The ATCC genome portal: 3,938 authenticated microbial reference genomes.

The ATCC Genome Portal (AGP, https://genomes.atcc.org/) is a database of authenticated genomes for bacteria, fungi, protists, and viruses held in ATCC's biorepository. It now includes 3,938 assemblies (253% increase) produced under ISO 9000 by ATCC. Here, we present new features and content added to the AGP for the research community.

Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications.

Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted by clinical microbiology laboratories due in part to the absence of standardized workflows. Here, we describe a sample-to-answer workflow called PanGIA (Pan-Genomics for Infectious Agents) that includes simplified, standardized wet-lab procedures and data analysis with an easy-to-use bioinformatics tool. PanGIA is an end-to-end, multi-use workflow that can be used for pathogen detection and related applications, such as biosurveillance and biothreat detection. We performed a comprehensive survey and assessment of current, commercially available wet-lab technologies and open-source bioinformatics tools for each workflow component. The workflow includes total nucleic acid extraction from clinical human whole blood and environmental microbial forensic swabs as sample inputs, host nucleic acid depletion, dual DNA and RNA library preparation, shotgun sequencing on an Illumina MiSeq, and sequencing data analysis. The PanGIA workflow can be completed within 24 h and is currently compatible with bacteria and viruses. Here, we present data from the development and application of the clinical and environmental workflows, enabling the specific detection of pathogens associated with bloodstream infections and environmental biosurveillance, without the need for targeted assay development.

Comparative Analysis and Data Provenance for 1,113 Bacterial Genome Assemblies.

The availability of public genomics data has become essential for modern life sciences research, yet the quality, traceability, and curation of these data have significant impacts on a broad range of microbial genomics research. While microbial genome databases such as NCBI's RefSeq database leverage the scalability of crowd sourcing for growth, genomics data provenance and authenticity of the source materials used to produce data are not strict requirements. Here, we describe the de novo assembly of 1,113 bacterial genome references produced from authenticated materials sourced from the American Type Culture Collection (ATCC), each with full genomics data provenance relating to bioinformatics methods, quality control, and passage history. Comparative genomics analysis of ATCC standard reference genomes (ASRGs) revealed significant issues with regard to NCBI's RefSeq bacterial genome assemblies related to completeness, mutations, structure, strain metadata, and gaps in traceability to the original biological source materials. Nearly half of RefSeq assemblies lack details on sample source information, sequencing technology, or bioinformatics methods. Deep curation of these records is not within the scope of NCBI's core mission in supporting open science, which aims to collect sequence records that are submitted by the public. Nonetheless, we propose that gaps in metadata accuracy and data provenance represent an "elephant in the room" for microbial genomics research. Effectively addressing these issues will require raising the level of accountability for data depositors and acknowledging the need for higher expectations of quality among the researchers whose research depends on accurate and attributable reference genome data. IMPORTANCE The traceability of microbial genomics data to authenticated physical biological materials is not a requirement for depositing these data into public genome databases. This creates significant risks for the reliability and data provenance of these important genomics research resources, the impact of which is not well understood. We sought to investigate this by carrying out a comparative genomics study of 1,113 ATCC standard reference genomes (ASRGs) produced by ATCC from authenticated and traceable materials using the latest sequencing technologies. We found widespread discrepancies in genome assembly quality, genetic variability, and the quality and completeness of the associated metadata among hundreds of reference genomes for ATCC strains found in NCBI's RefSeq database. We present a comparative analysis of de novo-assembled ASRGs, their respective metadata, and variant analysis using RefSeq genomes as a reference. Although assembly quality in RefSeq has generally improved over time, we found that significant quality issues remain, especially as related to genomic data and metadata provenance. Our work highlights the importance of data authentication and provenance for the microbial genomics community, and underscores the risks of ignoring this issue in the future.

The ATCC Genome Portal: Microbial Genome Reference Standards with Data Provenance.

Lack of data provenance negatively impacts scientific reproducibility and the reliability of genomic data. The ATCC Genome Portal (https://genomes.atcc.org) addresses this by providing data provenance information for microbial whole-genome assemblies originating from authenticated biological materials. To date, we have sequenced 1,579 complete genomes, including 466 type strains and 1,156 novel genomes.