RNAIII is linked with the pentose phosphate pathway through the activation of RpiRc in Staphylococcus aureus.

Staphylococcus aureus RNAIII is a dual-function regulatory RNA that controls the expression of multiple virulence genes and especially the transition from adhesion to the production of exotoxins. However, its contribution to S. aureus central metabolism remains unclear. Using MS2-affinity purification coupled with RNA sequencing, we uncovered more than 50 novel RNAIII-mRNA interactions. Among them, we demonstrate that RNAIII is a major activator of the rpiRc gene, encoding a regulator of the pentose phosphate pathway (PPP). RNAIII binds the 5' UTR of rpiRc mRNA to favor ribosome loading, leading to an increased expression of RpiRc and, subsequently, of two PPP enzymes. Finally, we show that RNAIII and RpiRc are involved in S. aureus fitness in media supplemented with various carbohydrate sources related to PPP and glycolysis. Collectively, our data depict an unprecedented phenotype associated with the RNAIII regulon, especially the direct implication of RNAIII in central metabolic activity modulation. These findings show that the contribution of RNAIII in Staphylococcus aureus adaptation goes far beyond what was initially reported. IMPORTANCE: Staphylococcus aureus is a major human pathogen involved in acute and chronic infections. Highly recalcitrant to antibiotic treatment, persistent infections are mostly associated with the loss of RNAIII expression, a master RNA regulator responsible for the switch from colonization to infection. Here, we used the MS2 affinity purification coupled with RNA sequencing approach to identify novel mRNA targets of RNAIII and uncover novel functions. We demonstrate that RNAIII is an activator of the expression of genes involved in the pentose phosphate pathway and is implicated in the adjustment of bacterial fitness as a function of carbohydrate sources. Taken together, our results demonstrate an unprecedented role of RNAIII that goes beyond the knowledge gained so far and contributes to a better understanding of the role of RNAIII in bacterial adaptation expression and the coordination of a complex regulatory network.

Immersive virtual reality for shoulder rehabilitation: evaluation of a physical therapy program executed with oculus quest 2.

BACKGROUND: Virtual Reality (VR) systems have been increasingly used across several medical fields. A crucial preliminary step for developing optimized VR-based applications for rehabilitation purposes is identifying potential interventions to meet the requirements necessary to satisfy end-users' needs. This study aims to assess the acceptability, usability, and appropriateness of a VR physical therapy program executed with Oculus Quest 2 by expert physiotherapists of shoulder musculoskeletal rehabilitation. METHODS: Eleven physiotherapists were enrolled to test a VR program for shoulder musculoskeletal rehabilitation. At the end of each session, physiotherapists completed three questionnaires about the acceptability, usability, and appropriateness of the VR system and application, investigating aspects such as wearability, safety, stability, ease of control, comfort, size, utility, playability, and use mode. RESULTS: The acceptability questionnaire revealed that all the physiotherapists found the VR system easy to wear and control, very confident, and safe. The usability questionnaire showed that most physiotherapists (73%) found the VR application entertaining, although only 45% said the system could be used independently by patients without the support of a therapist. Many physiotherapists found the use of the VR application appropriate for patients with rotator cuff tears treated conservatively (63.6%) or surgically (54.5%), for patients with shoulder osteoarthritis treated conservatively (72.7%), for patients with shoulder osteoarthritis after surgical treatment (63.6%). 91% of physiotherapists think it would be best for patients to use the VR system under the supervision of a therapist and not independently in a home setting. CONCLUSIONS: The use of VR in orthopaedic rehabilitation is encouraging, although further efforts are needed to increase the independent use of patients without the supervision of a physiotherapist. Moreover, future studies should strive to ensure the clinical effectiveness of VR rehabilitation in reaching therapeutic goal settings.

Performance Evaluation of an Immersive Virtual Reality Application for Rehabilitation after Arthroscopic Rotator Cuff Repair.

