Abstract
Aminoglycoside antibiotics are powerful bactericidal therapeutics that are often used in the treatment of critical Gram-negative systemic infections. The emergence and global spread of antibiotic resistance, however, has compromised the clinical utility of aminoglycosides to an extent similar to that found for all other antibiotic-drug classes. Apramycin, a drug candidate currently in clinical development, was suggested as a next-generation aminoglycoside antibiotic with minimal cross-resistance to all other standard-of-care aminoglycosides. Here, we analyzed 591,140 pathogen genomes deposited in the NCBI National Database of Antibiotic Resistant Organisms (NDARO) for annotations of apramycin-resistance genes, and compared them to the genotypic prevalence of carbapenem resistance and 16S-rRNA methyltransferase (RMTase) genes. The 3-N-acetyltransferase gene aac(3)-IV was found to be the only apramycin-resistance gene of clinical relevance, at an average prevalence of 0.7%, which was four-fold lower than that of RMTase genes. In the important subpopulation of carbapenemase-positive isolates, aac(3)-IV was nine-fold less prevalent than RMTase genes. The phenotypic profiling of selected clinical isolates and recombinant strains expressing the aac(3)-IV gene confirmed resistance to not only apramycin, but also gentamicin, tobramycin, and paromomycin. Probing the structure–activity relationship of such substrate promiscuity by site-directed mutagenesis of the aminoglycoside-binding pocket in the acetyltransferase AAC(3)-IV revealed the molecular contacts to His124, Glu185, and Asp187 to be equally critical in binding to apramycin and gentamicin, whereas Asp67 was found to be a discriminating contact. Our findings suggest that aminoglycoside cross-resistance to apramycin in clinical isolates is limited to the substrate promiscuity of a single gene, rendering apramycin best-in-class for the coverage of carbapenem- and aminoglycoside-resistant bacterial infections.
Highlights
Decreasing antibiotic efficacy in the treatment of drug-resistant bacterial infections is one of the greatest global health threats of our times, prompting the WHO to prioritize bacterial pathogens and define clinical needs for the development of new antibiotics [1]
Further chemical modification and scaffold evolution of aminoglycoside antibiotics are mandatory to restore the clinical utility of this drug class, which has long been listed as essential medicines by the WHO [7,8]
We studied the resistance-gene annotations of clinical isolates deposited in the National Database of Antibiotic Resistant Organisms (NDARO)
Summary
Decreasing antibiotic efficacy in the treatment of drug-resistant bacterial infections is one of the greatest global health threats of our times, prompting the WHO to prioritize bacterial pathogens and define clinical needs for the development of new antibiotics [1]. A major benefit of such an approach lies in the pre-existing clinical validation of both the molecular target and the drug class, and a proven clinical utility that facilitates early adoption by treatment guidelines, and market penetration [2]. One such success story is that of aminoglycosides, a drug class comprising potent antimicrobial agents with broad-spectrum activity that bind to the bacterial ribosome and inhibit bacterial protein-synthesis [3]. The efficacy of many clinically established aminoglycosides eroded over time due to the emergence and spread of aminoglycoside resistance. Further chemical modification and scaffold evolution of aminoglycoside antibiotics are mandatory to restore the clinical utility of this drug class, which has long been listed as essential medicines by the WHO [7,8]
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