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ABSTRACT Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the “life cycle” (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as “signatures” of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses. 

Wastewater treatment plants (WWTPs) receive a confluence of sewage containing antimicrobials, antibiotic resistant bacteria, antibiotic resistance genes (ARGs), and pathogens and thus are a key point of interest for antibiotic resistance surveillance. WWTP monitoring has the potential to inform with respect to the antibiotic resistance status of the community served as well as the potential for ARGs to escape treatment. However, there is lack of agreement regarding suitable sampling frequencies and monitoring targets to facilitate comparison within and among individual WWTPs. The objective of this study was to comprehensively evaluate patterns in metagenomic-derived indicators of antibiotic resistance through various stages of treatment at a conventional WWTP for the purpose of informing local monitoring approaches that are also informative for global comparison. Relative abundance of total ARGs decreased by ∼50% from the influent to the effluent, with each sampling location defined by a unique resistome (i.e., total ARG) composition. However, 90% of the ARGs found in the effluent were also detected in the influent, while the effluent ARG-pathogen taxonomic linkage patterns identified in assembled metagenomes were more similar to patterns in regional clinical surveillance data than the patterns identified in the influent. Analysis of core and discriminatory resistomes and general ARG trends across the eight sampling events (i.e., tendency to be removed, increase, decrease, or be found in the effluent only), along with quantification of ARGs of clinical concern, aided in identifying candidate ARGs for surveillance. Relative resistome risk characterization further provided a comprehensive metric for predicting the relative mobility of ARGs and likelihood of being carried in pathogens and can help to prioritize where to focus future monitoring and mitigation. Most antibiotics that were subject to regional resistance testing were also found in the WWTP, with the total antibiotic load decreasing by ∼40–50%, but no strong correlations were found between antibiotics and corresponding ARGs. Overall, this study provides insight into how metagenomic data can be collected and analyzed for surveillance of antibiotic resistance at WWTPs, suggesting that effluent is a beneficial monitoring point with relevance both to the local clinical condition and for assessing efficacy of wastewater treatment in reducing risk of disseminating antibiotic resistance. 

The first major goal of this project is to build a state-of-the-art information storage, retrieval, and analysis system that utilizes the latest technology and industry methods. This system is leveraged to accomplish another major goal, supporting modern search and browse capabilities for a large collection of tweets from the Twitter social media platform, web pages, and electronic theses and dissertations (ETDs). The backbone of the information system is a Docker container cluster running with Rancher and Kubernetes. Information retrieval and visualization is accomplished with containers in a pipelined fashion, whether in the cluster or on virtual machines, for Elasticsearch and Kibana, respectively. In addition to traditional searching and browsing, the system supports full-text and metadata searching. Search results include facets as a modern means of browsing among related documents. The system supports text analysis and machine learning to reveal new properties of collection data. These new properties assist in the generation of available facets. Recommendations are also presented with search results based on associations among documents and with logged user activity. The information system is co-designed by five teams of Virginia Tech graduate students, all members of the same computer science class, CS 5604. Although the project is an academic exercise, it is the practice of the teams to work and interact as though they are groups within a company developing a product. The teams on this project include three collection management groups -- Electronic Theses and Dissertations (ETD), Tweets (TWT), and Web-Pages (WP) -- as well as the Front-end (FE) group and the Integration (INT) group to help provide the overarching structure for the application. This submission focuses on the work of the Integration (INT) team, which creates and administers Docker containers for each team in addition to administering the cluster infrastructure. Each container is a customized application environment that is specific to the needs of the corresponding team. Each team will have several of these containers set up in a pipeline formation to allow scaling and extension of the current system. The INT team also contributes to a cross-team effort for exploring the use of Elasticsearch and its internally associated database. The INT team administers the integration of the Ceph data storage system into the CS Department Cloud and provides support for interactions between containers and the Ceph filesystem. During formative stages of development, the INT team also has a role in guiding team evaluations of prospective container components and workflows. The INT team is responsible for the overall project architecture and facilitating the tools and tutorials that assist the other teams in deploying containers in a development environment according to mutual specifications agreed upon with each team. The INT team maintains the status of the Kubernetes cluster, deploying new containers and pods as needed by the collection management teams as they expand their workflows. This team is responsible for utilizing a continuous integration process to update existing containers. During the development stage the INT team collaborates specifically with the collection management teams to create the pipeline for the ingestion and processing of new collection documents, crossing services between those teams as needed. The INT team develops a reasoner engine to construct workflows with information goal as input, which are then programmatically authored, scheduled, and monitored using Apache Airflow. The INT team is responsible for the flow, management, and logging of system performance data and making any adjustments necessary based on the analysis of testing results. The INT team has established a Gitlab repository for archival code related to the entire project and has provided the other groups with the documentation to deposit their code in the repository. This repository will be expanded using Gitlab CI in order to provide continuous integration and testing once it is available. Finally, the INT team will provide a production distribution that includes all embedded Docker containers and sub-embedded Git source code repositories. The INT team will archive this distribution on the Virginia Tech Docker Container Registry and deploy it on the Virginia Tech CS Cloud. The INT-2020 team owes a sincere debt of gratitude to the work of the INT-2019 team. This is a very large undertaking and the wrangling of all of the products and processes would not have been possible without their guidance in both direct and written form. We have relied heavily on the foundation they and their predecessors have provided for us. We continue their work with systematic improvements, but also want to acknowledge their efforts Ibid. Without them, our progress to date would not have been possible.