Tomato bacterial wilt disease outbreaks are accompanied by an increase in soil antibiotic resistance

The presence of soil-borne diseases obstacles and antibiotic resistance genes (ARGs) presenting in soil leads to serious economic losses and health risks to humans. However, little is known about the relationships between soil-borne disease obstacles and ARGs. One area that especially needs attention is the evolution of ARGs as pathogenic soil gradually develops, which introduces uncertainty to the dynamic prediction ability for ARGs of conventional farming models. Here, we investigated variations in tomato bacterial wilt disease accompanied by the resistome by metagenomic analysis in soils over 14 seasons of monoculture. The results showed that the abundance and diversity of ARGs and mobile genetic elements (MEGs) gradually increased during the accumulation of soil-borne pathogens (R. solanacearum), exhibiting a significant and positive correlation with that of the pathogen. Furthermore, the binning approach indicated that fluoroquinolone (qepA), tetracycline (tetA), multidrug resistance genes (MDR, mdtA, acrB, mexB, mexE), and beta-lactamases (ampc, blaGOB) carried by the pathogen itself were responsible for the increase in overall soil ARGs. The observed relationships between pathogens and related ARGs that might underlie the breakdown of soil ARGs were further studied in R. solanacearum invasion pot experiments. This study revealed the dynamics of soil ARGs as soil-borne diseases developed, indicating that these ecological trends can be anticipated. Overall, this study enhances our understanding of the factors driving ARGs in disease-causing soils.