Christophe Merlin

Tackling antibiotic resistance: the environmental framework

Antibiotic resistance is a threat to human and animal health worldwide, and key measures are required to reduce the risks posed by antibiotic resistance genes that occur in the environment. These measures include the identification of critical points of control, the development of reliable surveillance and risk assessment procedures, and the implementation of technological solutions that can prevent environmental contamination with antibiotic resistant bacteria and genes. In this Opinion article, we discuss the main knowledge gaps, the future research needs and the policy and management options that should be prioritized to tackle antibiotic resistance in the environment.

Biocompatible and stable ZnO quantum dots generated by functionalization with siloxane-core PAMAM dendrons

Despite the growing interest of quantum dots (QDs) in biological applications, there are many concerns regarding the potential accumulation and toxic effects of Cd-containing QDs in animals and humans. Zinc oxide QDs are promising alternatives for diagnosis and imaging but their aqueous instability has markedly limited their use. Generations 1, 2 and 3 (noted G1, G2, and G3, respectively) of new poly(amidoamine) (PAMAM) dendrons bearing a siloxane group at the focal point were prepared from 3-aminopropyltrimethoxysilane. Using tetramethylammonium hydroxide as cross-linking agent, hydrophobic oleate-capped ZnO QDs were functionalized with G1 or G2 dendrons, as evidenced by FT-IR, UV-visible and XPS analyses, and were successfully transferred in aqueous solution. AFM and TEM images show that ZnO@G1 and ZnO@G2 QDs have a spherical shape with average crystalline sizes of 5.3 and 5.1 nm, respectively. Immediately after dispersion in water, ZnO@G1 and ZnO@G2 QDs exhibit a broad and strong visible emission peak centered at 550 nm with a quantum yield of ca. 18%. A strong increase of photoluminescence quantum yields was observed over time and values up to 59% could be reached after ca. 20 days of storage in water at room temperature. The good quantum yields and the stabilities of PAMAM-dendron capped ZnO QDs ensured their potential applications in cell imaging. ZnO@G2 was successfully used for the labelling of the Gram+ bacterium Staphylococcus aureus. The biocompatibility of these QDs is markedly improved compared to Cd-based ones as growth inhibition tests showed that ZnO@G2 QDs could be used with concentrations up to 1 mM without altering the cell growth of the Escherichia coli bacterium while most Cd-containing QDs already exhibit cytotoxicity at the nM level.

The Biphenyl- and 4-Chlorobiphenyl-Catabolic Transposon Tn4371, a Member of a New Family of Genomic Islands Related to IncP and Ti Plasmids

ABSTRACT The nucleotide sequence of the biphenyl catabolic transposon Tn4371 has been completed and analyzed. It confirmed that the element has a mosaic structure made of several building blocks. In addition to previously identified genes coding for a tyrosine recombinase related to phage integrases and for biphenyl degradation enzymes very similar to those of Achromobacter georgiopolitanum KKS102, Tn4371 carries many plasmid-related genes involved in replication, partition, and other, as-yet-unknown, plasmid functions. One gene cluster contains most of the genes required to express a type IV secretion-mating pair formation apparatus coupled with a TraG ATPase, all of which are related to those found on IncP and Ti plasmids. Orthologues of all Tn4371 plasmid-related genes and of the tyrosine recombinase gene were found, with a very similar organization, in the chromosome of Ralstonia solanacearum and on the yet-to-be-determined genomic sequences of Erwinia chrysanthemi and Azotobacter vinelandii. In each of these chromosomal segments, conserved segments were separated by different groups of genes, which also differed from the Tn4371 bph genes. The conserved blocks of genes were also identified, in at least two copies, in the chromosome of Ralstonia metallidurans CH34. Tn4371 thus appears to represent a new family of potentially mobile genomic islands with a broad host range since they reside in a wide range of soil proteobacteria, including plant pathogens.

The exposure of bacteria to CdTe-core quantum dots: the importance of surface chemistry on cytotoxicity

A series of water-soluble CdTe-core quantum dots (QDs) with diameters below 5.0 nm and functionalized at their surface with polar ligands such as thioglycolic acid (TGA) or the tripeptide glutathione (GSH) were synthesized and characterized by UV-vis absorption spectroscopy, their photoluminescence measurements, atomic force microscopy (AFM) and transmission electron microscopy (TEM). Because cell elongations and growth inhibitions were observed during labeling experiments, the cytotoxicity of CdTe-core QDs was investigated. Using growth inhibition tests combining different bacterial strains with different CdTe-core QDs, it was possible to demonstrate that the cytotoxicity of QDs towards bacteria depends on exposure concentrations, surface chemistry and coating, and that it varied with the strain considered. Growth inhibition tests carried out with heavy-metal-resistant bacteria, as well as ICP-AES analyses of cadmium species released by CdTe@TGA QDs, demonstrated that the leakage of Cd2+ is not the main source of QD toxicity. Our study suggests that QD cytotoxicity is rather due to the formation of TeO2 and probably the existence of CdO formed by surface oxidation. In this respect, QDs possessing a CdO shell appeared very toxic.

