A Carotenoid- and Nuclease-Producing Bacterium Can Mitigate Enterococcus faecalis Transformation by Antibiotic Resistance Genes

Abstract

Dissemination of antibiotic resistance genes (ARGs) through natural transformation is facilitated by factors that stabilize extracellular DNA (eDNA) and that induce reactive oxygen species (ROS) that permeabilize receptor cells and upregulate transformation competence genes. In this study, we demonstrate that Deinococcus radiodurans can mitigate this ARG dissemination pathway by removing both eDNA and ROS that make recipient cells more vulnerable to transformation. We used plasmid RP4 as source of extracellular ARGs (tetA, aphA, and blaTEM-2) and the opportunistic pathogen Enterococcus faecalis as receptor. The presence of D. radiodurans significantly reduced the transformation frequency from 2.5 ± 0.7 × 10–6 to 7.4 ± 1.4 × 10–7 (p < 0.05). Based on quantification of intracellular ROS accumulation and superoxide dismutase (SOD) activity, and quantitative polymerase chain reaction (qPCR) and transcriptomic analyses, we propose two mechanisms by which D. radiodurans mitigates E. faecalis transformation by ARGs: (a) residual antibiotics induce D. radiodurans to synthesize liposoluble carotenoids that scavenge ROS and thus mitigate the susceptibility of E. faecalis for eDNA uptake, and (b) eDNA induces D. radiodurans to synthesize extracellular nucleases that degrade eARGs. This mechanistic insight informs biological strategies (including bioaugmentation) to curtail the spread of ARGs through transformation.

Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent

“…radiodurans cannot interfere with the functional evolution of indigenous microbial communities. Moreover, the products of eDNA biodegradation may also mitigate the spread of ARGs among bacteria by decreasing oxidative stress. ,, It has been reported that an eDNA product, deoxyguanosine monophosphate (dGMP), can act as a nutrient source for bacteria and enhance bacteria tolerance to oxidative stress, which makes bacteria more vulnerable to acquire ARG by HGT . Therefore, the synthetic microbiome may also reduce the risk of ARG spread by changing the microbial community and degrading eDNA.…”

“…In our previous study, we demonstrated that the nucleaseproducing Deinococcus could mitigate transformation of extracellular ARGs to Enterococcus faecalis by degrading eDNA. 18,19 Therefore, this study mainly demonstrates whether these nuclease-producing bacteria can reduce the risk of ARG dissemination in mixed bacteria sewage systems. In this study, a microbiome capable of degrading eDNA was constructed and operated by using Deinococcus radiodurans as the base microorganism.…”

Antibiotic-induced gut microbiota dysbiosis has a functional impact on purine metabolism

“…In addition, the present study only analyzed the number of enzymes related to the purine salvage pathway without further analyzing the specific mechanism. Therefore, we cannot yet fully explain why Enterococcus survived antibiotic treatment, suggesting that the antibiotic resistance genes of bacteria are non-negligible factors for antibiotic susceptibility and not just due to the purine salvage pathway alone ( Enterococcus are known to be resistant to ampicillin, and their resistance mechanisms have been clearly described) [ 47 ].…”

Nematodes Degrade Extracellular Antibiotic Resistance Genes by Secreting DNase II Encoded by the nuc-1 Gene

“…Generally, it is considered that microbes dominate the degradation process, including direct degradation through nucleases and indirectly mediated ARG attenuation. For example, Deinococcus radiodurans and Bdellovibrio bacteriovorus HD are crucial in ARG biodegradation as they produce nucleases. Multicellular organisms, such as earthworms, , Musca domestica larvae, and Hermetia illucens, can also mediate ARG biodegradation by affecting the microbial communities.…”