Introducing the Bacterial and Viral Bioinformatics Resource Center (BV-BRC): a resource combining PATRIC, IRD and ViPR.

The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Center (BRC) program to assist researchers with analyzing the growing body of genome sequence and other omics-related data. In this report, we describe the merger of the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD) and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) https://www.bv-brc.org/. The combined BV-BRC leverages the functionality of the bacterial and viral resources to provide a unified data model, enhanced web-based visualization and analysis tools, bioinformatics services, and a powerful suite of command line tools that benefit the bacterial and viral research communities.

Modified Harborview Risk Score accurately predicts mortality for patients with ruptured abdominal aortic aneurysm.

OBJECTIVE: The modified Harborview Risk Score (HRS) is a simple measure initially derived from a single institutional dataset used to predict ruptured abdominal aortic aneurysm (rAAA) repair survival preoperatively using basic labs and vital signs collected upon presentation. However, validation of this widely applicable scoring system has not been performed. This study aims to validate this scoring system using a large multi-institutional database. METHODS: All patients who underwent repair of an rAAA from 2011 to 2018 in the National Surgical Quality Improvement Program (NSQIP) and at a single academic medical center were included. The modified HRS was calculated by assigning 1 point for each of the following: age >76 years, creatinine >2 mg/dL, international normalized ratio >1.8, and any systolic blood pressure less than 70 mmHg. Assessment of the prediction model was then completed. Using a primary outcome measure of 30-day mortality, the receiver operating characteristic area under the curve was calculated. The discrimination between datasets was compared using a Delong test. Mortality rates for each score were compared between datasets using the Pearson χ2 test. Comparative analysis for patients with a score of 4 was limited due to a small sample size. RESULTS: A total of 1536 patients were identified using NSQIP, and 163 patients were assessed in the institutional dataset. There were 518 patients with a score of 0 (455 NSQIP, 63 institutional), 676 patients with a score of 1 (617 NSQIP, 59 institutional), 391 patients with a score of 2 (364 NSQIP, 27 institutional), 106 with a score of 3 (93 NSQIP, 13 institutional), and 8 patients with a score of 4 (7 NSQIP, 1 institutional). No difference was found in the receiver operating characteristic area under the curves between datasets (P = .78). Thirty-day mortality was 10% NSQIP vs 22% institutional for a score of 0; 28% NSQIP vs 36% institutional for a score of 1; 41% NSQIP vs 44% institutional for a score of 2; 45% NSQIP vs 69% institutional for a score of 3; and 57% NSQIP vs 100% institutional for a score of 4. Score 0 was the only score with a significant mortality rate difference between datasets (P = .01). CONCLUSIONS: The modified HRS is confirmed to be broadly applicable as a clinical decision-making tool for patients presenting with rAAAs. Therefore, this easily applicable model should be applied for all patients presenting with rAAAs to assist with provider and patient decision-making prior to proceeding with repair.

Early outcomes of endovascular repairs of the aortic arch using thoracic branch endoprosthesis.

OBJECTIVE: The only commercially available thoracic branched endoprosthesis (TBE) for treatment of the aortic arch was released in 2022. Limited data outside of clinical trial results have been reported. This study describes the demographics, anatomic details, and outcomes for patients treated for zone 0 to 2 using TBEs outside of a clinical trial. METHODS: All patients treated using TBEs for zone 0 to 2 were included. Patients treated as part of the clinical trial for zone 0 to 1 (n = 6) were excluded. Patient demographics, comorbidities, anatomic and operative details, and outcomes were reported. Outcomes and survival were then compared between groups. RESULTS: Of 40 patients, six patients underwent repair of zone 0, three of zone 1, and 31 of zone 2. There were no differences in demographics, comorbidities, or operative details by zone of treatment; however, the frequency of genetic aortopathy differed (zone 0: 0%; zone 1: 67%; and zone 2: 6.4%; P < .01). Seventy-three percent of patients were treated for dissection vs 27% with isolated aneurysms. Of the patients, 2.5% were treated for rupture, 22% were treated for symptomatic aneurysms, and 75% were treated electively. Forty-eight percent of repairs included a proximal cuff, and 83% received distal extension. Technical success was achieved in 100% of patients. Mean fluoroscopy time was 18 minutes, and median fluoroscopy dose was 416 mGy. Sixty percent of patients had prior aortic ascending/arch repair. TBE was planned as part of a complete thoracoabdominal repair in 45% of patients. Thirty-day mortality was 2.5% overall, with a single death in a zone 0 patient that occurred at day 1 due to a myocardial infarction. There were no reinterventions within 30 days. All other outcomes were similar. The 30-day stroke rate was 5.0%. The strokes occurred at day 6 (zone 1) and day 15 (zone 2); however, both were due to occlusion of a prior proximal surgical bypass and unrelated to the TBE side branch or embolization. Specifically, both patients had occlusion of a branch of their prior zone 1 or zone 2 arch replacement. An endoleak occurred in 7.5% of patients at 30-day follow-up (type II: 5.0%; unknown: 2.5%). At a mean follow-up of 6.6 months, 100% of side branches were patent. CONCLUSIONS: Repair of the aortic arch including TBE can be performed electively and urgently with acceptable stroke and death rates. TBE provides a valuable tool for patients requiring complete repair of a thoracoabdominal aneurysm. Continued investigation is underway to assess long-term safety and efficacy outside of the clinical trial.