Bacterial Surface Appendages Strongly Impact Nanomechanical and Electrokinetic Properties of Escherichia coli Cells Subjected to Osmotic Stress

The physicochemical properties and dynamics of bacterial envelope, play a major role in bacterial activity. In this study, the morphological, nanomechanical and electrohydrodynamic properties of Escherichia coli K-12 mutant cells were thoroughly investigated as a function of bulk medium ionic strength using atomic force microscopy (AFM) and electrokinetics (electrophoresis). Bacteria were differing according to genetic alterations controlling the production of different surface appendages (short and rigid Ag43 adhesins, longer and more flexible type 1 fimbriae and F pilus). From the analysis of the spatially resolved force curves, it is shown that cells elasticity and turgor pressure are not only depending on bulk salt concentration but also on the presence/absence and nature of surface appendage. In 1 mM KNO3, cells without appendages or cells surrounded by Ag43 exhibit large Young moduli and turgor pressures (∼700–900 kPa and ∼100–300 kPa respectively). Under similar ionic strength condition, a dramatic ∼50% to ∼70% decrease of these nanomechanical parameters was evidenced for cells with appendages. Qualitatively, such dependence of nanomechanical behavior on surface organization remains when increasing medium salt content to 100 mM, even though, quantitatively, differences are marked to a much smaller extent. Additionally, for a given surface appendage, the magnitude of the nanomechanical parameters decreases significantly when increasing bulk salt concentration. This effect is ascribed to a bacterial exoosmotic water loss resulting in a combined contraction of bacterial cytoplasm together with an electrostatically-driven shrinkage of the surface appendages. The former process is demonstrated upon AFM analysis, while the latter, inaccessible upon AFM imaging, is inferred from electrophoretic data interpreted according to advanced soft particle electrokinetic theory. Altogether, AFM and electrokinetic results clearly demonstrate the intimate relationship between structure/flexibility and charge of bacterial envelope and propensity of bacterium and surface appendages to contract under hypertonic conditions.

Persistence and dissemination of the multiple-antibiotic-resistance plasmid pB10 in the microbial communities of wastewater sludge microcosms.

Plasmid-mediated dissemination of antibiotic resistance genes is widely recognized to take place in many environmental compartments but remains difficult to study in a global perspective because of the complexity of the environmental matrices considered and the lack of exhaustive tools. In this report, we used a molecular approach based on quantitative PCR to monitor the fate of the antibiotic resistance plasmid pB10 and its donor host in microbial communities collected from various wastewater treatment plant (WWTP) sludges and maintained in microcosms under different conditions. In aerated activated sludge microcosms, pB10 did not persist because of an apparent loss of the donor bacteria. The persistence of the donor bacteria noticeably increased in non-aerated activated sludge microcosms or after amending antibiotics (sulfamethoxazole or amoxicillin) at sub-inhibitory concentrations, but the persistence of the donor bacteria did not stimulate the dissemination of pB10. The dissemination of the plasmid appeared as an increasing plasmid to donor ratio in microcosm setups with microbial communities collected in anaerobic digesters or the spatially organized communities from fixed biofilm reactors. As a whole, the data collected suggest that some WWTP processes, more than others, may sustain microbial communities that efficiently support the dissemination of the multiple-antibiotic-resistance plasmid pB10.

A GntR-like negative regulator of the biphenyl degradation genes of the transposon Tn4371.

Abstract Tn4371, a 55-kb catabolic transposon originally isolated from Ralstonia eutropha A5, carries genes for the degradation of biphenyl/4-chlorobiphenyl, which are clustered on a 13-kb DNA segment located in the middle of the element. DNA sequencing revealed that two potential regulatory genes, bphR and bphS, border this region. Transcriptional fusion experiments using bphC as a reporter gene, Northern hybridization and primer extension analysis led to the conclusion that the transposon-encoded genes bphEFGA1A2A3BCD form an operon transcribed from a σ70 promoter, pE. Transcription from pE was not influenced by deletion of the bphR gene of Tn4371, which should encode a LysR-like regulator. The bphS gene product negatively regulated pE, and displayed significant similarity to GntR-like regulators. This is the first reported example of a GntR-like regulator involved in the control of an aromatic degradation pathway.