Few studies have evaluated the effectiveness of shoulder rehabilitation in virtual environments. The objective of this study was to investigate the performance of a custom virtual reality application (VR app) with a stereophotogrammetric system considered the gold standard. A custom VR app was designed considering the recommended rehabilitation exercises following arthroscopic rotator cuff repair. Following the setting of the play space, the user's arm length, and height, five healthy volunteers performed four levels of rehabilitative exercises. Results for the first and second rounds of flexion and abduction displayed low total mean absolute error values and low numbers of unmet conditions. In internal and external rotation, the number of times conditions were not met was slightly higher; this was attributed to a lack of isolated shoulder movement. Data is promising, and volunteers were able to reach goal conditions more often than not. Despite positive results, more literature comparing VR applications with gold-standard clinical parameters is necessary. Nevertheless, results contribute to a body of literature that continues to encourage the application of VR to shoulder rehabilitation programs.

Stacked ensemble machine learning for porosity and absolute permeability prediction of carbonate rock plugs.

This study employs a stacked ensemble machine learning approach to predict carbonate rocks' porosity and absolute permeability with various pore-throat distributions and heterogeneity. Our dataset consists of 2D slices from 3D micro-CT images of four carbonate core samples. The stacking ensemble learning approach integrates predictions from several machine learning-based models into a single meta-learner model to accelerate the prediction and improve the model's generalizability. We used the randomized search algorithm to attain optimal hyperparameters for each model by scanning over a vast hyperparameter space. To extract features from the 2D image slices, we applied the watershed-scikit-image technique. We showed that the stacked model algorithm effectively predicts the rock's porosity and absolute permeability.

Virtual Reality for Shoulder Rehabilitation: Accuracy Evaluation of Oculus Quest 2.

Virtual reality (VR) systems are becoming increasingly attractive as joint kinematics monitoring systems during rehabilitation. This study aimed to evaluate the accuracy of the Oculus Quest 2 in measuring translational and rotational displacements. As the Oculus Quest 2 was chosen for future applications in shoulder rehabilitation, the translation range (minimum: ~200 mm, maximum: ~700 mm) corresponded to the forearm length of the 5th percentile female and the upper limb length of the 95th percentile male. The controller was moved on two structures designed to allow different translational displacements and rotations in the range 0-180°, to cover the range of motion of the upper limb. The controller measures were compared with those of a Qualisys optical capture system. The results showed a mean absolute error of 13.52 ± 6.57 mm at a distance of 500 mm from the head-mounted display along the x-direction. The maximum mean absolute error for rotational displacements was found to be 1.11 ± 0.37° for a rotation of 40° around the z-axis. Oculus Quest 2 is a promising VR tool for monitoring shoulder kinematics during rehabilitation. The inside-out movement tracking makes Oculus Quest 2 a viable alternative to traditional motion analysis systems.

Forecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches.

Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of sak and scn can discriminate strains based on their host specificity, while other genes such as mecA are often associated with virulent outcomes. Both GWAS and RF indicated the importance of intergenic regions (IGRs) and coding DNA sequence (CDS) but not sRNAs in forecasting an outcome. Additional transcriptomic analyses performed on the most prevalent clonal complex 8 (CC8) clonal types, in media mimicking nasal colonization or bacteremia, indicated three RNAs as potential RNA markers to forecast infection, followed by 30 others that could serve as infection severity predictors. Our report shows that genetic association and transcriptomics are complementary approaches that will be combined in a single analytical framework to improve our understanding of bacterial pathogenesis and ultimately identify potential predictive molecular markers. IMPORTANCE Predicting the outcome of bacterial colonization and infections, based on extensive genomic and transcriptomic data from a given pathogen, would be of substantial help for clinicians in treating and curing patients. In this report, genome-wide association studies and random forest algorithms have defined gene combinations that differentiate human from animal strains, colonization from diseases, and nonsevere from severe diseases, while it revealed the importance of IGRs and CDS, but not small RNAs (sRNAs), in anticipating an outcome. In addition, transcriptomic analyses performed on the most prevalent clonal types, in media mimicking either nasal colonization or bacteremia, revealed significant differences and therefore potent RNA markers. Overall, the use of both genomic and transcriptomic data in a single analytical framework can enhance our understanding of bacterial pathogenesis.

Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests.

Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup. Processing steps of quality controls have been developed in order (i) to avoid low-quality reads and sequences, (ii) to optimize abundance thresholds and profiles, (iii) to combine classifiers and reference databases for best classification of species and abundance profiles for both prokaryotic and eukaryotic sequences, and (iv) to introduce external positive control. We find that the best strategy is to use a pipeline composed of a combination of different but complementary classifiers such as Kraken2/Bracken and Kaiju. Such improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.

In vitro and in vivo activity of new strains of Bacillus subtilis against ESBL-producing Escherichia coli: an experimental study.

AIMS: The gastro-intestinal tract is a major reservoir of extended-spectrum beta-lactamase (ESBL) producing Escherichia coli. Bacillus spores may be used as probiotics to decrease digestive colonization by ESBL-E. coli. Our aim was to assess the in vitro and in vivo activity of new Bacillus strains against ESBL-E. coli. METHODS AND RESULTS: We screened the in vitro activity of 50 Bacillus strains against clinical isolates of ESBL-E. coli and selected B. subtilis strains CH311 and S3B. Both strains decreased ESBL-E. coli titers by 4 log10 CFU L-1 in an in vitro model of gut content, whereas the B. subtilis CU1 strain did not. In a murine model of intestinal colonization by ESBL-E. coli, CH311 and S3B did not decrease fecal titers of ESBL-E. coli. Ten sequences of putative antimicrobial peptides were identified in the genomes of CH311 and S3B, but not in CU1. CONCLUSIONS: Two new B. subtilis strains showed strong in vitro activity against ESBL-E. coli. SIGNIFICANCE AND IMPACT OF STUDY: Despite strong in vitro activities of new B. subtilis strains against ESBL-E. coli, intestinal colonisation was not altered by curative Bacillus treatment even if their spores proved to germinate in the gut. Thus, this work underlines the importance of in vivo experiments to identify efficient probiotics. The use of potential antimicrobial compounds identified by genome sequencing remains an attractive alternative to explore.

30 day predicted outcome in undifferentiated chest pain: multicenter validation of the HEART score in Tunisian population.

BACKGROUND: Chest pain remains one of the most challenging serious complaints in the emergency department (ED). A prompt and accurate risk stratification tool for chest pain patients is paramount to help physcian effectively progrnosticate outcomes. HEART score is considered one of the best scores for chest pain risk stratification. However, most validation studies of HEART score were not performed in populations different from those included in the original one. OBJECTIVE: To validate HEART score as a prognostication tool, among Tunisian ED patients with undifferentiated chest pain. METHODS: Our prospective, multicenter study enrolled adult patients presenting with chest pain at chest pain units. Patients over 30 years of age with a primary complaint of chest pain were enrolled. HEART score was calculated for every patient. The primary outcome was major cardiovascular events (MACE) occurrence, including all-cause mortality, non-fatal myocardial infarction (MI), and coronary revascularisation over 30 days following the ED visit. The discriminative power of HEART score was evaluated by the area under the ROC curve. A calibration analysis of the HEART score in this population was performed using Hosmer-Lemeshow goodness of test. RESULTS: We enrolled 3880 patients (age 56.3; 59.5% males). The application of HEART score showed that most patients were in intermediate risk category (55.3%). Within 30 days of ED visit, MACE were reported in 628 (16.2%) patients, with an incidence of 1.2% in the low risk group, 10.8% in the intermediate risk group and 62.4% in the high risk group. The area under receiver operating characteristic curve was 0.87 (95% CI 0.85-0.88). HEART score was not well calibrated (χ2 statistic = 12.34; p = 0.03). CONCLUSION: HEART score showed a good discrimination performance in predicting MACE occurrence at 30 days for Tunisian patients with undifferentiated acute chest pain. Heart score was not well calibrated in our population.

Genetic features of the poxtA linezolid resistance gene in human enterococci from France.

