Reads2Type: a web application for rapid microbial taxonomy identification

BACKGROUND: Identification of bacteria may be based on sequencing and molecular analysis of a specific locus such as 16S rRNA, or a set of loci such as in multilocus sequence typing. In the near future, healthcare institutions and routine diagnostic microbiology laboratories may need to sequence the entire genome of microbial isolates. Therefore we have developed Reads2Type, a web-based tool for taxonomy identification based on whole bacterial genome sequence data. RESULTS: Raw sequencing data provided by the user are mapped against a set of marker probes that are derived from currently available bacteria complete genomes. Using a dataset of 1003 whole genome sequenced bacteria from various sequencing platforms, Reads2Type was able to identify the species with 99.5 % accuracy and on the minutes time scale. CONCLUSIONS: In comparison with other tools, Reads2Type offers the advantage of not needing to transfer sequencing files, as the entire computational analysis is done on the computer of whom utilizes the web application. This also prevents data privacy issues to arise. The Reads2Type tool is available at http://www.cbs.dtu.dk/~dhany/reads2type.html

A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

Recent advances in whole genome sequencing have made the technology available for routine use in microbiological laboratories. However, a major obstacle for using this technology is the availability of simple and automatic bioinformatics tools. Based on previously published and already available web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates. The pipeline will automatically identify the bacterial species and, if applicable, assemble the genome, identify the multilocus sequence type, plasmids, virulence genes and antimicrobial resistance genes. A short printable report for each sample will be provided and an Excel spreadsheet containing all the metadata and a summary of the results for all submitted samples can be downloaded. The pipeline was benchmarked using datasets previously used to test the individual services. The reported results enable a rapid overview of the major results, and comparing that to the previously found results showed that the platform is reliable and able to correctly predict the species and find most of the expected genes automatically. In conclusion, a combined bioinformatics platform was developed and made publicly available, providing easy-to-use automated analysis of bacterial whole genome sequencing data. The platform may be of immediate relevance as a guide for investigators using whole genome sequencing for clinical diagnostics and surveillance. The platform is freely available at: https://cge.cbs.dtu.dk/services/CGEpipeline-1.1 and it is the intention that it will continue to be expanded with new features as these become available

Impact of environmental conditions on biomass yield, quality, and bio-mitigation capacity of Saccharina latissima

Seaweeds are attractive as a sustainable aquaculture crop for food, feed, bioenergy and biomolecules. Further, the non-value ecosystem services of seaweed cultivation (i.e. nutrient recapture) are gaining interest as an instrument towards sustainable aquaculture and for fulfilling the aims of the EU Marine Strategy Framework Directive. Environmental factors determine the yield and quality of the cultivated seaweed biomass and, in return, the seaweed aquaculture affects the marine environment by nutrient assimilation. Consequently, site selection is critical for obtaining optimal biomass yield and quality and for successful bio-mitigation. In this study, 5 sites for cultivation of Saccharina latissima were selected within a eutrophic water body to guide site selection for future kelp cultivation activities. Results were coupled to marine monitoring data to explore the relationship between environmental conditions and cultivation success. The biomass yields fluctuated 10-fold between sites due to local variations in light and nutrient availability. Yields were generally low, i.e. up to 510 g fresh weight (FW) per meter seeded line; however, the dry matter contents of protein and high-value pigments were high (up to 17% protein and 0.1% fucoxanthin). Growth performance, biomass quality and bio-mitigation potential was restricted by low availability of light and bioavailable phosphorus, and biofouling through juvenile suspension feeders was a critical factor at all cultivation sites. At specific sites, the tissue metal contents (Pb and Hg) exceeded the limit values for feed or food. Our results emphasize the importance of careful site selection before establishing large-scale cultivation, and stress the challenges and benefits of kelp cultivation in eutrophic waters

Diagnostic Yield of Genetic Testing in Young Patients With Atrioventricular Block of Unknown Cause

BACKGROUND: The cause of atrioventricular block (AVB) remains unknown in approximately half of young patients with the diagnosis. Although variants in several genes associated with cardiac conduction diseases have been identified, the contribution of genetic variants in younger patients with AVB is unknown. METHODS AND RESULTS: Using the Danish Pacemaker and Implantable Cardioverter Defibrillator (ICD) Registry, we identified all patients younger than 50 years receiving a pacemaker because of AVB in Denmark in the period from January 1, 1996 to December 31, 2015. From medical records, we identified patients with unknown cause of AVB at time of pacemaker implantation. These patients were invited to a genetic screening using a panel of 102 genes associated with inherited cardiac diseases. We identified 471 living patients with AVB of unknown cause, of whom 226 (48%) accepted participation. Median age at the time of pacemaker implantation was 39 years (interquartile range, 32–45 years), and 123 (54%) were men. We found pathogenic or likely pathogenic variants in genes associated with or possibly associated with AVB in 12 patients (5%). Most variants were found in the LMNA gene (n=5). LMNA variant carriers all had a family history of either AVB and/or sudden cardiac death. CONCLUSIONS: In young patients with AVB of unknown cause, we found a possible genetic cause in 1 out of 20 participating patients. Variants in the LMNA gene were most common and associated with a family history of AVB and/or sudden cardiac death, suggesting that genetic testing should be a part of the diagnostic workup in these patients to stratify risk and screen family members