MLVA Subtyping of Genovar E Chlamydia trachomatis Individualizes the Swedish Variant and Anorectal Isolates from Men who Have Sex with Men

This study describes a new multilocus variable number tandem-repeat (VNTR) analysis (MLVA) typing system for the discrimination of Chlamydia trachomatis genovar D to K isolates or specimens. We focused our MLVA scheme on genovar E which predominates in most populations worldwide. This system does not require culture and therefore can be performed directly on DNA extracted from positive clinical specimens. Our method was based on GeneScan analysis of five VNTR loci labelled with fluorescent dyes by multiplex PCR and capillary electrophoresis. This MLVA, called MLVA-5, was applied to a collection of 220 genovar E and 94 non-E genovar C. trachomatis isolates and specimens obtained from 251 patients and resulted in 38 MLVA-5 types. The genetic stability of the MLVA-5 scheme was assessed for results obtained both in vitro by serial passage culturing and in vivo using concomitant and sequential isolates and specimens. All anorectal genovar E isolates from men who have sex with men exhibited the same MLVA-5 type, suggesting clonal spread. In the same way, we confirmed the clonal origin of the Swedish new variant of C. trachomatis. The MLVA-5 assay was compared to three other molecular typing methods, ompA gene sequencing, multilocus sequence typing (MLST) and a previous MLVA method called MLVA-3, on 43 genovar E isolates. The discriminatory index was 0.913 for MLVA-5, 0.860 for MLST and 0.622 for MLVA-3. Among all of these genotyping methods, MLVA-5 displayed the highest discriminatory power and does not require a time-consuming sequencing step. The results indicate that MLVA-5 enables high-resolution molecular epidemiological characterisation of C. trachomatis genovars D to K infections directly from specimens

Impairment of gut microbial biotin metabolism and host biotin status in severe obesity: effect of biotin and prebiotic supplementation on improved metabolism

Objectives Gut microbiota is a key component in obesity and type 2 diabetes, yet mechanisms and metabolites central to this interaction remain unclear. We examined the human gut microbiome\u27s functional composition in healthy metabolic state and the most severe states of obesity and type 2 diabetes within the MetaCardis cohort. We focused on the role of B vitamins and B7/B8 biotin for regulation of host metabolic state, as these vitamins influence both microbial function and host metabolism and inflammation. Design We performed metagenomic analyses in 1545 subjects from the MetaCardis cohorts and different murine experiments, including germ-free and antibiotic treated animals, faecal microbiota transfer, bariatric surgery and supplementation with biotin and prebiotics in mice. Results Severe obesity is associated with an absolute deficiency in bacterial biotin producers and transporters, whose abundances correlate with host metabolic and inflammatory phenotypes. We found suboptimal circulating biotin levels in severe obesity and altered expression of biotin-associated genes in human adipose tissue. In mice, the absence or depletion of gut microbiota by antibiotics confirmed the microbial contribution to host biotin levels. Bariatric surgery, which improves metabolism and inflammation, associates with increased bacterial biotin producers and improved host systemic biotin in humans and mice. Finally, supplementing high-fat diet-fed mice with fructo-oligosaccharides and biotin improves not only the microbiome diversity, but also the potential of bacterial production of biotin and B vitamins, while limiting weight gain and glycaemic deterioration. Conclusion Strategies combining biotin and prebiotic supplementation could help prevent the deterioration of metabolic states in severe obesity

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network

Using the Cap Analysis of Gene Expression (CAGE) technology, the FANTOM5 consortium provided one of the most comprehensive maps of transcription start sites (TSSs) in several species. Strikingly, ~72% of them could not be assigned to a specific gene and initiate at unconventional regions, outside promoters or enhancers. Here, we probe these unassigned TSSs and show that, in all species studied, a significant fraction of CAGE peaks initiate at microsatellites, also called short tandem repeats (STRs). To confirm this transcription, we develop Cap Trap RNA-seq, a technology which combines cap trapping and long read MinION sequencing. We train sequence-based deep learning models able to predict CAGE signal at STRs with high accuracy. These models unveil the importance of STR surrounding sequences not only to distinguish STR classes, but also to predict the level of transcription initiation. Importantly, genetic variants linked to human diseases are preferentially found at STRs with high transcription initiation level, supporting the biological and clinical relevance of transcription initiation at STRs. Together, our results extend the repertoire of non-coding transcription associated with DNA tandem repeats and complexify STR polymorphism

