Sensitivity improvement of thin-film techniques by micro-sample analysis.

International audienceTwo types of thin-film techniques have been developed in the 90’s by W. Davison and H. Zhang, known under the name of DET (diffusive equilibrium in thin film) and DGT (diffusive gradient in thin film) technique. The solutes are equilibrated with the non-bound water of the hydrogel for the DET technique, whereas the solutes diffuse through a diffusive hydrogel before being accumulated by a binding gel for the DGT techniques. Elution of solutes is required for some chemical analysis. The analysis volume depends on the analytical tool consumption, such as 2-10 mL for classical elemental analysis, which is critical to the solute determination at trace levels in dilute eluent solution. Solute dilution is eventually compensated by its preconcentration with the DGT technique, contrary to the DET techniques. That’s a reason why the DGT application is currently most popular in environmental studies.Our laboratory has been recently equipped with a Tedelyne-Cetac MVX 7100 µL workstation (http://www.teledynecetac.com), which allows determining solute concentrations in small sample sizes (volumes ranging between 5 and 500 µL) once hyphenated to the Agilent 8800 ICP-MS/MS. The possibility to analyze small sample volumes meets the requirements of thin-film techniques notably by reducing to the minimum the volume of the eluent solution and thus by leading to the improvement of the technique sensitivity. However, ICP-MS/MS settings for analysis of small volumes are not a trivial issue. In this work, a number of key parameters such as sample flow rate, element integration time, number of replicates, were carefully evaluated and improved. The optimized performances of the MVX 7100 µL-ICP-MS/MS in terms of signal sensibility and stability were compared to the Agilent ALS-ICP-MS/MS (classical autosampler provided by the manufacturer). The developed method was applied for the determination of element concentrations (Fe, Mn and U) in pore waters of French river sediments. DET and Chelex-DGT devices were deployed simultaneously in river sediments. The DET samples were analyzed using the developed method, whereas Chelex-DGT samples were treated and analyzed using a classical protocol. Finally, a depth profile comparison between the two thin-film techniques will be presented and discussed

PPalign: optimal alignment of Potts models representing proteins with direct coupling information

International audienceTo assign structural and functional annotations to the ever increasing amount of sequenced proteins, the main approach relies on sequence-basedhomology search methods, e.g. BLAST or the current state-of-the-art methods based on profile Hidden Markov Models, which rely on significantalignments of query sequences to annotated proteins or protein families. While powerful, these approaches do not take coevolution between residuesinto account. Taking advantage of recent advances in the field of contact prediction, our approach, recently published in BMC Bioinformatics, proposesto represent proteins by Potts models, which model direct couplings between positions in addition to positional composition, and to compare proteins by aligning these models. Due to non-local dependencies, the problem of aligning Potts models is hard and remains the main computationalbottleneck for their use

Escherichia coli population structure and antibiotic resistance at a buffalo/cattle interface in Southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among Enterobacteriaceae (0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant E. coli strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (tet, dfrA, and blaTEM-1) in 26 isolated subdominant E. coli strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multihost systems. (Résumé d'auteur

An intensive care unit outbreak with multi-drug-resistant Pseudomonas aeruginosa – spotlight on sinks

Background: Pseudomonas aeruginosa and other Gram-negative bacteria have the ability to persist in moist environments in healthcare settings, but their spread from these areas can result in outbreaks of healthcare-associated infections. Methods: This study reports the investigation and containment of a multi-drug-resistant P. aeruginosa outbreak in three intensive care units of a Swiss university hospital. In total, 255 patients and 276 environmental samples were screened for the multi-drug-resistant P. aeruginosa outbreak strain. The environmental sampling and molecular characterization of patient and environmental strains, and control strategies implemented, including waterless patient care, are described. Results: Between March and November 2019, the outbreak affected 29 patients. Environmental sampling detected the outbreak strain in nine samples of sink siphons of three different intensive care units with a common water sewage system, and on one gastroscope. Three weeks after replacement of the sink siphons, the outbreak strain re-grew in siphon-derived samples and newly affected patients were identified. The outbreak ceased after removal of all sinks in the proximity of patients and in medication preparation areas, and minimization of tap water use. Multi-locus sequence typing indicated clonality (sequence type 316) in 28/29 patient isolates and all 10 environmental samples. Conclusions: Sink removal combined with the introduction of waterless patient care terminated the multi-drug-resistant P. aeruginosa outbreak. Sinks in intensive care units may pose a risk for point source outbreaks with P. aeruginosa and other bacteria persisting in moist environments. Keywords: Intensive care; Multi-drug resistance; Outbreak; Pseudomonas aeruginosa; Sink; Siphon; Waterless patient care

Inferring within-flock transmission dynamics of highly pathogenic avian influenza H5N8 virus in France, 2020.