OBJECTIVES: To describe the prevalence of poxtA among clinical linezolid-resistant enterococci (LRE) collected in France from 2016 to 2020 and to extensively characterize its genetic supports and environments. METHODS: All LRE clinical isolates received at the National Reference Centre for Enterococci from French hospitals between 2016 and 2020 were included. LRE isolates were screened for linezolid resistance genes (cfr-like, optrA and poxtA) by real-time PCR and phenotypically characterized. A collection of 11 representative poxtA-positive isolates (10 Enterococcus faecium and 1 Enterococcus faecalis) underwent WGS by hybrid assembly combining short-read (Illumina MiSeq) and long-read (MinION) approaches. Transferability of poxtA was attempted by filter-mating experiments. RESULTS: Out of 466 LRE received at the National Reference Centre for Enterococci over the period, 47 (10.1%) were poxtA-positive, including 42 E. faecium. The 11 isolates characterized by WGS were confirmed to be epidemiologically unrelated by core genome analysis and eight different STs were assigned to E. faecium isolates. The poxtA gene was found to be plasmid carried and flanked by IS1216E transposase genes in all isolates and frequently linked with fexB, tet(M) and tet(L). A total of seven distinct poxtA-harbouring plasmids were obtained after hybrid assembly and plasmid transfer of poxtA was successful in three cases. For the two poxtA/optrA-positive isolates, those genes were carried by different plasmids. CONCLUSIONS: The poxtA gene has been circulating among clinical enterococci in France since at least 2016, mostly in E. faecium and independently from optrA. The poxtA-carrying plasmids often co-carried resistance genes to phenicols and tetracyclines, and could have been co-selected through their veterinary use.

Avrilella dinanensis gen. nov., sp. nov., a novel bacterium of the family Flavobacteriaceae isolated from human blood.

Polyphasic taxonomic analysis was performed on a novel bacterium, designated UR159T, isolated in 2016 from human blood of a septic patient hospitalized in France. Preliminary 16S rRNA gene sequence-based phylogenetic analysis indicated that strain UR159T belonged to the family Flavobacteriaceae, forming a distinct phyletic line distantly related (<94% sequence similarity) to known species of the family. Further phenotypic, chemotaxonomic and genomic analyses were performed. Cells were non-motile, oxidase-negative, catalase-positive Gram-negative rods. It was strictly aerobic yielding yellow-pigmented colonies, and was metabolically rather inert. Major fatty acids were iso-branched fatty acids, predominantly iso-C15:0 (55.5%) and iso-C17:1ω9c (8.8%). Whole genome sequencing revealed a 2.3-Mbp genome encoding a total of 2262 putative genes with a genomic DNA G+C content at 37.6mol%. The average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) values between strain UR159T and the most closely related members of the Flavobacteriaceae family were <75% and <39%, respectively, much below the established cut-offs for ANI (<95-96%) and isDDH (<70%) for species and genus delineation. Average Amino Acid Identity (AAI) percentages were also estimated and were lower than 65% (cut-off proposed for genus delineation for uncultivated prokaryotes) in all cases, except for F. marinum that was just at the limit (65.1%). Based on these findings, we propose it as a new genus and species, Avrilella dinanensis gen. nov., sp. nov. (type strain UR159T=CIP 111616T=DSM 105483T).

Metagenomic Characterization of Indoor Dust Bacterial and Fungal Microbiota in Homes of Asthma and Non-asthma Patients Using Next Generation Sequencing.

