Study of the Aminoglycoside Subsistence Phenotype of Bacteria Residing in the Gut of Humans and Zoo Animals

Abstract

Recent studies indicate that next to antibiotic resistance, bacteria are able to subsist on antibiotics as a carbon source. Here we evaluated the potential of gut bacteria from healthy human volunteers and zoo animals to subsist on antibiotics. Nine gut isolates of Escherichia coli and Cellulosimicrobium sp. displayed increases in colony forming units (CFU) during incubations in minimal medium with only antibiotics added, i.e., the antibiotic subsistence phenotype. Furthermore, laboratory strains of E. coli and Pseudomonas putida equipped with the aminoglycoside 3′ phosphotransferase II gene also displayed the subsistence phenotype on aminoglycosides. In order to address which endogenous genes could be involved in these subsistence phenotypes, the broad-range glycosyl-hydrolase inhibiting iminosugar deoxynojirimycin (DNJ) was used. Addition of DNJ to minimal medium containing glucose showed initial growth retardation of resistant E. coli, which was rapidly recovered to normal growth. In contrast, addition of DNJ to minimal medium containing kanamycin arrested resistant E. coli growth, suggesting that glycosyl-hydrolases were involved in the subsistence phenotype. However, antibiotic degradation experiments showed no reduction in kanamycin, even though the number of CFUs increased. Although antibiotic subsistence phenotypes are readily observed in bacterial species, and are even found in susceptible laboratory strains carrying standard resistance genes, we conclude there is a discrepancy between the observed antibiotic subsistence phenotype and actual antibiotic degradation. Based on these results we can hypothesize that aminoglycoside modifying enzymes might first inactivate the antibiotic (i.e., by acetylation of amino groups, modification of hydroxyl groups by adenylation and phosphorylation respectively), before the subsequent action of catabolic enzymes. Even though we do not dispute that antibiotics could be used as a single carbon source, our observations show that antibiotic subsistence should be carefully examined with precise degradation studies, and that its mechanistic basis remains inconclusive.

Shared strategies for β-lactam catabolism in the soil microbiome

“…Finally, antibiotic-catabolizing enzymes have the potential to play an important industrial role in the production of next-generation antibiotics in the same way that the discovery of penicillin amidase spurred the development of semi-synthetic β-lactams through remodeling of natural penicillins. Characterization of hydrolytic enzymes responsible for the catabolism of other antibiotics, such as hypothetical glycosidases acting on aminoglycosides 16 , could catalyze an explosion of diverse semi-synthetic derivatives in other antibiotic classes. Antibiotic degradation may therefore paradoxically contribute to the development of the next generation of novel antibiotics.…”

“…However, controversy still remains over the characterization of resistant, but not metabolizing, versus subsistent growth phenotypes. To date, no specific genes or pathways have been identified that enable bacteria to use antibiotics as a sole carbon source 16 , 20 .…”

Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

“…The analysis of aminoglycosides in the sewage samples was performed as in Bello 53 , with adaptations as summarized in the following. For sample pretreatment, two 10-mL portions of each sample of sewage were weighed into separate 50-mL tubes, after which internal standards were added.…”

Dual RNase and β-lactamase Activity of a Single Enzyme Encoded in Archaea

“…Moreover, very recently, RNA-hydrolysis activity of bacterial class B metallo-β-lactamase IMP-1 has been reported experimentally [ 28 ]. The use of antibiotics as a source of nutrients for archaebacteria to degrade the molecules of β-lactam and use them as a source of carbon, as described in the bacteria, is a plausible hypothesis [ 20 , 29 , 30 , 31 ].…”