau; Nathalie Becker; Amal Moumène; Adrien Rieux; Paola Campos; Lionel Gagnevin; Myriam Gaudeul; Claudia Baider; Fréderic Chiroleu; Olivier Pruvost
• Keywords: DNA, Bacterial; Citrus; Xanthomonas; Asiatic Citrus canker; diagnostic; Gene Expression; Xanthomonas campestris citri; Real-Time Polymerase Chain Reaction; Microbiology; Real-time quantitative PCR; 03 medical and health sciences; http://aims.fao.org/aos/agrovoc/c_16411; Bacterial Proteins; http://aims.fao.org/aos/agrovoc/c_36120; [SDV.BV]Life Sciences [q-bio]/Vegetal Biology; Humans; http://aims.fao.org/aos/agrovoc/c_2238; Cycle cut-off; Diagnostics; surveillance épidémiologique; H20 - Maladies des plantes; Plant Diseases; 2. Zero hunger; 0303 health sciences; Surveillance; Bacteria; Ancient DNA; Methodology Article; Membrane Proteins; Reproducibility of Results; 600; http://aims.fao.org/aos/agrovoc/c_765; QR1-502; Bacterial Typing Techniques; Benchmarking; PCR; ROC Curve; http://aims.fao.org/aos/agrovoc/c_34079; [SDE]Environmental Sciences

Abstract Background Asiatic Citrus Canker, caused by Xanthomonas citri pv. citri, severely impacts citrus production worldwide and hampers international trade. Considerable regulatory procedures have been implemented to prevent the introduction and establishment of X. citri pv. citri into areas where it is not present. The effectiveness of this surveillance largely relies on the availability of specific and sensitive detection protocols. Although several PCR- or real-time PCR-based methods are available, most of them showed analytical specificity issues. Therefore, we developed new conventional and real-time quantitative PCR assays, which target a region identified by comparative genomic analyses, and compared them to existing protocols.

Results Our assays target the X. citri pv. citri XAC1051 gene that encodes for a putative transmembrane protein. The real-time PCR assay includes an internal plant control (5.8S rDNA) for validating the assay in the absence of target amplification. A receiver-operating characteristic approach was used in order to determine a reliable cycle cut-off for providing accurate qualitative results. Repeatability, reproducibility and transferability between real-time devices were demonstrated for this duplex qPCR assay (XAC1051-2qPCR). When challenged with an extensive collection of target and non-target strains, both assays displayed a high analytical sensitivity and specificity performance: LOD95% = 754 CFU ml− 1 (15 cells per reaction), 100% inclusivity, 97.2% exclusivity for XAC1051-2qPCR; LOD95% = 5234 CFU ml− 1 (105 cells per reaction), 100% exclusivity and inclusivity for the conventional PCR. Both assays can detect the target from naturally infected citrus fruit. Interestingly, XAC1051-2qPCR detected X. citri pv. citri from herbarium citrus samples. The new PCR-based assays displayed enhanced analytical sensitivity and specificity when compared with previously published PCR and real-time qPCR assays.

Conclusions We developed new valuable detection assays useful for routine diagnostics and surveillance of X. citri pv. citri in citrus material. Their reliability was evidenced through numerous trials on a wide range of bacterial strains and plant samples. Successful detection of the pathogen was achieved from both artificially and naturally infected plants, as well as from citrus herbarium samples, suggesting that these assays will have positive impact both for future applied and academic research on this bacterium.