Le test ET : test d'adéquation d'un modèle central à une queue de distribution

Ce travail est motivé par des questions de fiabilité structurale, où les lois usuelles appartiennent au domaine d'attraction de Gumbel, DA(Gumbel). Étant donné un échantillon iid, on veut vérifier si un modèle paramétrique $F_\theta$ appartenant au DA(Gumbel) permet d'obtenir une bonne approximation de la queue de distribution, plus précisément, au-delà de l'observation maximale. On suppose que les tests d'adéquation usuels ne rejettent pas l'hypothèse nulle $H_0$ : $\exists \theta ,$ $F=F_\theta$. De telles procédures testent essentiellement l'adéquation du modèle à la région centrale de l'échantillon. Le but du test ET est de vérifier l'adéquation aux observations extrêmes. Il s'agit de comparer sous $H_0$ deux estimateurs différents d'un quantile extrême, c'est-à-dire d'ordre $1-p$ avec $p<1/n$ : le premier est l'estimateur paramétrique du quantile, le second est \widehatq_{ET}, l'estimateur ET, basé sur une approximation exponentielle de la loi (possible parce que $F$ appartient au DA(Gumbel) sous $H_0$) des excès au-delà d'un seuil.\\ En approximant le vrai quantile par son estimateur ET, on commet deux types d'erreurs : une erreur d'estimation, et une erreur d'approximation, puisque nous approximons la loi des excès par une loi exponentielle. Sous $H_0$, la prise en compte de l'erreur d'approximation, ou une approximation raisonnable de celle-ci, dans les bornes de l'intervalle de confiance déduit de la loi limite %des fluctuations d'échantillonnage de \widehatq_{ET}- , produit un intervalle de confiance approché pour le vrai quantile. Le test ET ne rejette pas $H_0$ lorsque l'estimateur paramétrique appartient à cet intervalle. Nous proposons un seconde version du test ET dans laquelle nous approximons les fluctuations d'échantillonnage des estimateurs paramétrique et ET par booststrap paramétrique. Des simulations montrent que cette version du test est nettement plus puissante. Enfin, pour traiter le cas de lois dont les paramètres et donc les estimateurs paramètriques de quantiles sont difficiles à calculer (comme les modèles de mélange), nous proposons une version simplifiée du test ET boostrap paramétrique

Septic shock caused by Capnocytophaga canis after a cat scratch

Capnocytophaga canis is an uncommon cause of septic shock. Only three cases have been previously reported in the literature. In this article, we describe the case of a 70-year-old male admitted to the intensive care unit for septic shock of unknown origin. On day 2, one anaerobic bottle out of the two sets taken at admission turned positive with Gram-negative bacilli. The pathogen was identified by 16S rRNA gene as C. canis. The strain was characterized and compared with other clinical isolates of Capnocytophaga spp

Quasi-conjugate Bayes estimates for GPD parameters and application to heavy tails modelling

We present a quasi-conjugate Bayes approach for estimating Generalized Pareto Distribution (GPD) parameters, distribution tails and extreme quantiles within the Peaks-Over-Threshold framework. Damsleth conjugate Bayes structure on Gamma distributions is transfered to GPD. Bayes credibility intervals are defined, they provide assessment of the quality of the extreme events estimates. Posterior estimates are computed by Gibbs samplers with Hastings-Metropolis steps. Even if non-informative priors are used in this work, the suggested approach could incorporate informative priors, it brings solutions to the problem of estimating extreme events when data are scarce but expert opinion is available. It is shown that the obtained quasi-conjugate Bayes estimators compare well with the GPD standard estimators on simulated and real data sets

Extreme viral partitioning in a marine-derived High Arctic lake

ABSTRACT High-latitude, perennially stratified (meromictic) lakes are likely to be especially vulnerable to climate warming because of the importance of ice in maintaining their water column structure and associated distribution of microbial communities. This study aimed to characterize viral abundance, diversity, and distribution in a meromictic lake of marine origin on the far northern coast of Ellesmere Island, in the Canadian High Arctic. We collected triplicate samples for double-stranded DNA (dsDNA) viromics from five depths that encompassed the major features of the lake, as determined by limnological profiling of the water column. Viral abundance and virus-to-prokaryote ratios were highest at greater depths, while bacterial and cyanobacterial counts were greatest in the surface waters. The viral communities from each zone of the lake defined by salinity, temperature, and dissolved oxygen concentrations were markedly distinct, suggesting that there was little exchange of viral types among lake strata. Ten viral assembled genomes were obtained from our libraries, and these also segregated with depth. This well-defined structure of viral communities was consistent with that of potential hosts. Viruses from the monimolimnion, a deep layer of ancient Arctic Ocean seawater, were more diverse and relatively abundant, with few similarities to available viral sequences. The Lake A viral communities also differed from published records from the Arctic Ocean and meromictic Ace Lake in Antarctica. This first characterization of viral diversity from this sentinel environment underscores the microbial richness and complexity of an ecosystem type that is increasingly exposed to major perturbations in the fast-changing Arctic. IMPORTANCE The Arctic is warming at an accelerating pace, and the rise in temperature has increasing impacts on the Arctic biome. Lakes are integrators of their surroundings and thus excellent sentinels of environmental change. Despite their importance in the regulation of key microbial processes, viruses remain largely uncharacterized in Arctic lacustrine environments. We sampled a highly stratified meromictic lake near the northern limit of the Canadian High Arctic, a region in rapid transition due to climate change. We found that the different layers of the lake harbored viral communities that were strikingly dissimilar and highly divergent from known viruses. Viruses were more abundant in the deepest part of the lake containing ancient Arctic Ocean seawater that was trapped during glacial retreat and were genomically unlike any viruses previously described. This research demonstrates the complexity and novelty of viral communities in an environment that is vulnerable to ongoing perturbation