BACKGROUND: The exposure of house occupants to indoor air pollutants has increased in recent decades. Among microbiological contaminants, bacterial and fungal aerosols remain poorly studied and the debate on the impact of these aerosols on respiratory health is still open. This study aimed to assess the diversity of indoor microbial communities in relationship with the health of occupants. METHODS: Measurements were taken from dwellings of 2 cohorts in Brittany (France), one with children without any pathology and the other with children and adults with asthma. Thirty dust samples were analyzed by next generation sequencing with a 16S and 18S targeted metagenomics approach. Analysis of sequencing data was performed using qiime 2, and univariate and multivariate statistical analysis using R software and phyloseq package. RESULTS: A total of 2,637 prokaryotic (589 at genus level) and 2,153 eukaryotic taxa were identified (856 fungal taxa (39%) and 573 metazoa (26%)). The four main bacterial phyla were identified: Proteobacteria (53%), Firmicutes (27%), Actinobacteria (11%), Bacteroidetes (8%). Among Fungi, only 136 taxa were identified at genus level. Three main fungal phyla were identified: Ascomycota (84%), Basidiomycota (12%) and Mucoromycota (3%). No bacterial nor fungal phyla were significantly associated with asthma versus control group. A significant over representation in control group versus asthma was observed for Christensenellaceae family (p-value = 0.0015, adj. p-value = 0.033). Besides, a trend for over representation in control group was observed with Dermabacteraceae family (p-value = 0.0002, adj. p-value = 0.815). CONCLUSIONS: Our findings provide evidence that dust samples harbor a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples, a less easy strategy for the detection of eukaryotes at least using18S metagenomics approach. This study showed that the detection of some bacteria might be associated to indoor air of asthmatic patients. Regarding fungi, a higher number of samples and sequencing with more depth could allow reaching significant signatures.

Cross-reactivity between tumor MHC class I-restricted antigens and an enterococcal bacteriophage.

Intestinal microbiota have been proposed to induce commensal-specific memory T cells that cross-react with tumor-associated antigens. We identified major histocompatibility complex (MHC) class I-binding epitopes in the tail length tape measure protein (TMP) of a prophage found in the genome of the bacteriophage Enterococcus hirae Mice bearing E. hirae harboring this prophage mounted a TMP-specific H-2Kb-restricted CD8+ T lymphocyte response upon immunotherapy with cyclophosphamide or anti-PD-1 antibodies. Administration of bacterial strains engineered to express the TMP epitope improved immunotherapy in mice. In renal and lung cancer patients, the presence of the enterococcal prophage in stools and expression of a TMP-cross-reactive antigen by tumors correlated with long-term benefit of PD-1 blockade therapy. In melanoma patients, T cell clones recognizing naturally processed cancer antigens that are cross-reactive with microbial peptides were detected.

Molecular and functional analysis of the novel cfr(D) linezolid resistance gene identified in Enterococcus faecium.

OBJECTIVES: To characterize the novel cfr(D) gene identified in an Enterococcus faecium clinical isolate (15-307.1) collected from France. METHODS: The genome of 15-307.1 was entirely sequenced using a hybrid approach combining short-read (MiSeq, Illumina) and long-read (GridION, Oxford Nanopore Technologies) technologies in order to analyse in detail the genetic support and environment of cfr(D). Transfer of linezolid resistance from 15-307.1 to E. faecium BM4107 was attempted by filter-mating experiments. The recombinant plasmid pAT29Ωcfr(D), containing cfr(D) and its own promoter, was transferred to E. faecium HM1070, Enterococcus faecalis JH2-2 and Escherichia coli AG100A. RESULTS: As previously reported, 15-307.1 belonged to ST17 and was phenotypically resistant to linezolid (MIC, 16 mg/L), vancomycin and teicoplanin. A hybrid sequencing approach confirmed the presence of several resistance genes including vanA, optrA and cfr(D). Located on a 103 kb plasmid, cfr(D) encoded a 357 amino acid protein, which shared 64%, 64%, 48% and 51% amino acid identity with Cfr, Cfr(B), Cfr(C) and Cfr(E), respectively. Both optrA and cfr(D) were successfully co-transferred to E. faecium BM4107. When expressed in E. faecium HM1070 and E. faecalis JH2-2, pAT29Ωcfr(D) did not confer any resistance, whereas it was responsible for an expected PhLOPSA resistance phenotype in E. coli AG100A. Analysis of the genetic environment of cfr(D) showed multiple IS1216 elements, putatively involved in its mobilization. CONCLUSIONS: Cfr(D) is a novel member of the family of 23S rRNA methyltransferases. While only conferring a PhLOPSA resistance phenotype when expressed in E. coli, enterococci could constitute an unknown reservoir of cfr(D).

