Non contiguous-finished genome sequence and description of Bacillus timonensis sp. nov.

Bacillus timonensis strain MM10403188(T) sp. nov. is the type strain of a proposed new species within the genus Bacillus. This strain, whose genome is described here, was isolated from the fecal flora of a healthy patient. B. timonensis is an aerobic Gram-negative rod shaped bacterium. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,632,049 bp long genome (1 chromosome but no plasmid) contains 4,610 protein-coding and 74 RNA genes, including 5 rRNA genes

Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis

BackgroundNon-alcoholic steatohepatitis (NASH) has become a major public health issue as one of the leading causes of liver disease and transplantation worldwide. The instrumental role of the gut microbiota is emerging but still under investigation. Endogenous ethanol (EtOH) production by gut bacteria and yeasts is an emerging putative mechanism. Microbial metagenomics and culture studies targeting enterobacteria or yeasts have been reported, but no culturomics studies have been conducted so far.AimTo assess fecal EtOH and other biochemical parameters, characterize NASH-associated dysbiosis and identify EtOH-producing gut microbes associated with the disease, fecal samples from 41 NASH patients and 24 controls were analyzed. High-performance liquid chromatography (HPLC) was used for EtOH, glucose, total proteins, triglyceride and total cholesterol. Viable bacteria were assessed with microbial culturomics. Microbial genetic material was assessed using 16S metagenomics targeting the hypervariable V3V4 region.ResultsFecal EtOH and glucose was elevated in the stools of NASH patients (p < 0.05) but not triglyceride, total cholesterol or proteins. In culturomics, EtOH-producing Enterocloster bolteae and Limosilactobacillus fermentum were enriched in NASH. V3V4 16S rRNA amplicon sequencing confirmed the enrichment in EtOH-producing bacteria including L. fermentum, Mediterraneibacter gnavus and Streptococcus mutans, species previously associated with NASH and other dysbiosis-associated diseases. Strikingly, E. bolteae was identified only by culturomics. The well-known Lacticaseibacillus casei was identified in controls but never isolated in patients with NASH (p < 0.05).ConclusionElevated fecal EtOH and glucose is a feature of NASH. Several different EtOH-producing gut bacteria may play an instrumental role in the disease. Culturomics and metagenomics, two complementary methods, will be critical to identify EtOH-producing bacteria for future diagnostic markers and therapeutic targets for NASH. Suppression of EtOH-producing gut microbes and L. casei administration are options to be tested in NASH treatment

Outcomes of 3,737 COVID-19 patients treated with hydroxychloroquine/azithromycin and other regimens in Marseille, France: A retrospective analysis

Background: In our institute in Marseille, France, we initiated early and massive screening for coronavirus disease 2019 (COVID-19). Hospitalization and early treatment with hydroxychloroquine and azithromycin (HCQ-AZ) was proposed for the positive cases. Methods: We retrospectively report the clinical management of 3,737 screened patients, including 3,119 (83.5%) treated with HCQ-AZ (200 mg of oral HCQ, three times daily for ten days and 500 mg of oral AZ on day 1 followed by 250 mg daily for the next four days, respectively) for at least three days and 618 (16.5%) patients treated with other regimen (“others”). Outcomes were death, transfer to the intensive care unit (ICU), ≥ 10 days of hospitalization and viral shedding. Results: The patients’ mean age was 45 (sd 17) years, 45% were male, and the case fatality rate was 0.9%. We performed 2,065 low-dose computed tomography (CT) scans highlighting lung lesions in 592 of the 991 (59.7%) patients with minimal clinical symptoms (NEWS score = 0). A discrepancy between spontaneous dyspnoea, hypoxemia and lung lesions was observed. Clinical factors (age, comorbidities, NEWS-2 score), biological factors (lymphocytopenia; eosinopenia; decrease in blood zinc; and increase in D-dimers, lactate dehydrogenase, creatinine phosphokinase, and C-reactive protein) and moderate and severe lesions detected in low-dose CT scans were associated with poor clinical outcome. Treatment with HCQ-AZ was associated with a decreased risk of transfer to ICU or death (Hazard ratio (HR) 0.18 0.11- 0.27), decreased risk of hospitalization ≥10 days (odds ratios 95% CI 0.38 0.27-0.54) and shorter duration of viral shedding (time to negative PCR: HR 1.29 1.17-1.42). QTc prolongation (>60 ms) was observed in 25 patients (0.67%) leading to the cessation of treatment in 12 cases including 3 cases with QTc> 500ms. No cases of torsade de pointe or sudden death were observed. Conclusion Although this is a retrospective analysis, results suggest that early diagnosis, early isolation and early treatment of COVID-19 patients, with at least 3 days of HCQ-AZ lead to a significantly better clinical outcome and a faster viral load reduction than other treatments

