A5048908344- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Bacterial Identification and Susceptibility Testing
- Antifungal resistance and susceptibility
- Antibiotic Resistance in Bacteria
- Probiotics and Fermented Foods
- Microbial Community Ecology and Physiology
- Enterobacteriaceae and Cronobacter Research
- Cystic Fibrosis Research Advances
- Parasitic Infections and Diagnostics
- Bacteriophages and microbial interactions
- Mycobacterium research and diagnosis
- Fungal Infections and Studies
- Plant Pathogens and Fungal Diseases
- Infective Endocarditis Diagnosis and Management
- Parasites and Host Interactions
- Amoebic Infections and Treatments
- Plant Pathogenic Bacteria Studies
- Infections and bacterial resistance
- Identification and Quantification in Food
- Mosquito-borne diseases and control
- Microbial Metabolism and Applications
- Antimicrobial Resistance in Staphylococcus
- Molecular Biology Techniques and Applications
- Parasitic Diseases Research and Treatment
Méditerranée Infection Foundation
2016-2025
Aix-Marseille Université
2016-2025
Assistance Publique Hôpitaux de Marseille
2019-2025
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes
2010-2024
Inserm
2012-2024
Centre National de la Recherche Scientifique
2009-2024
Institut de Recherche pour le Développement
2015-2024
Centre de Recherche en Cancérologie de Marseille
2017
Cheikh Anta Diop University
2016
Institut de Neurobiologie de la Méditerranée
2008
Abstract Metagenomics revolutionized the understanding of relations among human microbiome, health and diseases, but generated a countless number sequences that have not been assigned to known microorganism 1 . The pure culture prokaryotes, neglected in recent decades, remains essential elucidating role these organisms 2 We recently introduced microbial culturomics, culturing approach uses multiple conditions matrix-assisted laser desorption/ionization–time flight 16S rRNA for identification...
Background There is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts cystic fibrosis (CF) patients. Methodology/Principal Findings Standard microbiological culture and phenotypic identification sputa from CF patients have been compared to molecular by use 16S rDNA amplification, cloning sequencing. Twenty-five were cultured yield 33 isolates (13 species) known be pathogens during CF. For cloning, 760 clones sequenced...
Staphylococcus aureus is a major human pathogen responsible for variety of nosocomial and community-acquired infections. Recent reports show that the prevalence Methicillin-Resistant S. (MRSA) infections in cystic fibrosis (CF) patients increasing. In 2006 Marseille, France, we have detected an atypical MRSA strain with specific antibiotic susceptibility profile unique growth phenotype. Because clinical importance spread such among CF decided to sequence genome one representative isolate...
Abstract Herein, the mycobiota was characterized in fecal samples from sick patients and healthy subjects, collected different geographical locations using both culturomics amplicon-based metagenomics approaches. Using approach, a total of 17,800 fungal colonies were isolated 14 samples, resulted isolation 41 species, which 10 species had not been previously reported human gut. Deep sequencing fungal-directed ITS1 ITS2 amplicons led to detection 142 OTUs 173 regions, respectively. Ascomycota...
Background Microbial eukaryotes represent an important component of the human gut microbiome, with different beneficial or harmful roles; some species are commensal mutualistic, whereas others opportunistic parasitic. The diversity inhabiting humans remains relatively unexplored because either low abundance these organisms in they have received limited attention from a whole-community perspective. Methodology/Principal Finding In this study, single fecal sample healthy African male was...
Blastocystis is the most common protozoan colonizing gut of vertebrates. It modulates human digestive microbiota in absence inflammation and gastrointestinal disease. Although it has been associated with diseases, including inflammatory bowel disease, its pathogenicity remains controversial. This study aimed to assess influence on bacterial communities healthy children. We conducted a cross-sectional 147 Blastocystis-colonized 149 Blastocystis-noncolonized Malian children, colonization...
Wild apes are considered to be the most serious reservoir and source of zoonoses. However, little data available about gut microbiota pathogenic bacteria in gorillas. For this propose, a total 48 fecal samples obtained from 21 Gorilla gorilla individuals (as revealed via microsatellite analysis) were screened for human bacterial pathogens using culturomics molecular techniques. By applying one index specific media supplemented by plants, we tested 12,800 colonies identified 147 different...
