Structural and phylogenetic analyses of resistance to next-generation aminoglycosides conferred by AAC(2′) enzymes

Abstract

Plazomicin is currently the only next-generation aminoglycoside approved for clinical use that has the potential of evading the effects of widespread enzymatic resistance factors. However, plazomicin is still susceptible to the action of the resistance enzyme AAC(2′)-Ia from Providencia stuartii. As the clinical use of plazomicin begins to increase, the spread of resistance factors will undoubtedly accelerate, rendering this aminoglycoside increasingly obsolete. Understanding resistance to plazomicin is an important step to ensure this aminoglycoside remains a viable treatment option for the foreseeable future. Here, we present three crystal structures of AAC(2′)-Ia from P. stuartii, two in complex with acetylated aminoglycosides tobramycin and netilmicin, and one in complex with a non-substrate aminoglycoside, amikacin. Together, with our previously reported AAC(2′)-Ia-acetylated plazomicin complex, these structures outline AAC(2′)-Ia’s specificity for a wide range of aminoglycosides. Additionally, our survey of AAC(2′)-I homologues highlights the conservation of residues predicted to be involved in aminoglycoside binding, and identifies the presence of plasmid-encoded enzymes in environmental strains that confer resistance to the latest next-generation aminoglycoside. These results forecast the likely spread of plazomicin resistance and highlight the urgency for advancements in next-generation aminoglycoside design.

Exposure ofMycobacterium tuberculosisto human alveolar lining fluid shows temporal and strain-specific adaptation to the lung environment

“…We also found several shared downregulated genes after 12 h of ALF exposure ( Figure 7A ). Genes associated with resistance to aminoglycosides ( acc , Rv0263c , Rv0264c ) (Bassenden et al 2021), lipid metabolism ( icl1 , fadB2 ), and osmotic stress response and persistence ( Rv0516c , mprA ) (Banerjee et al 2016) were consistently downregulated in all four M.tb strains. Further, fatty acid (FA) transporter mmpL12 was down in all M.tb strains but CDC1551.…”

Manuka honey in combination with azithromycin shows potential for improved activity against Mycobacterium abscessus

“…The lack of the amino group, replaced with a hydroxyl group in amikacin prevents the AAC(2′) from being effective. Furthermore, amikacin contains a (S)-4-amino-2-hydroxybutyrate (HABA) group at the N-1 position, which prevents hydrogen bonding with the enzyme and forces the enzyme to accommodate this group in a confirmation away from the active site ( Bassenden et al, 2021 ). These differences in chemical structure could be the reason why tobramycin was not as effective as amikacin when combined with manuka honey.…”

Inhibition of Enzymatic Acetylation-Mediated Resistance to Plazomicin by Silver Ions

“…It is active against multidrug-resistant Enterobacterales, including strains producing carbapenemases and extended-spectrum β-lactamases, while showing tolerable levels of nephrotoxicity and ototoxicity [ 29 , 32 , 33 ]. Unfortunately, despite the substitutions that make plazomicin a non-substrate for most aminoglycoside-modifying enzymes, the AAC(2′)-Ia enzyme identified in the chromosome of Providencia stuartii can catalyze the inactivation of the antibiotic molecule through transferring an acetyl group from the donor substrate acetyl-CoA to the amino group at the C-2′ position [ 34 , 35 ]. The crystal structures of this enzyme in complex with plazomicin and three other semisynthetic aminoglycosides have been recently reported [ 35 , 36 ].…”

“…Unfortunately, despite the substitutions that make plazomicin a non-substrate for most aminoglycoside-modifying enzymes, the AAC(2′)-Ia enzyme identified in the chromosome of Providencia stuartii can catalyze the inactivation of the antibiotic molecule through transferring an acetyl group from the donor substrate acetyl-CoA to the amino group at the C-2′ position [ 34 , 35 ]. The crystal structures of this enzyme in complex with plazomicin and three other semisynthetic aminoglycosides have been recently reported [ 35 , 36 ]. Although AAC(2′)-Ia is not usually found in clinical isolates, it is a matter of time before it disseminates and becomes prevalent if the use of plazomicin increases.…”