Emergence of eravacycline heteroresistance in carbapenem-resistant Acinetobacter baumannii isolates in China

Carbapenem-resistant Acinetobacter baumannii (CRAB) is resistant to almost all antibiotics. Eravacycline, a newer treatment option, has the potential to treat CRAB infections, however, the mechanism by which CRAB isolates develop resistance to eravacycline has yet to be clarified. This study sought to investigate the features and mechanisms of eravacycline heteroresistance among CRAB clinical isolates. A total of 287 isolates were collected in China from 2020 to 2022. The minimum inhibitory concentration (MIC) of eravacycline and other clinically available agents against A. baumannii were determined using broth microdilution. The frequency of eravacycline heteroresistance was determined by population analysis profiling (PAP). Mutations and expression levels of resistance genes in heteroresistant isolates were determined by polymerase chain reaction (PCR) and quantitative real-time PCR (qRT-PCR), respectively. Antisense RNA silencing was used to validate the function of eravacycline heteroresistant candidate genes. Twenty-five eravacycline heteroresistant isolates (17.36%) were detected among 144 CRAB isolates with eravacycline MIC values ≤4 mg/L while no eravacycline heteroresistant strains were detected in carbapenem-susceptible A. baumannii (CSAB) isolates. All eravacycline heteroresistant strains contained OXA-23 carbapenemase and the predominant multilocus sequence typing (MLST) was ST208 (72%). Cross-resistance was observed between eravacycline, tigecycline, and levofloxacin in the resistant subpopulations. The addition of efflux pump inhibitors significantly reduced the eravacycline MIC in resistant subpopulations and weakened the formation of eravacycline heteroresistance in CRAB isolates. The expression levels of adeABC and adeRS were significantly higher in resistant subpopulations than in eravacycline heteroresistant parental strains (P < 0.05). An ISAba1 insertion in the adeS gene was identified in 40% (10/25) of the resistant subpopulations. Decreasing the expression of adeABC or adeRS by antisense RNA silencing significantly inhibited eravacycline heteroresistance. In conclusion, this study identified the emergence of eravacycline heteroresistance in CRAB isolates in China, which is associated with high expression of AdeABC and AdeRS.

Virtual screening and biological activity evaluation of novel efflux pump inhibitors targeting AdeB

The AdeABC efflux pump is an important mechanism causing multidrug resistance in Acinetobacter baumannii, and its main component AdeB can recognize carbapenems, aminoglycosides, and other multi-class antibiotics and efflux them intracellularly, which is an ideal target for the development of anti-multidrug resistant bacteria drugs. Here, we combined multiple computer-aided drug design methods to target AdeB to identify promising novel structural inhibitors. Virtual screening was performed by molecular docking and molecular dynamics simulation (MD) and 12 potential compounds were identified from the databases. Meanwhile, their biological activities were validated by in vitro activity assays, and ChemDiv L676-2179 (γ-IFN), ChemDiv L676-1461, and Chembridge 53717615 were confirmed to suppress efflux effects and restore antibiotic susceptibility of resistant bacteria, which are expected to be developed as adjuvant drugs for the treatment of multi-drug resistant Acinetobacter baumannii clinical infections.

Antimicrobial and antibiofilm activities of Clostridium butyricum supernatant against Acinetobacter baumannii

Acinetobacter baumannii is the major nosocomial pathogen that causes serious infections such as ventilator-associated pneumonia and bacteremia due to its biofilms. Hence, this study investigated the antimicrobial and antibiofilm potentials of cell-free supernatants (CFS) obtained from Clostridium butyricum, as probiotic, against A. baumannii. Our results demonstrated that C. butyricum CFS inhibited A. baumannii cell growth in planktonic culture. Also, C. butyricum CFS not only inhibited the biofilm development and dispersed mature biofilms, but also suppressed the metabolic activity of biofilm cells, showing antibiofilm activity. The biofilm components reduced by C. butyricum CFS were observed via confocal laser scanning microscopy. In addition, C. butyricum CFS exhibited antivirulence effect by inhibiting the motility of A. baumannii. Furthermore, C. butyricum CFS significantly downregulated the expression of efflux pump-related genes including adeA, adeB and adeC in A. baumannii. Our data demonstrate that C. butyricum CFS showed antimicrobial and antibiofilm effects on A. baumannii. These effects are closely associated with suppression of motility and efflux pump-related genes in A. baumannii. The findings suggest that C. butyricum CFS can be used as a new therapeutic alternative against biofilm-associated infection caused by multidrug-resistant A. baumannii.

