Complete Genome Sequences of Two Methicillin-Resistant Staphylococcus haemolyticus Isolates of Multilocus Sequence Type 25, First Detected by Shotgun Metagenomics

The emergence of nosocomial infections by multidrug-resistantStaphylococcus haemolyticusisolates has been reported in several European countries. Here, we report the first two complete genome sequences ofS. haemolyticussequence type 25 (ST25) isolates 83131A and 83131B. Both isolates were isolated from the same clinical sample and were first identified through shotgun metagenomics

Differences in the Prevalence of Non-Communicable Disease between Slum Dwellers and the General Population in a Large Urban Area in Brazil.

Residents of urban slums are at greater risk for disease than their non-slum dwelling urban counterparts. We sought to contrast the prevalences of selected non-communicable diseases (NCDs) between Brazilian adults living in a slum and the general population of the same city, by comparing the age and sex-standardized prevalences of selected NCDs from a 2010 survey in Pau da Lima, Salvador Brazil, with a 2010 national population-based telephone survey. NCD prevalences in both populations were similar for hypertension (23.6% (95% CI 20.9⁻26.4) and 22.9% (21.2⁻24.6), respectively) and for dyslipidemia (22.7% (19.8⁻25.5) and 21.5% (19.7⁻23.4)). Slum residents had higher prevalences of diabetes mellitus (10.1% (7.9⁻12.3)) and of overweight/obesity (46.5% (43.1⁻49.9)), compared to 5.2% (4.2⁻6.1) and 40.6% (38.5⁻42.8) of the general population in Salvador. Fourteen percent (14.5% (12.1⁻17.0)) of slum residents smoked cigarettes compared to 8.3% (7.1⁻9.5) of the general population in Salvador. The national telephone survey underestimated the prevalence of diabetes mellitus, overweight/obesity, and smoking in the slum population, likely in part due to differential sampling inside and outside of slums. Further research and targeted policies are needed to mitigate these inequalities, which could have significant economic and social impacts on slum residents and their communities

Future potential of metagenomics in clinical laboratories

INTRODUCTION: Rapid and sensitive diagnostic strategies are necessary for patient care and public health. Most of the current conventional microbiological assays detect only a restricted panel of pathogens at a time or require a microbe to be successfully cultured from a sample. Clinical metagenomics next-generation sequencing (mNGS) has the potential to unbiasedly detect all pathogens in a sample, increasing the sensitivity for detection and enabling the discovery of unknown infectious agents. AREAS COVERED: High expectations have been built around mNGS; however, this technique is far from widely available. This review highlights the advances and currently available options in terms of costs, turnaround time, sensitivity, specificity, validation, and reproducibility of mNGS as a diagnostic tool in clinical microbiology laboratories. EXPERT OPINION: The need for a novel diagnostic tool to increase the sensitivity of microbial diagnostics is clear. mNGS has the potential to revolutionise clinical microbiology. However, its role as a diagnostic tool has yet to be widely established, which is crucial for successfully implementing the technique. A clear definition of diagnostic algorithms that include mNGS is vital to show clinical utility. Similarly to real-time PCR, mNGS will one day become a vital tool in any testing algorithm

Water, waste, energy and food nexus in Brazil: Identifying a resource interlinkage research agenda through a systematic review