Trials

BACKGROUND: The aim of this open-label, randomized controlled trial conducted in four African countries (Madagascar, Niger, Central African Republic, and Senegal) is to compare three strategies of renutrition for moderate acute malnutrition (MAM) in children based on modulation of the gut microbiota with enriched flours alone, enriched flours with prebiotics or enriched flours coupled with antibiotic treatment. METHODS: To be included, children aged between 6 months and 2 years are preselected based on mid-upper-arm circumference (MUAC) and are included based on a weight-for-height Z-score (WHZ) between - 3 and - 2 standard deviations (SD). As per current protocols, children receive renutrition treatment for 12 weeks and are assessed weekly to determine improvement. The primary endpoint is recovery, defined by a WHZ >/= - 1.5 SD after 12 weeks of treatment. Data collected include clinical and socioeconomic characteristics, side effects, compliance and tolerance to interventions. Metagenomic analysis of gut microbiota is conducted at inclusion, 3 months, and 6 months. The cognitive development of children is evaluated in Senegal using only the Developmental Milestones Checklist II (DMC II) questionnaire at inclusion and at 3, 6, and 9 months. The data will be correlated with renutrition efficacy and metagenomic data. DISCUSSION: This study will provide new insights for the treatment of MAM, as well as original data on the modulation of gut microbiota during the renutrition process to support (or not) the microbiota hypothesis of malnutrition. TRIAL REGISTRATION: ClinicalTrials.gov, ID: NCT03474276 Last update 28 May 2018

Caractérisation des altérations du microbiote digestif associées à l'obésité et rôle de la manipulation du microbiote digestif dans l'obésité

L'avènement des méthodes de séquençage moléculaire à large échelle a permis l'identification d'altérations du microbiote digestif spécifiquement associés à l'obésité notamment un ratio Bacteroidetes/Firmicutes diminué chez les obèses. Depuis, de nombreux travaux ont décrit de nouvelles altérations associées à l'obésité, notamment une augmentation des représentants du genre Lactobacillus mais l'ensemble de ces résultats sont souvent l'objet de controverses. Afin de clarifier si le genre Lactobacillus était associé à l'obésité, nous avons réalisé deux études cas témoins (la deuxième étant le prolongement de la première avec un effectif de 263 individus) qui nous ont permis d'identifier que les altérations du microbiote digestif sont plus reproductibles au niveau de l'espèce. A ce titre nous avons retrouvé une plus grande concentration de Lactobacillus reuteri dans le microbiote digestif de sujets obèses alors que les concentrations de Bifidobacterium animalis, Methanobrevibacter smithii et Escherichia coli étaient diminuées. Nous avons pu établir une relation dose-dépendante entre la concentration de Lactobacillus reuteri et l'indice de masse corporelle. Par ailleurs, nous avons réalisé une méta-analyse sur les résultats des études publiées et avons retrouvé une association entre les genres Bifidobacterium (6 études, 348 individus) et Methanobrevibacter (3 études, 195 individus) avec l'absence d'obésité (…)The revolution of large scale molecular sequencing methods allowed the identification of specific alterations in the gut microbiota associated with obesity such as a decreased Bacteroidetes / Firmicutes ratio in obese individuals. Since then, many studies have described different alterations associated with obesity, including an increase in members of the Lactobacillus genus, but results are often controversial. To clarify whether the genus Lactobacillus was associated with obesity, we conducted two case-control studies (the second being the follow-up of the first study with a total of 263 individuals) allowing us to understand that gut microbiota alterations are more reproducible at the species level. We found a greater concentration of Lactobacillus reuteri in the gut microbiota of obese while concentrations of Bifidobacterium animalis, Methanobrevibacter smithii and Escherichia coli were reduced. We were able to establish a dose-dependent relationship between the concentration of Lactobacillus reuteri and body mass index. In addition, we performed a meta-analysis on the results of published studies and we found an association between the Bifidobacterium (6 studies, 348 individuals) and Methanobrevibacter (3 studies, 195 individuals) with absence of obesity. (…

Association de taux élévés d'anticorps anticardiolipine IgG avec l'évolution vers une endocardite dans la fièvre Q aiguë

AIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocSudocFranceF

Suivi à long terme des endocardites de la fièvre Q (Identification de facteurs pronostiques sur la mortalité, le traitement chirurgical, la guérison et la récidive sérologique)

AIX-MARSEILLE2-BU Méd/Odontol. (130552103) / SudocSudocFranceF