A genomic data resource for predicting antimicrobial resistance from laboratory-derived antimicrobial susceptibility phenotypes.

Antimicrobial resistance (AMR) is a major global health threat that affects millions of people each year. Funding agencies worldwide and the global research community have expended considerable capital and effort tracking the evolution and spread of AMR by isolating and sequencing bacterial strains and performing antimicrobial susceptibility testing (AST). For the last several years, we have been capturing these efforts by curating data from the literature and data resources and building a set of assembled bacterial genome sequences that are paired with laboratory-derived AST data. This collection currently contains AST data for over 67 000 genomes encompassing approximately 40 genera and over 100 species. In this paper, we describe the characteristics of this collection, highlighting areas where sampling is comparatively deep or shallow, and showing areas where attention is needed from the research community to improve sampling and tracking efforts. In addition to using the data to track the evolution and spread of AMR, it also serves as a useful starting point for building machine learning models for predicting AMR phenotypes. We demonstrate this by describing two machine learning models that are built from the entire dataset to show where the predictive power is comparatively high or low. This AMR metadata collection is freely available and maintained on the Bacterial and Viral Bioinformatics Center (BV-BRC) FTP site ftp://ftp.bvbrc.org/RELEASE_NOTES/PATRIC_genomes_AMR.txt.

Association of Pre and Perioperative Vein Mapping with Hemodialysis Access Characteristics and Outcomes.

BACKGROUND: We investigated the utility of both pre and perioperative vein mapping for evaluating vessel suitability for both arteriovenous fistula (AVF) and arteriovenous graft (AVG) creation. In our practice, we used both mapping methods to detect arterial issues and to maximize AVF creation. We hypothesized that the patients whose operative plan changed based on their perioperative mapping would ultimately benefit from more optimal access placement with maintained rates of maturation and functional patency. METHODS: We performed a retrospective chart review evaluating patients who received initial hemodialysis (HD) access from January 1, 2017, to December 31, 2021, at the Veterans Affairs (VA) Puget Sound in Seattle, Washington. Patients were separated by whether their final procedure was congruent with the best access predicted from the preoperative vein mapping or noncongruent. The primary outcome was fistula maturation. Secondary outcomes were functional patency and number of procedures required to achieve maturation or to maintain functional patency. Results were analyzed using Pearson's chi-squared, Moods median, Student's t-tests, and Kaplan-Meier curves. RESULTS: Preoperative vein mapping uncovered arterial issues in 42% of the patient population. Initial HD access was created in 130 patients (n = 69 congruent, n = 61 noncongruent). Perioperative ultrasound led to a change in the created access in 47% of patients. Within the noncongruent group, 74% received access creation at a more anatomically favorable site compared to their predicted access, 47% were changed to forearm fistula, 20% to brachiocephalic (BC) from previously planned brachiobasilic (BB) or graft, and 7% to BB from previously planned graft. Maturation rates were similar in both groups (congruent 86% and noncongruent 82%), and there were no significant differences in the duration of functional patency or the number of procedures needed to achieve maturation or maintain functional patency. CONCLUSIONS: Utilization of pre and perioperative ultrasound for all patients resulted in higher rates of native AVF, forearm placement, and one-stage operations, with maintained maturation rates and functional patency in patients who were otherwise unsuitable candidates based on preoperative vein mapping alone.

The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities.

The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

PATRIC as a unique resource for studying antimicrobial resistance.

