Prevalence and genetic diversity of Salmonella in Iranian pistachio production during long-term storage: a metagenomic analysis

Salmonella enterica contamination remains a significant food safety concern for Iranian pistachios, a major export commodity, particularly due to its persistence in low-water-activity environments. This was highlighted by the 2025 Canadian outbreak linked to Iranian pistachio imports, which resulted in over 155 confirmed cases and prompted a temporary import ban. This study examines the prevalence and genetic diversity of Salmonella in Iranian pistachio production during extended storage to address region-specific knowledge gaps and inform supply chain improvements. An observational survey analysed 500 pistachio samples (100 g each) from five facilities in Kerman, Semnan, and Khorasan Razavi provinces, collected at pre-harvest, post-harvest, and 12-month storage stages under simulated commercial conditions (20–30°C, 40–60% RH). Methods included ISO 6579 enrichment, invA-targeted qPCR, Illumina MiSeq metagenomics, and whole-genome sequencing, with analysis via QIIME2, Snippy, and R-based statistical models. Salmonella was detected in 2.4% of samples (n=12), with stable relative abundance (0.15%; OR=1.04, p=0.192). Hull damage increased contamination risk 3.2-fold (p=0.004). Sequencing of 28 isolates identified 15 multilocus sequence types across eight serovars, dominated by desiccation-tolerant Senftenberg (36%) and Montevideo (26%), with moderate SNP variation (mean 1,245 SNPs) and upregulated csgD and rpoS genes, suggesting an 18.2-month half-life. Resident clades exhibited higher virulence (p=0.002) and were associated with specific facilities. These results underscore Salmonella persistence in low-water-activity foods, emphasising post-harvest vulnerabilities. Recommendations include enhanced hull inspections and humidity-controlled storage to reduce export risks. Metagenomic integration into routine monitoring could strengthen global food safety in arid agricultural systems.