Following the emergence of highly pathogenic avian influenza (H5N8) in France in early December 2020, we used duck mortality data from the index farm to investigate within-flock transmission dynamics. A stochastic epidemic model was fitted to the daily mortality data and model parameters were estimated using an approximate Bayesian computation sequential Monte Carlo (ABC-SMC) algorithm. The model predicted that the first bird in the flock was infected 5 days (95% credible interval, CI: 3-6) prior to the day of suspicion and that the transmission rate was 4.1 new infections per day (95% CI: 2.8-5.8). On average, ducks became infectious 4.1 h (95% CI: 0.7-9.1) after infection and remained infectious for 4.3 days (95% CI: 2.8-5.7). The model also predicted that 34% (50% prediction interval: 8%-76%) of birds would already be infectious by the day of suspicion, emphasizing the substantial latent threat this virus could pose to other poultry farms and to neighbouring wild birds. This study illustrates how mechanistic models can help provide rapid relevant insights that contribute to the management of infectious disease outbreaks of farmed animals. These methods can be applied to future outbreaks and the resulting parameter estimates made available to veterinary services within a few hours

Escherichia coli population structure and antibiotic resistance at a buffalo/cattle interface in southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacterial and antibiotic resistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibiotic resistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results (i) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, dominated by B1 (44.5%) and E (29.0%) phylogroups, with some variability in A phylogroup presence (from 1.9 to 12%); (ii) identified a significant gradient of antibiotic resistance from isolated buffalo to buffalo in contact with cattle and cattle populations expressed as the Murray score among Enterobacteriaceae (0.146, 0.258, and 0.340, respectively) and as the presence of tetracycline-, trimethoprim-, and amoxicillin-resistant subdominant E. coli strains (0, 5.7, and 38%, respectively); (iii) evidenced the dissemination of tetracycline, trimethoprim, and amoxicillin resistance genes (tet, dfrA, and blaTEM-1) in 26 isolated subdominant E. coli strains between nearby buffalo and cattle populations, that led us (iv) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and toward wildlife. The study of antibiotic resistance dissemination in multihost systems and at anthropized/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multihost systems.This study was implemented within the framework of the research Platform Conservation and Production in Partnership (www.rp-pcp.org) and in collaboration with CNRS within the framework of the Zone Atelier in the Hwange area.Agence Nationale de la Recherche (ANR) http://dx.doi.org/10.13039/501100001665ANR-11-CEPL-003.http://aem.asm.org2017-06-30Mammal Research Institut

Escherichia coli population structure and antibioresistance at a buffalo/cattle interface in Southern Africa

At a human/livestock/wildlife interface, Escherichia coli populations were used to assess the risk of bacteria and antibioresistance dissemination between hosts. We used phenotypic and genotypic characterization techniques to describe the structure and the level of antibioresistance of E. coli commensal populations and the resistant Enterobacteriaceae carriage of sympatric African buffalo (Syncerus caffer) and cattle populations characterized by their contact patterns in the southern part of Hwange ecosystem in Zimbabwe. Our results 1) confirmed our assumption that buffalo and cattle share similar phylogroup profiles, 2) identified a significant gradient of antibioresistance from isolated buffalo to buffalo in contact with cattle and cattle populations; 3) evidenced the dissemination of tetracycline, trimethoprim and amoxicillin resistance genes (tet, dfrA, blaTEM-1in 26 isolated sub-dominant E. coli strains between nearby buffalo and cattle populations that led us 4) to hypothesize the role of the human/animal interface in the dissemination of genetic material from human to cattle and towards wildlife. The study of antibiotic resistance dissemination in multi-host systems and at anthropised/natural interface is necessary to better understand and mitigate its multiple threats. These results also contribute to attempts aiming at using E. coli as a tool for the identification of pathogen transmission pathway in multi-host systems. (Texte intégral

Engaging rural Australian communities in National Science Week helps increase visibility for women researchers

During a week-long celebration of science, run under the federally-supported National Science Week umbrella, the Catch a Rising Star: women in Queensland research (CaRS) program flew scientists who identify as women to regional and remote communities in the Australian State of Queensland. The aim of the project was twofold: first, to bring science to remote and regional communities in a large, economically diverse state; and second, to determine whether media and public engagement provide career advancement opportunities for women scientists. This paper focuses on the latter goal. The data show: 1) a substantial majority (> 80%) of researchers thought the training and experience provided by the program would help develop her career as a research scientist in the future; 2) the majority (65%) thought the program would help relate her research to end users, industry partners, or stakeholders in the future; and, 3) analytics can help create a compelling narrative around engagement metrics and help to quantify influence. During the weeklong project, scientists reached 600,000 impressions on one social media platform (Twitter) using a program hashtag. The breadth and depth of the project outcomes indicate funding bodies and employers could use similar data as an informative source of metrics to support hiring and promotion decisions. Although this project focused on researchers who identify as women, the lessons learned are applicable to researchers representing a diverse range of backgrounds. Future surveys will help determine whether the CaRS program provided long-term career advantages to participating scientists and communities