Adsorption behavior of cationic and anionic dyes on magadiite-chitosan composite beads.

In this paper, the composite beads were obtained by the encapsulation of a lamellar polysilicate magadiite in chitosan. The composite beads were tested as adsorbents for the removal of anionic Congo red (CR) and cationic methylene blue (MB) dyes. The obtained material was characterized by different methods such as XRD, SEM, TGA and zeta potential analysis. The adsorption mechanism of both dyes was supported by UV-vis and (FTIR) spectroscopy. The results reveal that the magadiite was immobilized in the chitosan matrix by hydrogen bond and electrostatic interactions. The influence of contact time, adsorbent dose and initial concentration of dye were investigated. The adsorption kinetics of CR onto composite beads followed the linear form of pseudo-second-order model and their equilibrium data were fitted well to the linear Langmuir model as confirmed by the calculated values of R2, RMSE and SD. The adsorbed quantity registered for CR and MB dyes are 135.77 and 45.25 mg/g, respectively.

Analysis of the CodY RNome reveals RsaD as a stress-responsive riboregulator of overflow metabolism in Staphylococcus aureus.

In Staphylococcus aureus, the transcription factor CodY modulates the expression of hundreds of genes, including most virulence factors, in response to the availability of key nutrients like GTP and branched-chain amino acids. Despite numerous studies examining how CodY controls gene expression directly or indirectly, virtually nothing is known about the extent to which CodY exerts its effect through small regulatory RNAs (sRNAs). Herein, we report the first set of sRNAs under the control of CodY. We reveal that staphylococcal sRNA RsaD is overexpressed >20-fold in a CodY-deficient strain in three S. aureus clinical isolates and in S. epidermidis. We validated the CodY-dependent regulation of rsaD and demonstrated that CodY directly represses rsaD expression by binding the promoter. Using a combination of molecular techniques, we show that RsaD posttranscriptionally regulates alsS (acetolactate synthase) mRNA and enzyme levels. We further show that RsaD redirects carbon overflow metabolism, contributing to stationary phase cell death during exposure to weak acid stress. Taken together, our data delineate a role for CodY in controlling sRNA expression in a major human pathogen and indicate that RsaD may integrate nutrient depletion and other signals to mount a response to physiological stress experienced by S. aureus in diverse environments.

Alginate-whey an effective and green adsorbent for crystal violet removal: Kinetic, thermodynamic and mechanism studies.

In this study, a novel biocomposite beads is developed by gelling sodium alginate (ALG) solutions in acid whey (Aw). The formation of alginate-whey biocomposite (ALG-Aw) was confirmed by FTIR analysis where the corresponding spectrum showed the presence of characteristic absorption bands of both ALG and Aw. SEM analysis showed the presence of lactic bacteria immobilized in the alginate matrix leading to the formation of new porous structure. The adsorption properties of adsorbents were evaluated in crystal violet dye (CV) removal from aqueous solutions using a batch adsorption technique. The results showed that the maximum adsorption occurred at pH 6 and for an adsorbent dose of 0.4 g/L. The kinetic of CV removal onto ALG-Aw adsorbent can be described well by the pseudo-second order equation. The equilibrium adsorption data of ALG-Aw followed well the Redlich-Peterson isotherm which is coherent with the calculated R2, χ2 and ARE values. Calculated thermodynamic parameters such as Gibbs free energy (ΔG°), enthalpy (ΔH°), and entropy (ΔS°) shown that adsorption reaction is spontaneous and it is favored at low temperatures. Interactions of CV dye molecules with ALG-Aw composite beads were examined by FTIR and UV-visible DR spectroscopy.

Rapid genetic and phenotypic changes in Pseudomonas aeruginosa clinical strains during ventilator-associated pneumonia.

