IslandViewer (http://www.pathogenomics.sfu.ca/islandviewer/) is a widely-used webserver for the prediction and interactive visualization of genomic islands (GIs, regions of probable horizontal ...origin) in bacterial and archaeal genomes. GIs disproportionately encode factors that enhance the adaptability and competitiveness of the microbe within a niche, including virulence factors and other medically or environmentally important adaptations. We report here the release of IslandViewer 4, with novel features to accommodate the needs of larger-scale microbial genomics analysis, while expanding GI predictions and improving its flexible visualization interface. A user management web interface as well as an HTTP API for batch analyses are now provided with a secured authentication to facilitate the submission of larger numbers of genomes and the retrieval of results. In addition, IslandViewer's integrated GI predictions from multiple methods have been improved and expanded by integrating the precise Islander method for pre-computed genomes, as well as an updated IslandPath-DIMOB for both pre-computed and user-supplied custom genome analysis. Finally, pre-computed predictions including virulence factors and antimicrobial resistance are now available for 6193 complete bacterial and archaeal strains publicly available in RefSeq. IslandViewer 4 provides key enhancements to facilitate the analysis of GIs and better understand their role in the evolution of successful environmental microbes and pathogens.
Abstract
The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics ...tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD’s Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.
Abstract
Motivation
Many methods for microbial protein subcellular localization (SCL) prediction exist; however, none is readily available for analysis of metagenomic sequence data, despite growing ...interest from researchers studying microbial communities in humans, agri-food relevant organisms and in other environments (e.g. for identification of cell-surface biomarkers for rapid protein-based diagnostic tests). We wished to also identify new markers of water quality from freshwater samples collected from pristine versus pollution-impacted watersheds.
Results
We report PSORTm, the first bioinformatics tool designed for prediction of diverse bacterial and archaeal protein SCL from metagenomics data. PSORTm incorporates components of PSORTb, one of the most precise and widely used protein SCL predictors, with an automated classification by cell envelope. An evaluation using 5-fold cross-validation with in silico-fragmented sequences with known localization showed that PSORTm maintains PSORTb’s high precision, while sensitivity increases proportionately with metagenomic sequence fragment length. PSORTm’s read-based analysis was similar to PSORTb-based analysis of metagenome-assembled genomes (MAGs); however, the latter requires non-trivial manual classification of each MAG by cell envelope, and cannot make use of unassembled sequences. Analysis of the watershed samples revealed the importance of normalization and identified potential biomarkers of water quality. This method should be useful for examining a wide range of microbial communities, including human microbiomes, and other microbiomes of medical, environmental or industrial importance.
Availability and implementation
Documentation, source code and docker containers are available for running PSORTm locally at https://www.psort.org/psortm/ (freely available, open-source software under GNU General Public License Version 3).
Supplementary information
Supplementary data are available at Bioinformatics online.
Abstract
Protein subcellular localization (SCL) is important for understanding protein function, genome annotation, and aids identification of potential cell surface diagnostic markers, drug targets, ...or vaccine components. PSORTdb comprises ePSORTdb, a manually curated database of experimentally verified protein SCLs, and cPSORTdb, a pre-computed database of PSORTb-predicted SCLs for NCBI’s RefSeq deduced bacterial and archaeal proteomes. We now report PSORTdb 4.0 (http://db.psort.org/). It features a website refresh, in particular a more user-friendly database search. It also addresses the need to uniquely identify proteins from NCBI genomes now that GI numbers have been retired. It further expands both ePSORTdb and cPSORTdb, including additional data about novel secondary localizations, such as proteins found in bacterial outer membrane vesicles. Protein predictions in cPSORTdb have increased along with the number of available microbial genomes, from approximately 13 million when PSORTdb 3.0 was released, to over 66 million currently. Now, analyses of both complete and draft genomes are included. This expanded database will be of wide use to researchers developing SCL predictors or studying diverse microbes, including medically, agriculturally and industrially important species that have both classic or atypical cell envelope structures or vesicles.
Kombucha is a complex probiotic beverage made from fermented tea, yet despite extensive historical, anecdotal, and
evidence for its health benefits, no controlled trials have been published on its ...effect on humans.
We conducted a randomised placebo-controlled, cross-over study that examined the Glycemic Index (GI) and Insulin Index (II) responses after a standardised high-GI meal consumed with three different test beverages (soda water, diet lemonade soft drink and an unpasteurised kombucha) in 11 healthy adults. The study was prospectively registered with the Australian New Zealand Clinical Trials Registry (anzctr.org.au: 12620000460909). Soda water was used as the control beverage. GI or II values were calculated by expressing the 2-h blood glucose or insulin response as a percentage of the response produced by 50 g of glucose dissolved in water.
There was no statistically significant difference in GI or II between the standard meal consumed with soda water (GI: 86 and II: 85) or diet soft drink (GI: 84 and II: 81, (
= 0.929 for GI and
= 0.374 for II). In contrast, when kombucha was consumed there was a clinically significant reduction in GI and II (GI: 68,
= 0.041 and II: 70,
= 0.041) compared to the meal consumed with soda water.