The Pathosystems Resource Integration Center (PATRIC, www.patricbrc.org) is designed to provide researchers with the tools and services that they need to perform genomic and other 'omic' data analyses. In response to mounting concern over antimicrobial resistance (AMR), the PATRIC team has been developing new tools that help researchers understand AMR and its genetic determinants. To support comparative analyses, we have added AMR phenotype data to over 15 000 genomes in the PATRIC database, often assembling genomes from reads in public archives and collecting their associated AMR panel data from the literature to augment the collection. We have also been using this collection of AMR metadata to build machine learning-based classifiers that can predict the AMR phenotypes and the genomic regions associated with resistance for genomes being submitted to the annotation service. Likewise, we have undertaken a large AMR protein annotation effort by manually curating data from the literature and public repositories. This collection of 7370 AMR reference proteins, which contains many protein annotations (functional roles) that are unique to PATRIC and RAST, has been manually curated so that it projects stably across genomes. The collection currently projects to 1 610 744 proteins in the PATRIC database. Finally, the PATRIC Web site has been expanded to enable AMR-based custom page views so that researchers can easily explore AMR data and design experiments based on whole genomes or individual genes.

RNA-Rocket: an RNA-Seq analysis resource for infectious disease research.

MOTIVATION: RNA-Seq is a method for profiling transcription using high-throughput sequencing and is an important component of many research projects that wish to study transcript isoforms, condition specific expression and transcriptional structure. The methods, tools and technologies used to perform RNA-Seq analysis continue to change, creating a bioinformatics challenge for researchers who wish to exploit these data. Resources that bring together genomic data, analysis tools, educational material and computational infrastructure can minimize the overhead required of life science researchers. RESULTS: RNA-Rocket is a free service that provides access to RNA-Seq and ChIP-Seq analysis tools for studying infectious diseases. The site makes available thousands of pre-indexed genomes, their annotations and the ability to stream results to the bioinformatics resources VectorBase, EuPathDB and PATRIC. The site also provides a combination of experimental data and metadata, examples of pre-computed analysis, step-by-step guides and a user interface designed to enable both novice and experienced users of RNA-Seq data. AVAILABILITY AND IMPLEMENTATION: RNA-Rocket is available at rnaseq.pathogenportal.org. Source code for this project can be found at github.com/cidvbi/PathogenPortal. CONTACT: anwarren@vt.edu SUPPLEMENTARY INFORMATION: Supplementary materials are available at Bioinformatics online.

Minimizing delays to hemodialysis access maturation: A quality improvement analysis.

INTRODUCTION: Pre-operative process optimization can expedite time-to-intervention and reduce overall health care costs. We hypothesized that the longest delay to hemodialysis (HD) access creation would be from pre-operative vessel mapping (mandatory in our practice), and that this would be correlated with increased catheter days. METHODS: One hundred thirty patients (24 inpatients, 106 outpatients) who received initial hemodialysis (HD) access from 01/01/2017 to 12/31/2021, at the Veterans Affairs Puget Sound, Seattle, Washington, were identified. Median time differences between pre-operative events were compared between inpatients and outpatients using the Mann-Whitney U test. Outpatients were then stratified by time of catheter-based HD initiation (no catheter, pre-referral catheter, post-referral catheter) and compared. The impacts of mapping-related delays on catheter use were evaluated using regression. RESULTS: Inpatients had shorter referral to access maturation times (125 days inpatient vs 146 days outpatient; p = 0.03). This was driven by shorter referral to mapping (2 days inpatient vs 27 days outpatient; p < 0.01) and mapping to pre-surgical evaluation (1-day inpatient vs 6 days outpatients; p < 0.01) times. Pre-surgical evaluation to OR times represented the longest pre-operative delay in both groups (51 days inpatient vs 29 days outpatient; p = 0.59). Among outpatients, tunneled catheter placement post-referral resulted in longer maturation times (74 days no catheter vs 67 days pre-referral vs 149 days post-referral; p < 0.01) but not additional pre-operative delays. No trend existed between increased mapping times and catheter-based dialysis duration (R2 = 0.08). CONCLUSION: Preoperative vein mapping contributed up to 21% of referral to maturation times but was not associated with increased tunneled catheter duration. While tunneled catheter placement impacted access maturation it did not cause additional pre-operative delays. Earlier referrals for access creation and reduction of outpatient wait-time from referral to OR and increased AV graft placement may minimize catheter days in our system thereby mitigating the added delays caused by pre-operative vein mapping.

