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Demonstrates a genome-specific assay detects aggressive Pseudomonas syringae in various samples, suggesting effective monitoring methods.
Bacterial leaf spot of table beet and Swiss chard caused by Pseudomonas syringae pv. aptata is a seedborne threat lacking specific methods for detection from seed, plant, or soil samples. To address this, we developed a genotype-specific, genome-informed TaqMan™ qPCR assay targeting TIGR02646, a marker uniquely conserved in the aggressive MLST3 genotype, a highly virulent and predominant genotype, identified through a k-mer inclusion/exclusion screen of 421 P. syringae draft genomes. The assay showed 100% inclusivity for MLST3 (48/48 target isolates), including the P. syringae pv. aptata pathotype (ICMP459), and 100% exclusivity across 220 nontarget isolates under a predefined decision rule with Cq at or below 30 scored as positive. Analytical performance was consistent across relevant sample types; in pure culture, the assay was log-linear from 10 8 to 10 6 CFU/mL with 104% efficiency and a limit of detection of 10 3 CFU/reaction. In bacteria-spiked leaf extracts and seed extracts (1:10 dilution), the operational limit of detection was 10 3 and 10 4 CFU/reaction, respectively. In non-sterile soil, the limit of detection was 10 2 CFU/reaction with excellent linearity and acceptable efficiency despite typical inhibitors. Greenhouse spray-inoculation trials confirmed that the assay can track dose-responsive population dynamics and detect targets before the onset of severe symptoms. These results establish a genome-anchored, highly specific qPCR tool suitable for seed health testing, pre-plant risk assessment, and environmental surveillance of the aggressive P. syringae pv. aptata MLST3 genotype.
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Hamidizade et al. (2026) studied this question.
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