Although antifungals are available and usually used against fungal infections, multidrug-resistant (MDR) pathogens a growing problem for public health. Moreover, infections have become more prevalent nowadays due to the increasing number of people living with immunodeficiency. Thus, previously rarely-isolated and/or unidentified species including MDR yeast moulds emerged around world. Recent works indicate that polymyxin antibiotics (polymyxin B colistin) potential antifungal proprieties....
Efficient and easy-to-use DNA extraction purification methods are critical in implementing PCR-based diagnosis of pathogens. In order to optimize the routine clinical laboratory eukaryotic enteric pathogens, we compare, via quantitative PCR cycle threshold (Ct) values, efficiency two kits: semi-automated EZ1® (Qiagen) manual QIAamp® Stool Mini Kit (Qiagen), on six protozoa: Blastocystis spp., Cryptosporidium parvum/hominis, Cyclospora cayetanensis, Dientamoeba fragilis, Giardia intestinalis...
Cystic fibrosis afflicted lungs support the growth of many bacteria rarely implicated in other cases human infections.We report isolation and identification, by 16S rRNA amplification sequencing, two emerging pathogens resistant to colistin, Brevundimonas diminuta Ochrobactrum anthropi, a 17-year-old woman with cystic pneumonia. The patient eventually responded well 2-week regime imipenem tobramycin.Our results clearly re-emphasize emergence new colistin-resistant patients fibrosis.
An increasing body of evidence indicates that nondiphtheria corynebacteria may be responsible for respiratory tract infections. We report an outbreak Corynebacterium pseudodiphtheriticum infection in children with cystic fibrosis (CF). To identify 18 C. strains isolated from 13 French CF, we used molecular methods (partial rpoB gene sequencing) and matrix-assisted laser desorption ionization time-of-flight (MALDI-TOF) mass spectrometry. Clinical symptoms were exhibited by 10 (76.9%),...
The consumption of insects by apes has previously been reported based on direct observations and/or trail signs in feces. However, DNA-based diet analyses may have the potential to reveal trophic links for these wild species. Herein, we analyzed insect-diet diversity 9 feces obtained from three species African great apes, gorilla (Gorilla gorilla), chimpanzee (Pan troglodytes) and bonobo paniscus), using two mitochondrial amplifications arthropods. A total 1056 clones were sequenced Cyt-b...
Background Like other tropical African countries, Gabon is afflicted by many parasitic diseases, including filariases such as loiasis and mansonellosis. This study aimed to assess the prevalence of these two filarial diseases in febrile afebrile children using quantitative real-time PCR standard assays coupled with sequencing. Methodology/Principal Findings DNA from blood specimens 1,418 Gabonese (1,258 160 afebrile) were analyzed. Overall, was detected 95 (6.7%) children, 67 positive for M....
Research on the relationship between changes in gut microbiota and human disease, including AIDS, is a growing field. However, studies eukaryotic component of intestinal have just begun not yet been conducted HIV-infected patients. Moreover, community profiling influenced by use different methodologies at each step culture-independent techniques. Herein, initially, four DNA extraction protocols were compared to test efficiency method recovering from fecal samples. Our results revealed that...
Currently, Candida auris is among the most serious emerging pathogens that can be associated with nosocomial infections and outbreaks in intensive care units. Clinicians must able to identify manage it quickly.Here, we report for first time Algeria seven cases of C. infection or colonisation.The strains were isolated from clinical sites including bronchial aspirates (n = 4), wound swabs 1), urine sample 1) peritoneal fluid patients admitted unit. was identified both by MALDI-TOF sequencing...
The gut microbiota has recently been associated with malaria susceptibility/resistance in animal models and humans. This study aimed to assess its influence on attack Plasmodium parasitemia children living a malaria-endemic area of Mali. Healthy were enrolled 16-month cohort Bandiagara. Their bacteria fungi community structures characterized via 16S ITS metabarcoding at enrolment. Clinicians monitored attacks. Asymptomatic carriage was assessed by real-time polymerase chain reaction. Of the...