Impact du choix de la méthode de prise en soin du pied bot varus équin sur l’acquisition du développement moteur de l’enfant : proposition de protocole

Conservative methods are the gold standard for clubfoot treatment with either the Ponseti method or the functional method. Some parents and physical therapists express concern about Ponseti method affect on child’s motor development due to greater immobilization and lesser stimulation than functional method. The purpose of this study is to evaluate link between choice of treatment method and development of gross motor function in the management of clubfoot. Method : a non-systematic review following PRISMA guidelines was conducted across PubMed, Cochrane and PEDRO databases. Results : a total of 2 studies were included. Comparison between the two methods concerning acquisition of gross motor development is studied. Limits of these studies, warrant a research protocol on effect of treatment method’s choice on the acquisition of gross motor milestones from birth to 6 years in clubfoot disorder. Discussion : current literature show differences between the treatment methods when assessing motor development at different ages. These studies are heterogeneous, few in number and without real conclusions. Our study is the first to follow motor development from birth to 6 years by comparing the two treatment methods. It could provide further answers.Les méthodes conservatrices (méthode Ponseti, méthode fonctionnelle) constituent la référence pour le traitement du pied bot. Certains parents et kinésithérapeutes s'inquiètent de l'impact de la méthode Ponseti sur le développement moteur de l'enfant en raison d'une plus grande immobilisation et d'une moindre stimulation que la méthode fonctionnelle. L'objectif de cette étude est d'évaluer le lien entre le choix de la méthode de traitement et le développement moteur dans le traitement du pied bot. Méthode : une revue non systématique suivant les lignes directrices PRISMA a été menée en utilisant les bases de données PubMed, Cochrane et Pedro. Résultats : 2 études sur la comparaison entre les méthodes concernant l'acquisition du développement moteur ont été incluses. Les limites de ces études justifient un protocole de recherche sur l'effet du choix de la méthode de traitement du pied bot sur l'acquisition du développement moteur de la naissance à 6 ans. Discussion : la littérature actuelle montre des différences entre les méthodes lors de l'évaluation du développement moteur à différents âges. Ces études sont hétérogènes, peu nombreuses et sans réelles conclusions. Notre étude est la première à suivre le développement moteur de 0 à 6 ans en comparant les deux méthodes de traitement. Elle pourrait apporter des éléments de réponse complémentaires

Evaluation of two commercial real-time PCR assays for detection of <em>Mycoplasma genitalium</em> in urogenital specimens

International audienceThe performance of two commercial real-time PCR kits for the detection of Mycoplasma genitalium was evaluated in comparison to an in-house real-time PCR assay. Concordances of 96% and 93% were found for the TIB MOLBIOL and the Diagenode assays, respectively, compared to the results of the in-house assay

Cloning the Mycoplasma hominis PG21 Genome in <em>Saccharomyces cerevisiae</em> as a Yeast Centromeric Plasmid

International audienc

Molecular Typing Reveals Distinct Mycoplasma genitalium Transmission Networks among a Cohort of Men Who Have Sex with Men and a Cohort of Women in France

Mycoplasma genitalium causes sexually transmitted infecti.ons in men and women. Treatment failures to macrolides and fluoroquinolones have been reported worldwide. Although the mgpB typing method has often been used in M. genitalium-infected men who have sex with men (MSM), limited typing data are available for M. genitalium-infected women. In this study, we aimed to investigate the genetic relationship between M. genitalium strains and their antibiotic resistance profile in a cohort of MSM (86.2% on HIV preexposure prophylaxis [PrEP], 13.8% HIV positive) and a large cohort of women using mgpB/MG309 typing. The mgpB types were determined in 374 samples from 305 women and 65 MSM. Three MSM and one woman had two concurrent or subsequent samples. Macrolide and fluoroquinolone resistance-associated mutations were searched in the 23S rRNA as well as parC and gyrA genes. The mgpB phylogenetic construction revealed three large clusters that differed according to sexual practices and geographical origin of patients. The prevalence of macrolide and fluoroquinolone resistance was significantly higher in MSM compared with women (95.4% vs. 14.1% and 30.6% vs. 7.2%, p &lt; 0.001, respectively). The macrolide resistance spread was polyclonal in both populations, but clonal diffusion of two dual-resistant types was observed in PrEP users in association with high antibiotic pressure and dense connectivity in this population