Characterization of the Antibiotic and Copper Resistance of Emergent Species of Onion-Pathogenic <i>Burkholderia</i> Through Genome Sequence Analysis and High-Throughput Sequencing of Differentially Enriched Random Transposon Mutants

The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of <i>Burkholderia</i>, <i>B</i>. <i>cenocepacia</i> CCRMBC56 and <i>B</i>. <i>orbicola</i> CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of <i>B</i>. <i>cenocepacia</i> CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of <i>B. cenocepacia</i> CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of <i>B. cenocepacia</i> and other copper-resistant bacterial pathogens.