Overexpression of efflux pumps is a common mechanism of multidrug resistance (MDR), and antibiotic resistance genes are found in bacteria that are generally considered benign, which poses a risk. The global spread of bacterial infections and the increase in antibiotic resistance are two major problems that medical science is currently facing. One type of efflux pump that plays an important role in bacterial MDR is the ATP-binding cassette (ABC) transporter. ABC transporters hydrolyze ATP to facilitate the removal of antibiotics from the bacterial cell. An Escherichia coli ST131 treated with ciprofloxacin was analyzed using RNA-seq to determine whether molecular/gene networks were operationalized or non-operational by each antibiotic and the antibiotic resistance caused by ABC transporters. Gene expression assessment revealed that 589 genes have differential expression (FDR p-value < 0.05). Three of these genes, lolCDE, glnHPQ, and malEFG, exhibited ABC transporters as an enrichment function. In total, 22 substantial networks were found from these genes (PPI < 0.05). MalG, lolE, and glnP are the genes that serve as the hubs of these networks. Because MalEFG possesses two distinct enhanced functions—ABC transporters and two-component systems—it is more likely to be actively involved in antibiotic resistance. The first network may be activated by ciprofloxacin, while the other two networks may be inactivated, as malEFG is upregulated and the other two networks are downregulated.