Root Microbiota in Primary and Secondary Apical Periodontitis

Apical periodontitis is an inflammatory disease of the dental periradicular tissues triggered by bacteria colonizing necrotic root canals. Primary apical periodontitis results from the microbial colonization of necrotic pulp tissues. Secondary apical periodontitis results from a persistent infection of incorrectly treated root canals. The aim of this study was to characterize the microbiota present in primary and secondary intraradicular infections associated with apical periodontitis using 16S rRNA gene amplicon sequencing. Teeth exhibiting apical periodontitis with or without root canal treatment were extracted after informed consent. From each tooth, the intraradicular content as well as a dentin sample (control) were collected and subjected to DNA extraction. PCR amplicons of the V3–V4 region of the bacterial 16S rRNA gene were pooled and sequenced (2 × 300) on an Illumina MiSeq instrument. The bioinformatics analysis pipeline included quality filtering, merging of forward and reverse reads, clustering of reads into operational taxonomic units (OTUs), removal of putative contaminant OTUs and assigning taxonomy. The most prevalent and abundant OTU in both dentin and root canal samples was assigned to anaerobic bacterium Fusobacterium nucleatum. Multivariate analysis showed clustering of microbiota by sample type (dentin vs. intraradicular content) and, in root canals, by pathology (primary vs. secondary infection). The proportions of Enterococcus faecalis and F. nucleatum were, respectively, higher and lower when comparing secondary to primary infected root canals. Co-occurrence network analysis provided evidence of microbial interactions specific to the infection type. The identification of bacterial taxa differentially abundant in primary and secondary intraradicular infections may provide the basis for targeted therapeutic approaches aimed at reducing the incidence of apical periodontitis

Daptomycin resistance mechanisms in clinically derived Staphylococcus aureus strains assessed by a combined transcriptomics and proteomics approach

Objectives The development of daptomycin resistance in Staphylococcus aureus is associated with clinical treatment failures. The mechanism(s) of such resistance have not been clearly defined. Methods We studied an isogenic daptomycin-susceptible (DAPS) and daptomycin-resistant (DAPR) S. aureus strain pair (616; 701) from a patient with relapsing endocarditis during daptomycin treatment, using comparative transcriptomic and proteomic techniques. Results Minor differences in the genome content were found between strains by DNA hybridization. Transcriptomic analyses identified a number of genes differentially expressed in important functional categories: cell division; metabolism of bacterial envelopes; and global regulation. Of note, the DAPR isolate exhibited reduced expression of the major cell wall autolysis gene coincident with the up-regulation of genes involved in cell wall teichoic acid production. Using quantitative (q)RT-PCR on the gene cadre putatively involved in cationic peptide resistance, we formulated a putative regulatory network compatible with microarray data sets, mainly implicating bacterial envelopes. Of interest, qRT-PCR of this same gene cadre from two distinct isogenic DAPS/DAPR clinical strain pairs revealed evidence of other strain-dependent networks operative in the DAPR phenotype. Comparative proteomics of 616 versus 701 revealed a differential abundance of proteins in various functional categories, including cell wall-associated targets and biofilm formation proteins. Phenotypically, strains 616 and 701 showed major differences in their ability to develop bacterial biofilms in the presence of the antibacterial lipid, oleic acid. Conclusions Compatible with previous in vitro observations, in vivo-acquired DAPR in S. aureus is a complex, multistep phenomenon involving: (i) strain-dependent phenotypes; (ii) transcriptome adaptation; and (iii) modification of the lipid and protein contents of cellular envelope

Screening for Staphylococcal Superantigen Genes Shows No Correlation with the Presence or the Severity of Chronic Rhinosinusitis and Nasal Polyposis

BACKGROUND: Staphylococcus aureus secretes numerous exotoxins which may exhibit superantigenic properties. Whereas the virulence of several of them is well documented, their exact biological effects are not fully understood. Exotoxins may influence the immune and inflammatory state of various organs, including the sinonasal mucosa: their possible involvement in chronic rhinosinusitis has been suggested and is one of the main trends in current research. The aim of this study was to investigate whether the presence of any of the 22 currently known staphylococcal exotoxin genes could be correlated with chronic rhinosinusitis. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a prospective, multi-centred European study, analysing 93 Staphylococcus aureus positive swabs taken from the middle meatus of patients suffering from chronic rhinosinusitis, with or without nasal polyposis, and controls. Strains were systematically tested for the presence of the 22 currently known exotoxin genes and genotyped according to their agr groups. No direct correlation was observed between chronic rhinosinusitis, with or without nasal polyposis, and either agr groups or the presence of the most studied exotoxins genes (egc, sea, seb, pvl, exfoliatins or tsst-1). However, genes for enterotoxins P and Q were frequently observed in nasal polyposis for the first time, but absent in the control group. The number of exotoxin genes detected was not statistically different among the 3 patient groups. CONCLUSIONS/SIGNIFICANCE: Unlike many previous studies have been suggesting, we did not find any evident correlation between staphylococcal exotoxin genes and the presence or severity of chronic rhinosinusitis with or without nasal polyposis

Decontamination of 16S rRNA gene amplicon sequence datasets based on bacterial load assessment by qPCR

Identification of unexpected taxa in 16S rRNA surveys of low-density microbiota, diluted mock communities and cultures demonstrated that a variable fraction of sequence reads originated from exogenous DNA. The sources of these contaminants are reagents used in DNA extraction, PCR, and next-generation sequencing library preparation, and human (skin, oral and respiratory) microbiota from the investigators