Infected breast milk associated with late-onset and recurrent group B streptococcal infection in neonatal twins: a genetic analysis

The original publication is available at www.springerlink.comInternational audienceAsymptomatic excretion of group B streptococcus (GBS) in breast milk may be an underrecognized cause of neonatal and recurrent infection. We report the case of late-onset and recurrent infection in newborn twins resulting from ingestion of maternal breast milk infected with GBS. Genetic analysis of isolates is equally presented

Sacroiliitis secondary to catheter-related bacteremia due to Mycobacterium abscessus (sensu stricto).

International audienceWe describe a case of sacroiliitis secondary to catheter-related bacteremia due to Mycobacterium abscessus (sensu stricto). This case confirms that MultiLocus sequence typing and variable-number tandem-repeat methods are very robust techniques to identify the pathogen species and to validate molecular epidemiological links among complex M. abscessus isolates

Proposal of a quantitative PCR-based protocol for an optimal Pseudomonas aeruginosa detection in patients with cystic fibrosis

BACKGROUND: The lung of patients with cystic fibrosis (CF) is particularly sensitive to Pseudomonas aeruginosa. This bacterium plays an important role in the poor outcome of CF patients. During the disease progress, first acquisition of P. aeruginosa is the key-step in the management of CF patients. Quantitative PCR (qPCR) offers an opportunity to detect earlier the first acquisition of P. aeruginosa by CF patients. Given the lack of a validated protocol, our goal was to find an optimal molecular protocol for detection of P. aeruginosa in CF patients. METHODS: We compared two formerly described qPCR formats in early detection of P. aeruginosa in CF sputum samples: a qPCR targeting oprL gene, and a multiplex PCR targeting gyrB and ecfX genes. RESULTS: Tested in vitro on a large panel of P. aeruginosa isolates and others gram-negative bacilli, oprL qPCR exhibited a better sensitivity (threshold of 10 CFU/mL versus 730 CFU/mL), whereas the gyrB/ecfX qPCR exhibited a better specificity (90% versus 73%). These results were validated ex vivo on 46 CF sputum samples positive for P. aeruginosa in culture. Ex vivo assays revealed that qPCR detected 100 times more bacterial cells than culture-based method did. CONCLUSION: Based on these results, we proposed a reference molecular protocol combining the two qPCRs, which offers a sensitivity of 100% with a threshold of 10 CFU/mL and a specificity of 100%. This combined qPCR-based protocol can be adapted and used for other future prospective studies

Role of mobile genetic elements on the evolution and virulence of Streptococcus agalactiae

Nous avons étudié le rôle des éléments génétiques mobiles (EGM) dans l’évolution et la virulence de Streptococcus agalactiae, bactérie pathogène opportuniste responsable d'infections chez l’homme. La structure génétique de la population a été analysée par multilocus sequence typing à partir d’un souchier représentatif de la diversité de l’espèce. La distribution de 11 EGM (sept séquences d’insertion, trois transposases, un intron) a été confrontée à la structure de la population. Cette confrontation a permis i) de démontrer que l’acquisition des EGM corrélait avec l’évolution de l’espèce, ii) de proposer une hypothèse de la chronologie d’acquisition des EGM, iii) d’identifier certains EGM comme marqueurs de l’écosystème d’origine des souches, et iv) de conforter l’hypothèse de l’émergence du clone humain invasif CC17 à partir d’un ancêtre bovin. Nous avons également cartographié les copies des EGM présentes sur le génome de S. agalactiae, puis nous avons identifié huit nouveaux sites d’insertion, dont deux sont significativement associés à l’origine écologique de la souche.We studied the role of mobile genetic elements (MGE) on the evolution and the virulence of Streptococcus agalactiae, an opportunistic bacterium responsible for human infections. The genetic population structure was analyzed by multilocus sequence typing using a collection representative of the species diversity. The distribution of 11 MGE (seven insertion sequences, three transposases, one intron) was compared to the population structure. We demonstrated that the MGE prevalence strongly correlates with the genetic lineages. We proposed an evolutionary scheme for the acquisition of the MGE. Several MGE appeared to be markers of the origin of the strains. MGE analysis brought evidence for a bovine origin of the human virulent clone CC17. We also identified the position of the MGE copies on the S. agalactiae genome and we identified eight new MGE insertion sites, from which two were significantly associated with the ecological origin of the isolates

Healthy Patients Are Not the Best Controls for Microbiome-Based Clinical Studies: Example of Sjögren’s Syndrome in a Systematic Review