Targeting Outer Membrane Protein Component AdeC for the Discovery of Efflux Pump Inhibitor against AdeABC Efflux Pump of Multidrug Resistant Acinetobacter baumannii

The structure and functioning of multidrug efflux systems provide us with a better understanding of the transport of various antibiotics, thus giving a path for the discovery of effective compounds for combating the multidrug resistance in Acinetobacter baumannii. In the present study, a number of computational techniques have been used to search for an inhibitor for the RND efflux pump, AdeABC, of A. baumannii targeting specifically its outermost component, i.e., AdeC. We have prepared the three-dimensional structure for AdeC using MODELLER v9.16 and identified its active binding site using SiteMap. Using high-throughput virtual screening, we identified compounds from a large library of biogenic compounds on the basis of their effective interaction at the binding site of AdeC. The validation of docking step was performed by plotting ROC curve (enrichment calculations). The docked complexes were further analyzed for their binding free energies by molecular mechanics using Generalized Born model and Solvent Accessibility (MMGBSA). The molecular dynamics simulation was performed for AdeC-ZINC77257599 complex using GROMACS. The present rational drug designing, molecular mechanics and molecular dynamics data provided an inhibitor, i.e, ZINC77257599 [(3R,4Z,6E,8E)-3-hydroxy-2,2,4-trimethyl-10-oxazol-5-yl-deca-4,6,8-trienamide], for the outer membrane protein component (AdeC) of efflux pump AdeABC of A. baumannii.

Role of insertion sequence Aba-1 and AdeS in reduced tigecycline susceptibility in MDR-Acinetobacter baumannii clinical isolates from Cairo, Egypt

Infections caused by multidrug resistant (MDR) Acinetobacter baumannii (A. baumannii) especially in intensive care units have limited therapeutic options. Overexpression of the adeABC efflux pump may be caused either by the ISAba-1 insertion or by specific point mutations in adeR and adeS, therefore, plays a major role in conferring MDR-A. baumannii. We aimed in our study to monitor the tigecycline (TGC) susceptibility and to study the role of ISAba-1 and the adeS regulator within the AdeABC efflux pump among MDR-A. baumannii clinical isolates. MDR-A. baumannii (63) isolated from ICU patients were identified by detection of OXA-51-like gene. TGC MIC was determined by E-test and broth microdilution. PCR analysis of adeR, adeS, adeB and ISAba1 genes were done with further sequencing of adeS gene. Reduced susceptibility to TGC (MIC: 3-4 mg/L) was noticed in 6/63 (9.5%) MDR-A. baumannii isolates, ISAba-1 was detected in three isolates that two of which showed amino acid substitutions in the adeS operon. We concluded that the amino acids mutations in the adeS gene in presence of insertion ISAba-1 may play a role in conferring reduced TGC susceptibility of MDR-A. baumannii.

AdeR protein regulates adeABC expression by binding to a direct-repeat motif in the intercistronic spacer

Overexpression of the efflux pump AdeABC is associated with tigecycline resistance of multi-drug resistant Acinetobacter baumannii (MDRAB). A two-component regulatory system, sensor AdeS and regulator AdeR proteins regulate the pump. However, the detailed mechanism of the AdeR protein to enhance the expression of adeABC operon is not well defined. We illustrated the biological characteristics of AdeR proteins by comparing a mutant AdeR protein of a tigecycline resistant MDRAB to the wild AdeR protein. By analyzing a series of deletion constructs, a minimal gene cassette of the intercistronic spacer DNA fragment specifically bound with the adeR protein and resulted in band shifting in electrophoresis mobility shifting assays (EMSA). A conserve direct repeat motif was observed in the intercistronic spacer DNA. We demonstrated the AdeR protein was a direct-repeat-binding protein. Two common residue mutations on the AdeR proteins of tigecycline resistant MDRAB isolates could reduce their binding affinity with the intercistronic spacer. The free intercistronic spacer may then more efficiently support the read-through of the adeABC operon during the co-transcriptional translation in tigecycline resistant MDRAB isolates.