Impact of Internal RNA on Aggregation and Electrokinetics of Viruses: Comparison between MS2 Phage and Corresponding Virus-Like Particles

ABSTRACT We compare for the first time the electrokinetic and aggregation properties of MS2 phage (pH 2.5 to 7, 1 to 100 mM NaNO3 electrolyte concentration) with those of the corresponding virus-like particles (VLPs), which lack entirely the inner viral RNA component. In line with our previous work (J. Langlet, F. Gaboriaud, C. Gantzer, and J. F. L. Duval, Biophys. J. 94:3293-3312, 2008), it is found that modifying the content of RNA within the virus leads to very distinct electrohydrodynamic and aggregation profiles for MS2 and MS2 VLPs. Under the given pH and concentration conditions, MS2 VLPs exhibit electrophoretic mobility larger in magnitude than that of MS2, and both have similar isoelectric point (IEP) values (∼4). The electrokinetic results reflect a greater permeability of MS2 VLPs to electroosmotic flow, developed within/around these soft particles during their migration under the action of the applied electrical field. Results also support the presence of some remaining negatively charged component within the VLPs. In addition, MS2 phage systematically forms aggregates at pH values below the IEP, regardless of the magnitude of the solution ionic strength, whereas MS2 VLPs aggregate under the strict condition where the pH is relatively equal to the IEP at sufficiently low salt concentrations (<10 mM). It is argued that the stability of VLPs against aggregation and the differences between electrokinetics of MS2 and corresponding VLPs conform to recently developed formalisms for the stability and electrohydrodynamics of soft multilayered particles. The differences between the surface properties of these two kinds of particles reported here suggest that VLPs may not be appropriate for predicting the behavior of pathogenic viruses in aqueous media.

Occurrence of Tn4371-Related Mobile Elements and Sequences in (Chloro)biphenyl-Degrading Bacteria

ABSTRACT Tn4371, a 55-kb transposable element involved in the degradation and biphenyl or 4-chlorobiphenyl identified inRalstonia eutropha A5, displays a modular structure including a phage-like integrase gene (int), aPseudomonas-like (chloro)biphenyl catabolic gene cluster (bph), and RP4- and Ti-plasmid-like transfer genes (trb) (C. Merlin, D. Springael, and A. Toussaint, Plasmid 41:40–54, 1999). Southern blot hybridization was used to examine the presence of different regions of Tn4371 in a collection of (chloro)biphenyl-degrading bacteria originating from different habitats and belonging to different bacterial genera. Tn4371-related sequences were never detected on endogenous plasmids. Although the gene probes containing only bph sequences hybridized to genomic DNA from most strains tested, a limited selection of strains, all β-proteobacteria, displayed hybridization patterns similar to the Tn4371 bph cluster. Homology between Tn4371 and DNA of two of those strains, originating from the same area as strain A5, extended outside the catabolic genes and covered the putative transfer region of Tn4371. On the other hand, none of the (chloro)biphenyl degraders hybridized with the outer left part of Tn4371 containing the int gene. Thebph catabolic determinant of the two strains displaying homology to the Tn4371 transfer genes and a third strain isolated from the A5 area could be mobilized to a R. eutropha recipient, after insertion into an endogenous or introduced IncP1 plasmid. The mobilized DNA of those strains included all Tn4371 homologous sequences previously identified in their genome. Our observations show that the bph genes present on Tn4371 are highly conserved between different (chloro)biphenyl-degrading hosts, isolated globally but belonging mainly to the β-proteobacteria. On the other hand, Tn4371-related mobile elements carrying bphgenes are apparently only found in isolates from the environment that provided the Tn4371-bearing isolate A5.

Incidence of the core composition on the stability, the ROS production and the toxicity of CdSe quantum dots

Mercaptosuccinic acid-capped CdSe and alloyed CdSe(S) QDs were prepared in aqueous solution at 100 and 170°C, respectively. These dots were characterized by transmission electron microscopy (TEM), X-ray diffraction (XRD), and UV-vis and photoluminescence spectroscopies. The dots were found to be of similar size (ca. 2nm) but differ in their composition and surface chemistry. The photostability of the QDs was found to correlate with their ability to produce reactive oxygen species (ROS) upon light activation. CdSe QDs produce hydroxyl radicals immediately after irradiation due to their modest photostability, while CdSe(S) QDs start to generate the hydroxyl radicals only once they start to be bleached (ca. 30min). Cytotoxicity experiments conducted on Escherichia coli cells revealed that CdSe QDs were the more toxic despite being the least loaded in cadmium. In addition, consistent with ROS assays, the cytotoxicity of the CdSe QDs appeared light-dependent and is in accordance with a light-dependent oxidative stress observed with an oxyR-based whole cell biosensor. Our results demonstrate the crucial role played by nanoparticles synthesis process on their PL properties, their stability and their toxicity.