Unveiling the Invisible Threat: Cutting-Edge Methods for Detecting Fungus and Oomycete Plant Pathogens and Mycotoxins

Early detection of fungal and oomycete pathogens and accurate monitoring of mycotoxins are critical for ensuring food safety and sustaining agricultural productivity. This review provides a critical overview of current diagnostic tools, covering traditional morphological assessments, serological assays, and advanced molecular approaches such as PCR variants, isothermal amplification (LAMP, RPA), DNA hybridization, and next-generation sequencing. Analytical strategies for mycotoxin detection are also described, including solvent-based extraction, immunoassays, and liquid chromatography coupled with mass spectrometry, alongside emerging biosensor technologies. A distinctive contribution of this review is in the comparative assessment of these methodologies based on shared performance criteria sensitivity, specificity, turnaround time, field applicability, and cost, offering a transversal framework for method selection across phytosanitary contexts. Special attention is given to quarantine pathogens and mycotoxigenic fungi affecting the citrus supply chain, where early and accurate diagnosis is pivotal to prevent yield losses and trade restrictions. The review highlights that method selection should be guided by the specific diagnostic objective, available resources, and regulatory requirements, with integrated strategies often representing the most practical solution to ensure both food safety and phytosanitary security.