These results suggest live kombucha can produce reductions in acute postprandial hyperglycemia. Further studies examining the mechanisms and potential therapeutic benefits of kombucha are warranted.
Metagenomic methods enable the simultaneous characterization of microbial communities without time-consuming and bias-inducing culturing. Metagenome-assembled genome (MAG) binning methods aim to ...reassemble individual genomes from this data. However, the recovery of mobile genetic elements (MGEs), such as plasmids and genomic islands (GIs), by binning has not been well characterized. Given the association of antimicrobial resistance (AMR) genes and virulence factor (VF) genes with MGEs, studying their transmission is a public-health priority. The variable copy number and sequence composition of MGEs makes them potentially problematic for MAG binning methods. To systematically investigate this issue, we simulated a low-complexity metagenome comprising 30 GI-rich and plasmid-containing bacterial genomes. MAGs were then recovered using 12 current prediction pipelines and evaluated. While 82-94 % of chromosomes could be correctly recovered and binned, only 38-44 % of GIs and 1-29 % of plasmid sequences were found. Strikingly, no plasmid-borne VF nor AMR genes were recovered, and only 0-45 % of AMR or VF genes within GIs. We conclude that short-read MAG approaches, without further optimization, are largely ineffective for the analysis of mobile genes, including those of public-health importance, such as AMR and VF genes. We propose that researchers should explore developing methods that optimize for this issue and consider also using unassembled short reads and/or long-read approaches to more fully characterize metagenomic data.
Antibiotic-resistant superbug bacteria represent a global health problem with no imminent solutions. Here we demonstrate that the combination (termed AB569) of acidified nitrite (A-NO₂⁻) and Na2-EDTA ...(disodium ethylenediaminetetraacetic acid) inhibited all Gram-negative and Gram-positive bacteria tested. AB569 was also efficacious at killing the model organism Pseudomonas aeruginosa in biofilms and in a murine chronic lung infection model. AB569 was not toxic to human cell lines at bactericidal concentrations using a basic viability assay. RNA-Seq analyses upon treatment of P. aeruginosa with AB569 revealed a catastrophic loss of the ability to support core pathways encompassing DNA, RNA, protein, ATP biosynthesis, and iron metabolism. Electrochemical analyses elucidated that AB569 produced more stable SNO proteins, potentially explaining one mechanism of bacterial killing. Our data implicate that AB569 is a safe and effective means to kill pathogenic bacteria, suggesting that simple strategies could be applied with highly advantageous therapeutic/toxicity index ratios to pathogens associated with a myriad of periepithelial infections and related disease scenarios.
Editor: We congratulate Kilgore and associates1 on their retrospective, population-based, case-control study that showed that hormonal contraceptives, particularly the oral contraceptive pill (OCP), ...are not associated with idiopathic intracranial hypertension (IIH). ...they did not exclude coagulopathies, which is vital because the World Health Organization warns that the OCP in this environment is associated with an unacceptable health risk.2 Kilgore and associates1 are concerned that because the OCP and IIH are not causally associated, the investigation of a specific etiology may not be pursued. ...Kilgore and associates1 consider that the patient should be given a diagnosis of IIH only when all underlying etiologies, after appropriate investigations, have been excluded, thereby permitting the best patient management.
Background The Pipeline Flex Embolization Device (PED) with Shield Technology (PED‐Shield) is a third‐generation flow diverting stents with surface modification designed to reduce platelet adhesion ...and thrombogenicity. We report the long‐term safety and effectiveness of the PED‐Shield in the treatment of unruptured intracranial aneurysms in an Australian cohort. Methods SCOPE‐AUS (Safety and Clinical Effectiveness Of Pipeline Shield Embolization Device for Treatment of Intracranial Aneurysms in Australia) is a multicenter, single‐arm, retrospective study of patients with unruptured intracranial aneurysms treated with the PED‐Shield flow diverting stents at 3 high‐volume neurointervention centers in Australia between May 1, 2015, and June 30, 2018, evaluating safety and efficacy. The primary outcome was neurologic adverse event or neurologic‐related death at 1 year, and the secondary outcome was long‐term complete aneurysm occlusion. Results A total of 238 patients (mean age 55.8±11.0 years, 73.1% 174/238 female) and 278 aneurysms were treated via 247 procedures. Two (0.7%) aneurysms were retreated during the 18‐month follow‐up. Overall occlusion rates at 18 months or at last follow‐up imaging were 92.5% (233/252). There were 35 (14.7%) total primary end point events. The 12‐month neurologic morbidity and mortality rates were 3.8% (9/238) and 1.3% (3/238), respectively. For the subgroup of internal carotid artery aneurysms, mortality (0.7%) and morbidity (2.0%) rates were low, and the complete occlusion rate was 92.5% (147/155). Conclusions In this multicenter study, which includes a wide variety of both distal bifurcation and proximal unruptured intracranial aneurysms, the occlusion rates and safety outcomes of the PED‐Shield flow diverting stent demonstrate a high proportion of complete aneurysm occlusion, extremely low retreatment rates, and low complication rates.
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