| Criteria | Kanamycin A | Kanamycin B | Remarks |
| Chemical Structure | Composed of 2-deoxystreptamine linked to 3-amino-3-deoxy-α-D-glucopyranose and 6-amino-6-deoxy-α-D-glucopyranose | Structurally similar but differs in the sugar moiety attached to the core aminocyclitol ring | Minor structural differences lead to variation in activity and stability |
| Natural Source | Produced by Streptomyces kanamyceticus | Also produced by Streptomyces kanamyceticus as a minor component | Kanamycin A is the major active form in clinical and research use |
| Antibacterial Activity | Broad-spectrum activity against Gram-negative and some Gram-positive bacteria | Lower antimicrobial potency compared to Kanamycin A | Kanamycin A is preferred in clinical and research applications |
| Usage in Research and Medicine | Widely used for bacterial selection in molecular cloning and in clinical treatments | Rarely used independently; present as an impurity in kanamycin sulfate mixtures | Kanamycin A is purified and marketed for most antibiotic purposes |
| Toxicity Profile | Known for ototoxicity and nephrotoxicity at high doses | Similar toxicity, though less well-characterized due to limited use | Monitoring is important during therapeutic use |
| Resistance Mechanism | Inactivation via aminoglycoside-modifying enzymes (e.g., phosphotransferases) | Likely susceptible to the same resistance mechanisms | Resistance impacts both forms due to structural similarities |
| Analytical Distinction | Can be separated by HPLC or mass spectrometry | Requires advanced analytical methods to distinguish from A | Quality control is important in pharmaceutical-grade kanamycin formulations |