Clinicopathologic Characterization of 2 Individuals With TBK1 Variants-1 Novel Splice Variant, 2 Proteinopathies: A Case Series.

Objectives: Here, we report detailed clinicopathologic evaluation of 2 individuals with pathogenic variants in TBK1, including one novel likely pathogenic splice variant. We describe the striking diversity of clinical phenotypes among family members and also the brain and spinal cord neuropathology associated with these 2 distinct TBK1 variants. Methods: Two individuals with pathogenic variants in TBK1 and their families were clinically characterized, and the probands subsequently underwent extensive postmortem neuropathologic examination of their brains and spinal cords. Results: Multiple affected individuals within a single family were found to carry a previously unreported c.358+3A>G variant, predicted to alter splicing. Detailed histopathologic evaluation of our 2 TBK1 variant carriers demonstrated distinct TDP-43 pathologic subtypes, but shared argyrophilic grain disease (AGD) tau pathology. Discussion: Although all pathogenic TBK1 variants are associated with TDP-43 pathology, the clinical and histologic features can be highly variable. Within one family, we describe distinct neurologic presentations which we propose are all caused by a novel c.358+3A>G variant. AGD is typically associated with older age, but it has been described as a copathologic finding in other TBK1 variant carriers and may be a common feature in FTLD-TDP due to TBK1.

Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance.

As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NIAID) established the Bioinformatics Resource Centers (BRC) to assist researchers with their analysis of genome sequence and other omics-related data. Recently, the PAThosystems Resource Integration Center (PATRIC), the Influenza Research Database (IRD), and the Virus Pathogen Database and Analysis Resource (ViPR) BRCs merged to form the Bacterial and Viral Bioinformatics Resource Center (BV-BRC) at https://www.bv-brc.org/ . The combined BV-BRC leverages the functionality of the original resources for bacterial and viral research communities with a unified data model, enhanced web-based visualization and analysis tools, and bioinformatics services. Here we demonstrate how antimicrobial resistance data can be analyzed in the new resource.

Missing genes in the annotation of prokaryotic genomes.

BACKGROUND: Protein-coding gene detection in prokaryotic genomes is considered a much simpler problem than in intron-containing eukaryotic genomes. However there have been reports that prokaryotic gene finder programs have problems with small genes (either over-predicting or under-predicting). Therefore the question arises as to whether current genome annotations have systematically missing, small genes. RESULTS: We have developed a high-performance computing methodology to investigate this problem. In this methodology we compare all ORFs larger than or equal to 33 aa from all fully-sequenced prokaryotic replicons. Based on that comparison, and using conservative criteria requiring a minimum taxonomic diversity between conserved ORFs in different genomes, we have discovered 1,153 candidate genes that are missing from current genome annotations. These missing genes are similar only to each other and do not have any strong similarity to gene sequences in public databases, with the implication that these ORFs belong to missing gene families. We also uncovered 38,895 intergenic ORFs, readily identified as putative genes by similarity to currently annotated genes (we call these absent annotations). The vast majority of the missing genes found are small (less than 100 aa). A comparison of select examples with GeneMark, EasyGene and Glimmer predictions yields evidence that some of these genes are escaping detection by these programs. CONCLUSIONS: Prokaryotic gene finders and prokaryotic genome annotations require improvement for accurate prediction of small genes. The number of missing gene families found is likely a lower bound on the actual number, due to the conservative criteria used to determine whether an ORF corresponds to a real gene.

Functional bias in molecular evolution rate of Arabidopsis thaliana.

BACKGROUND: Characteristics derived from mutation and other mechanisms that are advantageous for survival are often preserved during evolution by natural selection. Some genes are conserved in many organisms because they are responsible for fundamental biological function, others are conserved for their unique functional characteristics. Therefore one would expect the rate of molecular evolution for individual genes to be dependent on their biological function. Whether this expectation holds for genes duplicated by whole genome duplication is not known. RESULTS: We empirically demonstrate here, using duplicated genes generated from the Arabidopsis thaliana alpha-duplication event, that the rate of molecular evolution of genes duplicated in this event depend on biological function. Using functional clustering based on gene ontology annotation of gene pairs, we show that some duplicated genes, such as defense response genes, are under weaker purifying selection or under stronger diversifying selection than other duplicated genes, such as protein translation genes, as measured by the ratio of nonsynonymous to synonymous divergence (dN/dS). CONCLUSIONS: These results provide empirical evidence indicating that molecular evolution rate for genes duplicated in whole genome duplication, as measured by dN/dS, may depend on biological function, which we characterize using gene ontology annotation. Furthermore, the general approach used here provides a framework for comparative analysis of molecular evolution rate for genes based on their biological function.

