Identification and characterization of a novel chromosomal aminoglycoside 3'--phosphotransferase, APH(3')-Id, from DW18 isolated from the sewage of an animal farm.

Background: Aminoglycosides, as important clinical antimicrobials, are used as second-line drugs for treating multidrug-resistant tuberculosis or combined with β-lactam drugs for treating severe infections such as sepsis. Aminoglycoside-modifying enzyme (AME) is the most important mechanism of aminoglycoside resistance and deserves more attention.

Methods: The bacterium DW18 was isolated from the sewage of an animal farm using the conventional method. The agar dilution method was used to determine the minimum inhibitory concentrations (MICs) of antimicrobials. A novel resistance gene was cloned, and the enzyme was expressed. The kinetic parameters were measured by a SpectraMax M5 multifunctional microplate reader. Bioinformatic analysis was performed to reveal the genetic context of the gene and its phylogenetic relationship with other AMEs.

Results: A novel aminoglycoside 3'--phosphotransferase gene designated was identified in DW18 and shared the highest amino acid identity of 77.49% with the functionally characterized aminoglycoside 3'--phosphotransferase APH(3')-Ia. The recombinant plasmid carrying the novel resistance gene (pMD19-/ DH5α) showed 1,024-, 512-, 128- and 16-fold increased MIC levels for kanamycin, ribostamycin, paromomycin and neomycin, respectively, compared with the reference strain DH5α. APH(3')-Id showed the highest catalytic efficiency for ribostamycin [ of (4.96 ± 1.63) × 10 M/s], followed by paromomycin [ of (2.18 ± 0.21) × 10 M/s], neomycin [ of (1.73 ± 0.20) × 10 M/s], and kanamycin [ of (1.10 ± 0.18) × 10 M/s]. Three conserved functional domains of the aminoglycoside phosphotransferase family and ten amino acid residues responsible for the phosphorylation of kanamycin were found in the amino acid sequence of APH(3')-Id. No mobile genetic element (MGE) was discovered surrounding the gene.

Conclusion: In this work, a novel aminoglycoside 3'--phosphotransferase gene designated encoded in the chromosome of the environmental isolate DW18 was identified and characterized. These findings will help clinicians select effective antimicrobials to treat infections caused by pathogens with this kind of resistance gene.