Treatment with antibiotics leads to the selection of isolates with increased resistance. We investigated if evolution towards resistance was associated with virulence changes, in the context of P. aeruginosa ventilator-associated pneumonia (VAP). Four patients were selected because they had multiple VAP episodes during short periods (12 days to 5 weeks), with emergence of resistance. We performed whole-genome sequencing of 12 P. aeruginosa from bronchoalveolar lavages or blood culture (3 isolates per patient). Production of quorum sensing-dependent virulence factors, serum resistance, cytotoxicity against A549 cells, biofilm production, and twitching motility were studied. Each patient was infected with a unique strain. For all patients, resistance development was explained by genetic events in ampD, mexR or oprD. Additional variations were detected in virulence- and/or fitness-associated genes (algB, gacA, groEL, lasR, mpl, pilE, pilM, rhlR) depending on the strain. We noticed a convergence towards quorum sensing deficiency, correlated with a decrease of pyocyanin and protease production, survival in serum, twitching motility and cytotoxicity. In one patient, changes in pilM and pilE were related to enhanced twitching. We show that the emergence of resistance in P. aeruginosa is associated with virulence modification, even in acute infections. The consequences of this short-term pathoadaptation need to be explored.

Emergence of optrA-mediated linezolid resistance in enterococci from France, 2006-16.

OBJECTIVES: To describe the epidemiological trend of linezolid-resistant enterococci (LRE) collected in France from 2006 to 2016 and to extensively characterize LRE isolates. METHODS: The National Reference Center for Enterococci (NRC-Enc) received enterococcal isolates suspected to be VRE and/or LRE from all French hospitals between 2006 and 2016. LRE isolates were phenotypically characterized and their genomes were entirely sequenced by Miseq (Illumina). Transfer of linezolid resistance was attempted by filter mating experiments. RESULTS: Out of 3974 clinical isolates of enterococci received at the NRC-Enc over the period, 9 (0.2%) were LRE (MICs 8 to >32 mg/L), including 6 Enterococcus faecium and 3 Enterococcus faecalis. This overall prevalence significantly increased over the study period, reaching 0.8% in 2016. The five LRE isolated before 2016 were vanA-positive E. faecium whereas strains isolated in 2016 (one E. faecium and three E. faecalis) were susceptible to vancomycin. None of these isolates was part of an outbreak, while E. faecium strains were assigned to four different STs [17 (1), 80 (3), 412 (1) and 650 (1)] and all three E. faecalis belonged to ST480. Except for the strain isolated in 2010, all LRE were positive for optrA, which was located on plasmids (5/8) or in the chromosome (3/8). Plasmid transfer of optrA was successful in three cases. CONCLUSIONS: There has been a significant increase in the prevalence of LRE in France over time; this is due to the spread of optrA among E. faecium and E. faecalis human clinical isolates (VRE or not).

CuNPs-magadiite/chitosan nanocomposite beads as advanced antibacterial agent: Synthetic path and characterization.

In this work, an inorganic-organic nanocomposite was prepared by combining copper exchanged-magadiite (Cu-magadiite) with chitosan. The synthesis was carried out by direct dispersion of the Cu-magadiite in the chitosan matrix. The mixture obtained is shaped into beads with an average diameter of about 1-1.2 mm. These beads were then contacted with a solution of NaBH4 in order to reduce loaded copper ions into copper nanoparticles species. The resulting nanocomposite (Cu-NPs-magadiite/chitosan) was characterized by XRD, FTIR, SEM, TG, UV-visible DR and EDX analysis. The results show that the magadiite was completely exfoliated confirming the formation of the organic-inorganic composite. Indeed, the encapsulation of magadiite was confirmed by the SEM images, which is presented as micron free aggregates included in the cavities of a continuous polysaccharide matrix. Otherwise, they confirm also the formation of CuNPs which are probably immobilized inside the magadiite-chitosan solid matrix. The antibacterial activity against E. coli and S. aureus was highlighted by the disc inhibition method and the minimum inhibitory concentration (MIC) was determined. The CuNPs-magadiite/chitosan nanocomposite showed a very efficient bactericidal effect against both pathogen bacteria. Additionally, the MIC values obtained for nanocomposite are of 0.25 µg/L against S. aureus and of 0.50 µg/L against E. coli.