Genomic insights into ST85 and ST158 belonging to recently emerged global clones of multidrug-resistant Acinetobacter baumannii isolates from Egypt: In vitro assessment of repurposed drug–antibiotic combinations

Background: The strikingly rapid increase in multidrug-resistant Acinetobacter baumannii (MDRAB) incidence rates represents a major challenge in healthcare settings. This is due to the limitation of the currently available treatment options to combat tenacious A. baumannii infections. MDRAB isolates belonging to recently emerged global clones GC9 and GC10 are on the rise, especially in the Middle East and Africa, which warrants a thorough investigation of these global clones.

Methods: Thirteen A. baumannii isolates belonging to less well-studied global clones were selected from 46 isolates collected in Alexandria, Egypt, after determining their clone using MLST. Susceptibility to multiple antibiotic classes was determined by the Kirby-Bauer disk diffusion method. Testing of carbapenemase activity and selected virulence phenotypes was done. Whole genome sequencing, phylogenetic analysis, and molecular characterization of the resistance and virulence genotypes were performed. Checkerboard assay was employed for testing the combination of each of ciclopirox and N-acetylcysteine (NAC), as potential repurposed drugs, with each of meropenem and levofloxacin antibiotics against MDRAB isolates.

Results: All the isolates displayed multidrug resistance and were carbapenemase-positive. One isolate showed strong biofilm formation, whereas 4 and 8 isolates were moderate and weak biofilm formers, respectively. Twelve out of thirteen isolates were positive twitchers. The isolates showed moderate phospholipase and strong protease activities. However, low phospholipase production was detected in one isolate. The genomic analysis revealed that 3 and 10 isolates belonged to ST85 (GC9) and ST158 (GC10), respectively. All 13 isolates harbored multiple resistance genes including oxa23 and carried an RP-T1 rep type plasmid. Phylogenetic analysis demonstrated that the isolates were clustered together forming subclades with others from Alexandria/Egypt. The AbGRI3-2 resistance island (RI) was detected in ST158 isolates carrying R3-T60 rep type and 9 antibiotic resistance genes. The combination of NAC with each of meropenem or levofloxacin showed a synergistic action against 3 and one isolate(s), respectively, using the checkerboard assay.

Conclusion: The current study provides an in-depth characterization of the collected MDRAB isolates from the global clones GC9 and GC10. The endemicity of these clones necessitates strategies to mitigate ongoing MDRAB outbreaks in countries like Egypt. Combination of NAC with meropenem or levofloxacin represents a promising treatment option against the newly emerged global clones that needs further in vivo testing.