The Genome Reverse Compiler: an explorative annotation tool.

BACKGROUND: As sequencing costs have decreased, whole genome sequencing has become a viable and integral part of biological laboratory research. However, the tools with which genes can be found and functionally characterized have not been readily adapted to be part of the everyday biological sciences toolkit. Most annotation pipelines remain as a service provided by large institutions or come as an unwieldy conglomerate of independent components, each requiring their own setup and maintenance. RESULTS: To address this issue we have created the Genome Reverse Compiler, an easy-to-use, open-source, automated annotation tool. The GRC is independent of third party software installs and only requires a Linux operating system. This stands in contrast to most annotation packages, which typically require installation of relational databases, sequence similarity software, and a number of other programming language modules. We provide details on the methodology used by GRC and evaluate its performance on several groups of prokaryotes using GRC's built in comparison module. CONCLUSION: Traditionally, to perform whole genome annotation a user would either set up a pipeline or take advantage of an online service. With GRC the user need only provide the genome he or she wants to annotate and the function resource files to use. The result is high usability and a very minimal learning curve for the intended audience of life science researchers and bioinformaticians. We believe that the GRC fills a valuable niche in allowing users to perform explorative, whole-genome annotation.

Thermodynamic analysis of additivity between the heavy and light chains in affinity maturation of an antibody.

In a recent article published in Molecular Immunology [Furukawa, K., Shimizu, T., Murakami, A., Kono, R., Nakagawa, M., Sagawa, T., Yamato, I., Azuma, T., 2007. Strategy for affinity maturation of an antibody with high evolvability to (4-hydroxy-3-nitrophenyl) acetyl hapten. Mol. Immunol. 44, 2436-2445], the authors measure thermodynamic parameters of the antigen-antibody interaction for a set of antibodies using an isothermal titration calorimetry to quantitatively assess the contribution of amino acid replacements to an increase in affinity during antibody maturation. One of the findings in their study is that the binding free energy change elicited by mutations in the heavy and light chains is additive. In this letter, we report our analysis of their results in terms of equilibrium thermodynamics to show that enthalpy-entropy compensation is responsible for the additivity.

Enthalpy-entropy compensation in the transition of a monospecific antibody towards antigen-binding promiscuity.

In a recent article published in Molecular Immunology (Dimitrov, J.D., Lacroix-Desmazes, S., Kaveri, S.V., Vassilev, T.L., 2007. Transition towards antigen-binding promiscuity of a monospecific antibody. Mol. Immunol. 44, 1854-1863.), the authors perform kinetic and thermodynamic analyses using a surface plasmon resonance-based technique to explain polyspecificity of antibodies in terms of molecular mechanisms. They found that after the antibody was exposed to urea, a protein destabilizing agent, it had the same affinity as the native state and that the two forms of the antibody use two distinct thermodynamic pathways for binding to the same antigen. In this letter, we report our analysis of these results in terms of equilibrium thermodynamics to show that the specificity transition of the antibody exhibits enthalpy-entropy compensation.

Whole Exome Sequencing to Identify Genetic Variants Associated with Raised Atherosclerotic Lesions in Young Persons.

We investigated the influence of genetic variants on atherosclerosis using whole exome sequencing in cases and controls from the autopsy study "Pathobiological Determinants of Atherosclerosis in Youth (PDAY)". We identified a PDAY case group with the highest total amounts of raised lesions (n = 359) for comparisons with a control group with no detectable raised lesions (n = 626). In addition to the standard exome capture, we included genome-wide proximal promoter regions that contain sequences that regulate gene expression. Our statistical analyses included single variant analysis for common variants (MAF > 0.01) and rare variant analysis for low frequency and rare variants (MAF < 0.05). In addition, we investigated known CAD genes previously identified by meta-analysis of GWAS studies. We did not identify individual common variants that reached exome-wide significance using single variant analysis. In analysis limited to 60 CAD genes, we detected strong associations with COL4A2/COL4A1 that also previously showed associations with myocardial infarction and arterial stiffness, as well as coronary artery calcification. Likewise, rare variant analysis did not identify genes that reached exome-wide significance. Among the 60 CAD genes, the strongest association was with NBEAL1 that was also identified in gene-based analysis of whole exome sequencing for early onset myocardial infarction.