Functional network analysis identifies multiple virulence and antibiotic resistance targets in Stenotrophomonas maltophilia

Protein-protein interaction network study of metallo-beta-lactamase-L1 present in Stenotrophomonas maltophilia and identification of potential drug targets

Microorganisms are evolving to withstand the effect of antimicrobial agents and thereby pose a global threat known as antimicrobial resistance. Resistance towards multiple drugs due to various intrinsic as well environmental factors leads to an even more dangerous drug resistance property known as multi-drug resistance (MDR). WHO has recognized MDR bacteria as a top global threat as they complicate the treatment and augment mortality and morbidity risks. Gram-negative bacteria produce beta-lactamase enzymes that can hydrolyze beta-lactam antibiotics, impacting drug susceptibility. Stenotrophomonas maltophilia, an opportunistic pathogen, exemplifies MDR due to the production of two types of beta-lactamases. The metallo-beta-lactamase (MBL) L1 produced by the bacteria is a class B1 zinc-dependent MBL that is broadly substrate-specific and is a challenge to the currently available treatment options. This study constructs and analyzes a protein-protein interaction network of L1 beta-lactamase to comprehend its role in the MDR property of the bacteria. The network encompasses 51 proteins including L1 MBL (Smlt2667) and 382 interactions, revealing key players in MDR and potential drug targets. The network analysis aids the discernment of antimicrobial gene impact on cellular function, informing drug discovery strategies. This research addresses the emerging challenge of antibiotic resistance and identifies pathways for therapeutic intervention.

Supplementary Information

The online version contains supplementary material available at 10.1007/s40203-024-00270-9.

Constitutive Activation of RpoH and the Addition of L-arabinose Influence Antibiotic Sensitivity of PHL628 E. coli

Antibiotics are used to combat the ever-present threat of infectious diseases, but bacteria are continually evolving an assortment of defenses that enable their survival against even the most potent treatments. While the demand for novel antibiotic agents is high, the discovery of a new agent is exceedingly rare. We chose to focus on understanding how different signal transduction pathways in the gram-negative bacterium Escherichia coli (E. coli) influence the sensitivity of the organism to antibiotics from three different classes: tetracycline, chloramphenicol, and levofloxacin. Using the PHL628 strain of E. coli, we exogenously overexpressed two transcription factors, FliA and RpoH.I54N (a constitutively active mutant), to determine their influence on the minimum inhibitory concentration (MIC) and minimum duration of killing (MDK) concentration for each of the studied antibiotics. We hypothesized that activating these pathways, which upregulate genes that respond to specific stressors, could mitigate bacterial response to antibiotic treatment. We also compared the exogenous overexpression of the constitutively active RpoH mutant to thermal heat shock that has feedback loops maintained. While FliA overexpression had no impact on MIC or antibiotic tolerance, RpoH.I54N overexpression reduced the MIC for tetracycline and chloramphenicol but had no independent impact on antibiotic tolerance. Thermal heat shock alone also did not affect MIC or antibiotic tolerance. L-arabinose, the small molecule used to induce expression in our system, unexpectedly independently increased the MICs for tetracycline (>2-fold) and levofloxacin (3-fold). Additionally, the combination of thermal heat shock and arabinose provided a synergistic, 5-fold increase in MIC for chloramphenicol. Arabinose increased the tolerance, as assessed by MDK99, for chloramphenicol (2-fold) and levofloxacin (4-fold). These experiments highlight the potential of the RpoH pathway to modulate antibiotic sensitivity and the emerging implication of arabinose in enhanced MIC and antibiotic tolerance.