The resource nexus consists of a framework to address interlinkages between natural resources and systems that provide water, energy, food and waste management. It transcends traditional assessments conducted in “silos”, raising trade-offs and synergies that are rarely acknowledged. The nexus framework is intrinsically context-specific, as each respective region has particularities in terms of critical interlinkages. Brazil is the world's eighth largest economy [1] and is heavily reliant on natural resources. This paper considers Brazil to be a textbook case for nexus research that identifies critical interlinkages that are neglected by literature, which is typically based on single-resource analysis. It proposes a research agenda to advance resource nexus assessments and improve resource governance in Brazil. We propose a novel method for nexus research, systematically reviewing geographical context-specific papers in relevant single nexus dimensions and establishing resource interlinkages that characterise research gaps and policy priorities. We found that 36% of practices reviewed involve more than one resource at a time, characterising interlinkages not analysed by the literature. Lastly, selected quantitative indicators were used to identify critical interlinkages by analysing the representativeness of practices in the national context, and the relevance of synergies or trade-offs for Brazil. Critical interlinkages in Brazil were found to be irrigation for energy crop expansion (water, food and energy); transport biofuels and fuelwood (water, energy, food); deforestation for new pasture (water, energy, food); and hydropower generation (water and energy). These are, therefore, priorities for future nexus research and for efforts to address synergies and trade-offs in resource governance

Complete Coding Sequences of Five Dengue Virus Type 2 Clinical Isolates from Venezuela Obtained through Shotgun Metagenomics

Dengue is a disease endemic in Latin American countries, like Venezuela, and has become one of the most important public health problems. We report five complete coding sequences of dengue virus serotype 2 (DENV-2) isolated from DENV-infected patients in Venezuela. Phylogenetic analysis placed the isolates within the American/Asian genotype

Comparison of CDMS [100] and [111] oriented germanium detectors

The Cryogenic Dark Matter Search (CDMS) utilizes large mass, 3" diameter $\times$ 1" thick target masses as particle detectors. The target is instrumented with both phonon and ionization sensors and comparison of energy in each channel provides event-by-event classification of electron and nuclear recoils. Fiducial volume is determined by the ability to obtain good phonon and ionization signal at a particular location. Due to electronic band structure in germanium, electron mass is described by an anisotropic tensor with heavy mass aligned along the symmetry axis defined by the [111] Miller index (L valley), resulting in large lateral component to the transport. The spatial distribution of electrons varies significantly for detectors which have their longitudinal axis orientations described by either the [100] or [111] Miller indices. Electric fields with large fringing component at high detector radius also affect the spatial distribution of electrons and holes. Both effects are studied in a 3 dimensional Monte Carlo and the impact on fiducial volume is discussed.Comment: Low Temperature Detector 14 conference proceedings to be published in the Journal of Low Temperature Physic

Elucidating vancomycin-resistant Enterococcus faecium outbreaks:the role of clonal spread and movement of mobile genetic elements

Background: Vancomycin-resistant Enterococcus faecium (VREfm) has emerged as a nosocomial pathogen worldwide. The dissemination of VREfm is due to both clonal spread and spread of mobile genetic elements (MGEs) such as transposons.Objectives: We aimed to combine vanB-carrying transposon data with core-genome MLST (cgMLST) typing and epidemiological data to understand the pathways of transmission in nosocomial outbreaks.Methods: Retrospectively, 36 VREfm isolates obtained from 34 patients from seven VREfm outbreak investigations in 2014 were analysed. Isolates were sequenced on a MiSeq and a MinION instrument. De novo assembly was performed in CLC Genomics Workbench and the hybrid assemblies were obtained through Unicycler v0.4.1. Ridom SeqSphere+ was used to extract MLST and cgMLST data. Detailed analysis of each transposon and their integration points was performed using the Artemis Comparison Tool (ACT) and multiple blast analyses.Results: Four different vanB transposons were found among the isolates. cgMLST divided ST80 isolates into three cluster types (CTs); CT16, CT104 and CT106. ST117 isolates were divided into CT24, CT103 and CT105. Within VREfm isolates belonging to CT103, two different vanB transposons were found. In contrast, VREfm isolates belonging to CT104 and CT106 harboured an identical vanB transposon.Conclusions: cgMLST provides a high discriminatory power for the epidemiological analysis of VREfm. However, additional transposon analysis is needed to detect horizontal gene transfer. Combining these two methods allows investigation of both clonal spread as well as the spread of MGEs. This leads to new insights and thereby better understanding of the complex transmission routes in VREfm outbreaks.</p