International audienceIntroduction It has been hypothesized that gut and oral dysbiosis may contribute to the development of primary Sjögren’s syndrome (pSS). The aim of this systematic review was to assemble available data regarding the oral and gut microbiota in pSS and to compare them to data from healthy individuals and patients with dry symptoms without a diagnosis of Sjögren’s syndrome or lupus disease to identify dysbiosis and discuss the results. Methodology Using the PRISMA guidelines, we systematically reviewed studies that compared the oral and gut microbiota of Sjögren’s patients and controls. The PubMed database and Google Scholar were searched. Results Two-hundred and eighty-nine studies were found, and 18 studies were included: 13 referred to the oral microbiota, 4 referred to the gut microbiota, and 1 referred to both anatomical sites. The most frequent controls were healthy volunteers and patients with sicca symptoms. The most common analysis method used was 16S-targeted metagenomics. The results were mostly heterogeneous, and the results regarding diversity were not always in accordance. Dysbiosis in pSS was not confirmed, and reduced salivary secretion seems to explain more microbial changes than the underlying disease. Conclusion These heterogeneous results might be explained by the lack of a standardized methodology at each step of the process and highlight the need for guidelines. Our review provides evidence that sicca patients seem to be more relevant than healthy subjects as a control group

The Microbiome in Cystic Fibrosis Pulmonary Disease

International audienceCystic fibrosis (CF) is a genetic disease with mutational changes leading to profound dysbiosis, both pulmonary and intestinal, from a very young age. This dysbiosis plays an important role in clinical manifestations, particularly in the lungs, affected by chronic infection. The range of microbiological tools has recently been enriched by metagenomics based on next-generation sequencing (NGS). Currently applied essentially in a gene-targeted manner, metagenomics has enabled very exhaustive description of bacterial communities in the CF lung niche and, to a lesser extent, the fungi. Aided by progress in bioinformatics, this now makes it possible to envisage shotgun sequencing and opens the door to other areas of the microbial world, the virome, and the archaeome, for which almost everything remains to be described in cystic fibrosis. Paradoxically, applying NGS in microbiology has seen a rebirth of bacterial culture, but in an extended manner (culturomics), which has proved to be a perfectly complementary approach to NGS. Animal models have also proved indispensable for validating microbiome pathophysiological hypotheses. Description of pathological microbiomes and correlation with clinical status and therapeutics (antibiotic therapy, cystic fibrosis transmembrane conductance regulator (CFTR) modulators) revealed the richness of microbiome data, enabling description of predictive and follow-up biomarkers. Although monogenic, CF is a multifactorial disease, and both genotype and microbiome profiles are crucial interconnected factors in disease progression. Microbiome-genome interactions are thus important to decipher

Interbreeding between Neanderthals and modern humans: Remarks and methodological dangers of a dental calculus microbiome analysis

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Les bactéries anaérobies, ces inconnues du microbiote pulmonaire

La médecine a longtemps considéré le poumon comme un organe stérile. Il est désormais évident qu’il est colonisé par des microorganismes, y compris chez les sujets sains. Parmi les bactéries présentes dans le microbiote pulmonaire, une part importante est anaérobie (strictes ou facultatives). Si l’intérêt et l’impact du microbiote, en général, et pulmonaire en particulier, vont grandissant, peu d’études s’intéressent à ces inconnues que représentent ces bactéries anaérobies résidentes des poumons. Cette synthèse bibliographique décrit la biodiversité des anaérobies en situation physiologique et dans différentes maladies respiratoires chroniques (mucoviscidose, BPCO, asthme), abordant tour à tour leurs rôles dans l’effet de flore barrière, dans l’inflammation, ou encore comme potentiel biomarqueur de certaines maladies pulmonaires

Une anthropologie biologique de la disparition de l’homme de Néandertal : données récentes

Quelles ont pu être les causes de la disparition de l’homme de Néandertal ? On tentera ici de faire une synthèse entre l’un des questionnements fondamentaux de l’anthropologie biologique relatifs à l’évolution humaine (hypothèses sur les causes de l’extinction des Néandertaliens) et des concepts bio-médicaux évolutionnistes, dont certains ont été récemment reformulés grâce aux progrès de la paléogénomique (héritages ancestraux du système immunitaire humain actuel, paléo-microbiologie, relation hôte-pathogène, etc.)

Porphyromonas: A neglected potential key genus in human microbiomes

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